0s autopkgtest [22:15:47]: starting date and time: 2024-03-26 22:15:47+0000
  0s autopkgtest [22:15:47]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [22:15:47]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p3bhnms6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed --apt-upgrade tombo --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.10.0-1ubuntu2 python3-defaults/3.12.2-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-5.secgroup --name adt-noble-s390x-tombo-20240326-221547-juju-7f2275-prod-proposed-migration-environment-2-fd4e7b60-569b-44c6-85fe-f2350e325dc0 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
116s autopkgtest [22:17:43]: testbed dpkg architecture: s390x
117s autopkgtest [22:17:44]: testbed apt version: 2.7.12
117s autopkgtest [22:17:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup
118s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
118s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4000 kB]
120s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [55.4 kB]
120s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B]
120s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
120s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [693 kB]
120s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B]
120s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B]
120s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B]
120s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4123 kB]
120s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B]
120s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [48.3 kB]
120s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B]
121s Fetched 9554 kB in 3s (3282 kB/s)
122s Reading package lists...
123s Reading package lists...
124s Building dependency tree...
124s Reading state information...
124s Calculating upgrade...
124s The following packages will be upgraded:
124s   psmisc
124s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
124s Need to get 178 kB of archives.
124s After this operation, 28.7 kB disk space will be freed.
124s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x psmisc s390x 23.7-1 [178 kB]
125s Fetched 178 kB in 0s (367 kB/s)
125s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52170 files and directories currently installed.)
125s Preparing to unpack .../psmisc_23.7-1_s390x.deb ...
125s Unpacking psmisc (23.7-1) over (23.6-2) ...
125s Setting up psmisc (23.7-1) ...
125s Processing triggers for man-db (2.12.0-3) ...
125s Reading package lists...
126s Building dependency tree...
126s Reading state information...
126s 0 upgraded, 0 newly installed, 0 to remove and 244 not upgraded.
126s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
126s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
126s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
127s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
128s Reading package lists...
128s Reading package lists...
128s Building dependency tree...
128s Reading state information...
128s Calculating upgrade...
128s The following packages were automatically installed and are no longer required:
128s   libaio1 libnetplan0 python3-distutils python3-lib2to3
128s Use 'sudo apt autoremove' to remove them.
128s The following packages will be REMOVED:
128s   libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1
128s   libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11
128s   libhogweed6 libmagic1 libnettle8 libnpth0 libnvme1 libparted2 libperl5.38
128s   libpng16-16 libpsl5 libreadline8 libreiserfscore0 libssl3 libtirpc3 liburcu8
128s   libuv1
128s The following NEW packages will be installed:
128s   bpfcc-tools bpftrace fontconfig-config fonts-dejavu-core fonts-dejavu-mono
128s   hwdata ieee-data libaio1t64 libapt-pkg6.0t64 libarchive13t64 libatm1t64
128s   libbpfcc libc-dev-bin libc-devtools libc6-dev libclang-cpp18 libclang1-18
128s   libcrypt-dev libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libdeflate0
128s   libdw1t64 libelf1t64 libext2fs2t64 libfontconfig1 libfreetype6 libgd3
128s   libgdbm-compat4t64 libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libgpgme11t64
128s   libhogweed6t64 libjbig0 libjpeg-turbo8 libjpeg8 libllvm18 libmagic1t64
128s   libnetplan1 libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64
128s   libperl5.38t64 libpng16-16t64 libpsl5t64 libreadline8t64 libreiserfscore0t64
128s   libsharpyuv0 libssl3t64 libtiff6 libtirpc3t64 liburcu8t64 libuv1t64 libwebp7
128s   libxpm4 linux-headers-6.8.0-20 linux-headers-6.8.0-20-generic
128s   linux-image-6.8.0-20-generic linux-libc-dev linux-modules-6.8.0-20-generic
128s   linux-modules-extra-6.8.0-20-generic linux-tools-6.8.0-20
128s   linux-tools-6.8.0-20-generic linux-tools-common manpages manpages-dev
128s   python3-bpfcc python3-netaddr rpcsvc-proto ubuntu-kernel-accessories
128s   xdg-user-dirs
128s The following packages have been kept back:
128s   s390-tools
128s The following packages will be upgraded:
128s   apparmor apt apt-utils base-files bash bind9-dnsutils bind9-host bind9-libs
128s   binutils binutils-common binutils-s390x-linux-gnu bolt bsdextrautils
128s   bsdutils btrfs-progs coreutils cryptsetup-bin curl dbus dbus-bin dbus-daemon
128s   dbus-session-bus-common dbus-system-bus-common dbus-user-session dhcpcd-base
128s   dirmngr dmsetup dpkg dpkg-dev e2fsprogs e2fsprogs-l10n eject fdisk file ftp
128s   fwupd gawk gcc-13-base gcc-14-base gir1.2-girepository-2.0 gir1.2-glib-2.0
128s   gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv
128s   groff-base ibverbs-providers inetutils-telnet info initramfs-tools
128s   initramfs-tools-bin initramfs-tools-core install-info iproute2 jq keyboxd
128s   kmod kpartx krb5-locales libapparmor1 libaudit-common libaudit1 libbinutils
128s   libblkid1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3
128s   libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3
128s   libblockdev-utils3 libblockdev3 libbpf1 libbrotli1 libcap-ng0 libcom-err2
128s   libcryptsetup12 libctf-nobfd0 libctf0 libdbus-1-3 libdebconfclient0
128s   libdevmapper1.02.1 libdpkg-perl libevent-core-2.1-7 libexpat1 libfdisk1
128s   libfido2-1 libftdi1-2 libfwupd2 libgcc-s1 libgirepository-1.0-1
128s   libglib2.0-data libgssapi-krb5-2 libgudev-1.0-0 libgusb2 libibverbs1
128s   libjcat1 libjq1 libjson-glib-1.0-0 libjson-glib-1.0-common libk5crypto3
128s   libkmod2 libkrb5-3 libkrb5support0 libldap-common libldap2
128s   liblocale-gettext-perl liblzma5 libmagic-mgc libmbim-glib4 libmbim-proxy
128s   libmm-glib0 libmount1 libnghttp2-14 libnsl2 libnss-systemd libpam-modules
128s   libpam-modules-bin libpam-runtime libpam-systemd libpam0g libplymouth5
128s   libpolkit-agent-1-0 libpolkit-gobject-1-0 libproc2-0 libprotobuf-c1
128s   libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib
128s   libpython3.12-minimal libpython3.12-stdlib libqmi-glib5 libqmi-proxy
128s   libqrtr-glib0 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db
128s   libseccomp2 libselinux1 libsemanage-common libsemanage2 libsframe1 libslang2
128s   libsmartcols1 libsqlite3-0 libss2 libssh-4 libstdc++6 libsystemd-shared
128s   libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtirpc-common
128s   libudev1 libudisks2-0 libusb-1.0-0 libuuid1 libvolume-key1 libxml2 libxmlb2
128s   libxmuu1 linux-generic linux-headers-generic linux-headers-virtual
128s   linux-image-generic linux-image-virtual linux-virtual logsave lshw lsof
128s   man-db motd-news-config mount mtr-tiny multipath-tools netplan-generator
128s   netplan.io openssh-client openssh-server openssh-sftp-server openssl parted
128s   perl perl-base perl-modules-5.38 pinentry-curses plymouth
128s   plymouth-theme-ubuntu-text procps python-apt-common python3 python3-apt
128s   python3-cryptography python3-dbus python3-distutils python3-gdbm python3-gi
128s   python3-lib2to3 python3-minimal python3-netplan python3-pkg-resources
128s   python3-pyrsistent python3-setuptools python3-typing-extensions python3-yaml
128s   python3.11 python3.11-minimal python3.12 python3.12-minimal readline-common
128s   rsync rsyslog s390-tools-data shared-mime-info sudo systemd systemd-dev
128s   systemd-resolved systemd-sysv systemd-timesyncd tcpdump telnet tnftp
128s   ubuntu-pro-client ubuntu-pro-client-l10n udev udisks2 usb.ids util-linux
128s   uuid-runtime vim-common vim-tiny wget xxd xz-utils zlib1g
129s 243 upgraded, 73 newly installed, 28 to remove and 1 not upgraded.
129s Need to get 228 MB of archives.
129s After this operation, 524 MB of additional disk space will be used.
129s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x motd-news-config all 13ubuntu8 [5098 B]
129s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x base-files s390x 13ubuntu8 [74.2 kB]
129s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bash s390x 5.2.21-2ubuntu3 [845 kB]
129s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdutils s390x 1:2.39.3-9ubuntu2 [96.1 kB]
129s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbrotli1 s390x 1.1.0-2build1 [375 kB]
130s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgssapi-krb5-2 s390x 1.20.1-6ubuntu1 [149 kB]
130s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5-3 s390x 1.20.1-6ubuntu1 [360 kB]
130s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5support0 s390x 1.20.1-6ubuntu1 [34.6 kB]
130s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libk5crypto3 s390x 1.20.1-6ubuntu1 [90.3 kB]
130s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu2 [22.9 kB]
130s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu1 [75.7 kB]
130s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build6 [58.4 kB]
130s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x udisks2 s390x 2.10.1-6 [298 kB]
130s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libudisks2-0 s390x 2.10.1-6 [179 kB]
130s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblkid1 s390x 2.39.3-9ubuntu2 [128 kB]
130s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblzma5 s390x 5.6.0-0.2 [137 kB]
130s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main s390x kmod s390x 31+20240202-2ubuntu4 [107 kB]
130s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkmod2 s390x 31+20240202-2ubuntu4 [56.3 kB]
130s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-dev all 255.4-1ubuntu5 [103 kB]
130s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-timesyncd s390x 255.4-1ubuntu5 [35.3 kB]
130s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB]
130s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libaudit-common all 1:3.1.2-2.1 [5674 B]
130s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcap-ng0 s390x 0.8.4-2build1 [15.7 kB]
130s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libaudit1 s390x 1:3.1.2-2.1 [48.9 kB]
130s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam0g s390x 1.5.3-5ubuntu3 [69.8 kB]
130s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libselinux1 s390x 3.5-2ubuntu1 [84.7 kB]
130s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl4t64 s390x 8.5.0-2ubuntu8 [363 kB]
130s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main s390x curl s390x 8.5.0-2ubuntu8 [227 kB]
130s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpsl5t64 s390x 0.21.2-1.1 [57.6 kB]
130s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main s390x wget s390x 1.21.4-1ubuntu2 [351 kB]
131s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main s390x tnftp s390x 20230507-2build1 [107 kB]
131s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main s390x tcpdump s390x 4.99.4-3ubuntu2 [490 kB]
131s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd-shared s390x 255.4-1ubuntu5 [2131 kB]
133s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-resolved s390x 255.4-1ubuntu5 [304 kB]
133s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main s390x sudo s390x 1.9.15p5-3ubuntu3 [968 kB]
133s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main s390x rsync s390x 3.2.7-1build1 [446 kB]
133s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-cryptography s390x 41.0.7-4build2 [918 kB]
133s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB]
133s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssh-sftp-server s390x 1:9.6p1-3ubuntu11 [39.0 kB]
133s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssh-client s390x 1:9.6p1-3ubuntu11 [935 kB]
133s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssh-server s390x 1:9.6p1-3ubuntu11 [529 kB]
133s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssh-4 s390x 0.10.6-2build1 [189 kB]
133s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsasl2-modules s390x 2.1.28+dfsg1-5ubuntu1 [76.6 kB]
133s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.12 s390x 3.12.2-4build3 [645 kB]
133s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.12-minimal s390x 3.12.2-4build3 [2419 kB]
133s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.12-minimal s390x 3.12.2-4build3 [829 kB]
133s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libparted2t64 s390x 3.6-3.1build2 [172 kB]
133s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main s390x parted s390x 3.6-3.1build2 [44.6 kB]
133s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.11 s390x 3.11.8-1build4 [589 kB]
133s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3.11-minimal s390x 3.11.8-1build4 [2280 kB]
133s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.11-minimal s390x 3.11.8-1build4 [838 kB]
133s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.11-stdlib s390x 3.11.8-1build4 [1944 kB]
133s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main s390x shared-mime-info s390x 2.4-1build1 [474 kB]
133s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gir1.2-girepository-2.0 s390x 1.79.1-1ubuntu6 [24.5 kB]
133s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gir1.2-glib-2.0 s390x 2.79.3-3ubuntu5 [180 kB]
133s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgirepository-1.0-1 s390x 1.79.1-1ubuntu6 [84.0 kB]
133s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-gi s390x 3.47.0-3build1 [236 kB]
133s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-dbus s390x 1.3.2-5build2 [100 kB]
133s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnetplan1 s390x 1.0-1 [123 kB]
133s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-netplan s390x 1.0-1 [23.0 kB]
133s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main s390x netplan-generator s390x 1.0-1 [59.1 kB]
133s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main s390x initramfs-tools-bin s390x 0.142ubuntu23 [20.5 kB]
133s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main s390x initramfs-tools-core all 0.142ubuntu23 [50.1 kB]
133s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main s390x initramfs-tools all 0.142ubuntu23 [9058 B]
133s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main s390x netplan.io s390x 1.0-1 [65.4 kB]
133s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxmlb2 s390x 0.3.15-1build1 [70.6 kB]
133s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgpgme11t64 s390x 1.18.0-4.1ubuntu3 [150 kB]
133s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libvolume-key1 s390x 0.3.12-7build1 [40.8 kB]
133s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libqrtr-glib0 s390x 1.2.2-1ubuntu3 [17.5 kB]
133s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libqmi-glib5 s390x 1.35.2-0ubuntu1 [918 kB]
133s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libqmi-proxy s390x 1.35.2-0ubuntu1 [6122 B]
133s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpolkit-agent-1-0 s390x 124-1ubuntu1 [17.8 kB]
133s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpolkit-gobject-1-0 s390x 124-1ubuntu1 [48.3 kB]
133s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmm-glib0 s390x 1.23.4-0ubuntu1 [251 kB]
133s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmbim-glib4 s390x 1.31.2-0ubuntu2 [238 kB]
133s Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmbim-proxy s390x 1.31.2-0ubuntu2 [6154 B]
133s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjson-glib-1.0-common all 1.8.0-2build1 [4210 B]
133s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjson-glib-1.0-0 s390x 1.8.0-2build1 [68.4 kB]
133s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgusb2 s390x 0.4.8-1build1 [39.0 kB]
133s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgudev-1.0-0 s390x 1:238-3ubuntu2 [15.7 kB]
133s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libarchive13t64 s390x 3.7.2-1.1ubuntu2 [419 kB]
133s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main s390x fwupd s390x 1.9.15-2 [4435 kB]
133s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl3t64-gnutls s390x 8.5.0-2ubuntu8 [356 kB]
133s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfwupd2 s390x 1.9.15-2 [136 kB]
133s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev3 s390x 3.1.0-1build1 [52.3 kB]
133s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-utils3 s390x 3.1.0-1build1 [19.2 kB]
133s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-swap3 s390x 3.1.0-1build1 [7778 B]
133s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-part3 s390x 3.1.0-1build1 [15.4 kB]
133s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnvme1t64 s390x 1.8-3 [78.7 kB]
133s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-nvme3 s390x 3.1.0-1build1 [18.3 kB]
133s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-mdraid3 s390x 3.1.0-1build1 [13.2 kB]
133s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-loop3 s390x 3.1.0-1build1 [7138 B]
133s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main s390x e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B]
133s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu2 [22.5 kB]
133s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu2 [235 kB]
133s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu2 [615 kB]
133s Get:97 http://ftpmaster.internal/ubuntu noble/main s390x libreiserfscore0t64 s390x 1:3.6.27-7.1 [85.5 kB]
133s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main s390x btrfs-progs s390x 6.6.3-1.1build1 [959 kB]
133s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-fs3 s390x 3.1.0-1build1 [36.5 kB]
133s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblockdev-crypto3 s390x 3.1.0-1build1 [21.6 kB]
133s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bolt s390x 0.9.6-2build1 [142 kB]
133s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-0t64 s390x 2.79.3-3ubuntu5 [1566 kB]
134s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjcat1 s390x 0.2.0-2build2 [34.4 kB]
134s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libldap2 s390x 2.6.7+dfsg-1~exp1ubuntu6 [202 kB]
134s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ubuntu-pro-client-l10n s390x 31.2.2 [19.4 kB]
134s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ubuntu-pro-client s390x 31.2.2 [214 kB]
134s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gnupg-utils s390x 2.4.4-2ubuntu15 [116 kB]
134s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main s390x keyboxd s390x 2.4.4-2ubuntu15 [83.1 kB]
134s Get:109 http://ftpmaster.internal/ubuntu noble/main s390x libnpth0t64 s390x 1.6-3.1 [8148 B]
134s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgv s390x 2.4.4-2ubuntu15 [165 kB]
134s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg-wks-client s390x 2.4.4-2ubuntu15 [76.8 kB]
134s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg-agent s390x 2.4.4-2ubuntu15 [240 kB]
134s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg s390x 2.4.4-2ubuntu15 [589 kB]
134s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dirmngr s390x 2.4.4-2ubuntu15 [340 kB]
134s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gnupg all 2.4.4-2ubuntu15 [359 kB]
134s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-apt s390x 2.7.7 [171 kB]
134s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt-utils s390x 2.7.14 [214 kB]
134s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapt-pkg6.0t64 s390x 2.7.14 [1014 kB]
134s Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnettle8t64 s390x 3.9.1-2.2 [210 kB]
134s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libhogweed6t64 s390x 3.9.1-2.2 [204 kB]
134s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu2 [1044 kB]
134s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt s390x 2.7.14 [1390 kB]
135s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgconf s390x 2.4.4-2ubuntu15 [111 kB]
135s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgsm s390x 2.4.4-2ubuntu15 [244 kB]
135s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libreadline8t64 s390x 8.2-4 [170 kB]
135s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gawk s390x 1:5.2.1-2build2 [496 kB]
135s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main s390x fdisk s390x 2.39.3-9ubuntu2 [124 kB]
135s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3.12-stdlib s390x 3.12.2-4build3 [2046 kB]
135s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-base s390x 5.38.2-3.2 [1961 kB]
135s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
135s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-gdbm s390x 3.12.2-3ubuntu1.1 [19.0 kB]
135s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main s390x man-db s390x 2.12.0-3build4 [1246 kB]
135s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm6t64 s390x 1.23-5.1 [36.4 kB]
135s Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm-compat4t64 s390x 1.23-5.1 [6880 B]
135s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libperl5.38t64 s390x 5.38.2-3.2 [5007 kB]
136s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl s390x 5.38.2-3.2 [231 kB]
136s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-6 [763 kB]
136s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsasl2-modules-db s390x 2.1.28+dfsg1-5ubuntu1 [21.1 kB]
136s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsasl2-2 s390x 2.1.28+dfsg1-5ubuntu1 [57.8 kB]
136s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfido2-1 s390x 1.14.0-1build1 [81.0 kB]
136s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu2 [264 kB]
136s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dhcpcd-base s390x 1:10.0.6-1ubuntu2 [217 kB]
136s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuv1t64 s390x 1.48.0-1.1 [101 kB]
136s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bind9-host s390x 1:9.18.24-0ubuntu3 [50.5 kB]
136s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bind9-dnsutils s390x 1:9.18.24-0ubuntu3 [162 kB]
136s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bind9-libs s390x 1:9.18.24-0ubuntu3 [1243 kB]
136s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB]
136s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnss-systemd s390x 255.4-1ubuntu5 [166 kB]
136s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libudev1 s390x 255.4-1ubuntu5 [178 kB]
136s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd s390x 255.4-1ubuntu5 [3533 kB]
136s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main s390x udev s390x 255.4-1ubuntu5 [1887 kB]
136s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-sysv s390x 255.4-1ubuntu5 [11.9 kB]
136s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-systemd s390x 255.4-1ubuntu5 [242 kB]
136s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd0 s390x 255.4-1ubuntu5 [443 kB]
136s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-modules-bin s390x 1.5.3-5ubuntu3 [57.4 kB]
136s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-modules s390x 1.5.3-5ubuntu3 [289 kB]
136s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB]
136s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-user-session s390x 1.14.10-4ubuntu2 [9960 B]
136s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapparmor1 s390x 4.0.0-beta3-0ubuntu2 [50.8 kB]
136s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libexpat1 s390x 2.6.1-2 [94.8 kB]
136s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB]
136s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-bin s390x 1.14.10-4ubuntu2 [41.4 kB]
136s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus s390x 1.14.10-4ubuntu2 [24.3 kB]
136s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dbus-daemon s390x 1.14.10-4ubuntu2 [118 kB]
136s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdbus-1-3 s390x 1.14.10-4ubuntu2 [213 kB]
136s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmount1 s390x 2.39.3-9ubuntu2 [138 kB]
136s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libseccomp2 s390x 2.5.5-1ubuntu2 [53.4 kB]
136s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu2 [142 kB]
136s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuuid1 s390x 2.39.3-9ubuntu2 [35.6 kB]
136s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfdisk1 s390x 2.39.3-9ubuntu2 [151 kB]
136s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mount s390x 2.39.3-9ubuntu2 [119 kB]
136s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu1 [747 kB]
136s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-14-base s390x 14-20240315-1ubuntu1 [47.0 kB]
136s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgcc-s1 s390x 14-20240315-1ubuntu1 [35.9 kB]
136s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libstdc++6 s390x 14-20240315-1ubuntu1 [908 kB]
136s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg s390x 1.22.6ubuntu5 [1278 kB]
136s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-minimal s390x 3.12.2-0ubuntu1 [27.1 kB]
136s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3 s390x 3.12.2-0ubuntu1 [24.1 kB]
136s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpython3-stdlib s390x 3.12.2-0ubuntu1 [9804 B]
136s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsmartcols1 s390x 2.39.3-9ubuntu2 [67.9 kB]
136s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdextrautils s390x 2.39.3-9ubuntu2 [76.3 kB]
136s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main s390x groff-base s390x 1.23.0-3build1 [1049 kB]
136s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main s390x pinentry-curses s390x 1.2.1-3ubuntu4 [37.6 kB]
136s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main s390x readline-common all 8.2-4 [56.4 kB]
136s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxml2 s390x 2.9.14+dfsg-1.3ubuntu2 [818 kB]
137s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbpf1 s390x 1:1.3.0-2build1 [176 kB]
137s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libelf1t64 s390x 0.190-1.1build2 [69.7 kB]
137s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc-common all 1.3.4+ds-1.1 [8018 B]
137s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main s390x lsof s390x 4.95.0-1build2 [248 kB]
137s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnsl2 s390x 1.3.0-3build2 [44.1 kB]
137s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc3t64 s390x 1.3.4+ds-1.1 [85.8 kB]
137s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main s390x iproute2 s390x 6.1.0-1ubuntu5 [1156 kB]
137s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-yaml s390x 6.0.1-2build1 [121 kB]
137s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libusb-1.0-0 s390x 2:1.0.27-1 [54.8 kB]
137s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libprotobuf-c1 s390x 1.4.1-1ubuntu3 [23.4 kB]
137s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnghttp2-14 s390x 1.59.0-1build1 [77.8 kB]
137s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu2 [60.1 kB]
137s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main s390x procps s390x 2:4.0.4-4ubuntu2 [724 kB]
137s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main s390x coreutils s390x 9.4-3ubuntu3 [1482 kB]
137s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main s390x util-linux s390x 2.39.3-9ubuntu2 [1143 kB]
137s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main s390x file s390x 1:5.45-3 [22.2 kB]
137s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmagic-mgc s390x 1:5.45-3 [305 kB]
137s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmagic1t64 s390x 1:5.45-3 [93.1 kB]
137s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libplymouth5 s390x 24.004.60-1ubuntu6 [151 kB]
137s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpng16-16t64 s390x 1.6.43-3 [200 kB]
137s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main s390x multipath-tools s390x 0.9.4-5ubuntu6 [318 kB]
137s Get:207 http://ftpmaster.internal/ubuntu noble/main s390x liburcu8t64 s390x 0.14.0-3.1 [67.3 kB]
137s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblocale-gettext-perl s390x 1.07-6ubuntu4 [15.8 kB]
137s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main s390x uuid-runtime s390x 2.39.3-9ubuntu2 [33.4 kB]
137s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdebconfclient0 s390x 0.271ubuntu2 [11.4 kB]
137s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsemanage-common all 3.5-1build4 [10.1 kB]
137s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsemanage2 s390x 3.5-1build4 [96.7 kB]
137s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main s390x install-info s390x 7.1-3build1 [64.5 kB]
137s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-13-base s390x 13.2.0-21ubuntu1 [48.3 kB]
137s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu2 [17.2 kB]
138s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dmsetup s390x 2:1.02.185-3ubuntu2 [80.4 kB]
138s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main s390x eject s390x 2.39.3-9ubuntu2 [26.2 kB]
138s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main s390x krb5-locales all 1.20.1-6ubuntu1 [13.8 kB]
138s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
138s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libslang2 s390x 2.3.3-3build1 [501 kB]
138s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtext-charwidth-perl s390x 0.04-11build2 [9484 B]
138s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtext-iconv-perl s390x 1.7-8build2 [13.8 kB]
138s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python-apt-common all 2.7.7 [19.8 kB]
138s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-setuptools all 68.1.2-2ubuntu1 [396 kB]
138s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB]
138s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main s390x rsyslog s390x 8.2312.0-3ubuntu7 [536 kB]
138s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main s390x vim-tiny s390x 2:9.1.0016-1ubuntu6 [879 kB]
138s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main s390x vim-common all 2:9.1.0016-1ubuntu6 [385 kB]
138s Get:229 http://ftpmaster.internal/ubuntu noble/main s390x xdg-user-dirs s390x 0.18-1 [18.5 kB]
138s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main s390x xxd s390x 2:9.1.0016-1ubuntu6 [63.5 kB]
138s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apparmor s390x 4.0.0-beta3-0ubuntu2 [710 kB]
138s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ftp all 20230507-2build1 [4724 B]
138s Get:233 http://ftpmaster.internal/ubuntu noble-proposed/main s390x inetutils-telnet s390x 2:2.5-3ubuntu3 [105 kB]
138s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main s390x info s390x 7.1-3build1 [152 kB]
138s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxmuu1 s390x 2:1.1.3-3build1 [8860 B]
138s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main s390x lshw s390x 02.19.git.2021.06.19.996aaad9c7-2build2 [346 kB]
138s Get:237 http://ftpmaster.internal/ubuntu noble/main s390x manpages all 6.05.01-1 [1340 kB]
138s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mtr-tiny s390x 0.95-1.1build1 [57.0 kB]
138s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main s390x plymouth-theme-ubuntu-text s390x 24.004.60-1ubuntu6 [10.2 kB]
138s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main s390x plymouth s390x 24.004.60-1ubuntu6 [147 kB]
138s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main s390x telnet all 0.17+2.5-3ubuntu3 [3682 B]
138s Get:242 http://ftpmaster.internal/ubuntu noble-proposed/main s390x usb.ids all 2024.03.18-1 [223 kB]
138s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main s390x xz-utils s390x 5.6.0-0.2 [274 kB]
138s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libctf0 s390x 2.42-4ubuntu1 [98.4 kB]
138s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libctf-nobfd0 s390x 2.42-4ubuntu1 [100 kB]
138s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main s390x binutils-s390x-linux-gnu s390x 2.42-4ubuntu1 [2270 kB]
138s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbinutils s390x 2.42-4ubuntu1 [477 kB]
138s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main s390x binutils s390x 2.42-4ubuntu1 [3056 B]
138s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main s390x binutils-common s390x 2.42-4ubuntu1 [217 kB]
138s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsframe1 s390x 2.42-4ubuntu1 [14.2 kB]
138s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libllvm18 s390x 1:18.1.2-1ubuntu2 [33.4 MB]
139s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libclang-cpp18 s390x 1:18.1.2-1ubuntu2 [16.1 MB]
140s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libbpfcc s390x 0.29.1+ds-1ubuntu4 [697 kB]
140s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x python3-bpfcc all 0.29.1+ds-1ubuntu4 [40.2 kB]
140s Get:255 http://ftpmaster.internal/ubuntu noble/main s390x ieee-data all 20220827.1 [2113 kB]
140s Get:256 http://ftpmaster.internal/ubuntu noble/main s390x python3-netaddr all 0.8.0-2ubuntu1 [319 kB]
140s Get:257 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x bpfcc-tools all 0.29.1+ds-1ubuntu4 [687 kB]
140s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libclang1-18 s390x 1:18.1.2-1ubuntu2 [9349 kB]
140s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdw1t64 s390x 0.190-1.1build2 [286 kB]
140s Get:260 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x bpftrace s390x 0.20.2-1ubuntu1 [1139 kB]
140s Get:261 http://ftpmaster.internal/ubuntu noble-proposed/main s390x cryptsetup-bin s390x 2:2.7.0-1ubuntu2 [211 kB]
140s Get:262 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg-dev all 1.22.6ubuntu5 [1074 kB]
140s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdpkg-perl all 1.22.6ubuntu5 [269 kB]
140s Get:264 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB]
140s Get:265 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB]
140s Get:266 http://ftpmaster.internal/ubuntu noble-proposed/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu1 [37.4 kB]
140s Get:267 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB]
140s Get:268 http://ftpmaster.internal/ubuntu noble/main s390x hwdata all 0.379-1 [29.1 kB]
140s Get:269 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libibverbs1 s390x 50.0-2build1 [70.0 kB]
140s Get:270 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ibverbs-providers s390x 50.0-2build1 [408 kB]
140s Get:271 http://ftpmaster.internal/ubuntu noble-proposed/main s390x jq s390x 1.7.1-3 [66.5 kB]
140s Get:272 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjq1 s390x 1.7.1-3 [168 kB]
140s Get:273 http://ftpmaster.internal/ubuntu noble/main s390x libaio1t64 s390x 0.3.113-6 [7290 B]
140s Get:274 http://ftpmaster.internal/ubuntu noble/main s390x libatm1t64 s390x 1:2.5.1-5.1 [24.5 kB]
140s Get:275 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.39-0ubuntu6 [20.2 kB]
140s Get:276 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfreetype6 s390x 2.13.2+dfsg-1build2 [437 kB]
140s Get:277 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu1 [150 kB]
140s Get:278 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB]
140s Get:279 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B]
140s Get:280 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB]
140s Get:281 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB]
140s Get:282 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsharpyuv0 s390x 1.3.2-0.4build2 [14.9 kB]
140s Get:283 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libwebp7 s390x 1.3.2-0.4build2 [207 kB]
140s Get:284 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu1 [218 kB]
140s Get:285 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxpm4 s390x 1:3.5.17-1build1 [41.4 kB]
140s Get:286 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgd3 s390x 2.3.3-9ubuntu3 [141 kB]
140s Get:287 http://ftpmaster.internal/ubuntu noble/main s390x libc-devtools s390x 2.39-0ubuntu6 [30.6 kB]
140s Get:288 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-libc-dev s390x 6.8.0-20.20 [1592 kB]
141s Get:289 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB]
141s Get:290 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu6 [64.7 kB]
141s Get:291 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.39-0ubuntu6 [1629 kB]
141s Get:292 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libevent-core-2.1-7 s390x 2.1.12-stable-9build1 [94.3 kB]
141s Get:293 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libftdi1-2 s390x 1.5-6build4 [29.3 kB]
141s Get:294 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB]
141s Get:295 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-modules-6.8.0-20-generic s390x 6.8.0-20.20 [21.0 MB]
141s Get:296 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-image-6.8.0-20-generic s390x 6.8.0-20.20 [9872 kB]
141s Get:297 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-modules-extra-6.8.0-20-generic s390x 6.8.0-20.20 [11.7 MB]
142s Get:298 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-generic s390x 6.8.0-20.20+1 [1734 B]
142s Get:299 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-image-generic s390x 6.8.0-20.20+1 [9688 B]
142s Get:300 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-virtual s390x 6.8.0-20.20+1 [1682 B]
142s Get:301 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-image-virtual s390x 6.8.0-20.20+1 [9700 B]
142s Get:302 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-headers-virtual s390x 6.8.0-20.20+1 [1642 B]
142s Get:303 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB]
142s Get:304 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-headers-6.8.0-20-generic s390x 6.8.0-20.20 [2579 kB]
143s Get:305 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-headers-generic s390x 6.8.0-20.20+1 [9608 B]
143s Get:306 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-tools-common all 6.8.0-20.20 [437 kB]
143s Get:307 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-tools-6.8.0-20 s390x 6.8.0-20.20 [2674 kB]
143s Get:308 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-tools-6.8.0-20-generic s390x 6.8.0-20.20 [1724 B]
143s Get:309 http://ftpmaster.internal/ubuntu noble/main s390x manpages-dev all 6.05.01-1 [2018 kB]
143s Get:310 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-distutils all 3.12.2-3ubuntu1.1 [133 kB]
143s Get:311 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-lib2to3 all 3.12.2-3ubuntu1.1 [79.1 kB]
143s Get:312 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-pyrsistent s390x 0.20.0-1build1 [55.8 kB]
143s Get:313 http://ftpmaster.internal/ubuntu noble-proposed/main s390x python3-typing-extensions all 4.10.0-1 [60.7 kB]
143s Get:314 http://ftpmaster.internal/ubuntu noble-proposed/main s390x s390-tools-data all 2.31.0-0ubuntu3 [17.8 kB]
143s Get:315 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-kernel-accessories s390x 1.536build1 [10.5 kB]
143s Get:316 http://ftpmaster.internal/ubuntu noble-proposed/main s390x kpartx s390x 0.9.4-5ubuntu6 [32.8 kB]
144s Preconfiguring packages ...
144s Fetched 228 MB in 15s (15.7 MB/s)
144s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
144s Preparing to unpack .../motd-news-config_13ubuntu8_all.deb ...
144s Unpacking motd-news-config (13ubuntu8) over (13ubuntu7) ...
144s Preparing to unpack .../base-files_13ubuntu8_s390x.deb ...
144s Unpacking base-files (13ubuntu8) over (13ubuntu7) ...
144s Setting up base-files (13ubuntu8) ...
145s motd-news.service is a disabled or a static unit not running, not starting it.
145s (Reading database ... 
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(Reading database ... 52167 files and directories currently installed.)
145s Preparing to unpack .../bash_5.2.21-2ubuntu3_s390x.deb ...
145s Unpacking bash (5.2.21-2ubuntu3) over (5.2.21-2ubuntu2) ...
145s Setting up bash (5.2.21-2ubuntu3) ...
145s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
145s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
145s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_s390x.deb ...
145s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ...
145s Setting up bsdutils (1:2.39.3-9ubuntu2) ...
145s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
145s Preparing to unpack .../0-libbrotli1_1.1.0-2build1_s390x.deb ...
145s Unpacking libbrotli1:s390x (1.1.0-2build1) over (1.1.0-2) ...
145s Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-6ubuntu1_s390x.deb ...
145s Unpacking libgssapi-krb5-2:s390x (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
145s Preparing to unpack .../2-libkrb5-3_1.20.1-6ubuntu1_s390x.deb ...
145s Unpacking libkrb5-3:s390x (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
145s Preparing to unpack .../3-libkrb5support0_1.20.1-6ubuntu1_s390x.deb ...
145s Unpacking libkrb5support0:s390x (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
145s Preparing to unpack .../4-libk5crypto3_1.20.1-6ubuntu1_s390x.deb ...
145s Unpacking libk5crypto3:s390x (1.20.1-6ubuntu1) over (1.20.1-5build1) ...
145s Preparing to unpack .../5-libcom-err2_1.47.0-2.4~exp1ubuntu2_s390x.deb ...
145s Unpacking libcom-err2:s390x (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
145s Preparing to unpack .../6-zlib1g_1%3a1.3.dfsg-3.1ubuntu1_s390x.deb ...
145s Unpacking zlib1g:s390x (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ...
145s Setting up zlib1g:s390x (1:1.3.dfsg-3.1ubuntu1) ...
145s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
145s Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d.1-2build6_s390x.deb ...
145s Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build6) over (2.4+20151223.gitfa8646d.1-2build4) ...
145s Preparing to unpack .../udisks2_2.10.1-6_s390x.deb ...
145s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ...
145s Preparing to unpack .../libudisks2-0_2.10.1-6_s390x.deb ...
145s Unpacking libudisks2-0:s390x (2.10.1-6) over (2.10.1-1ubuntu2) ...
145s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_s390x.deb ...
145s Unpacking libblkid1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
145s Setting up libblkid1:s390x (2.39.3-9ubuntu2) ...
145s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
145s Preparing to unpack .../liblzma5_5.6.0-0.2_s390x.deb ...
145s Unpacking liblzma5:s390x (5.6.0-0.2) over (5.4.5-0.3) ...
145s Setting up liblzma5:s390x (5.6.0-0.2) ...
146s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
146s Preparing to unpack .../0-kmod_31+20240202-2ubuntu4_s390x.deb ...
146s Unpacking kmod (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ...
146s Preparing to unpack .../1-libkmod2_31+20240202-2ubuntu4_s390x.deb ...
146s Unpacking libkmod2:s390x (31+20240202-2ubuntu4) over (30+20230601-2ubuntu1) ...
146s Preparing to unpack .../2-systemd-dev_255.4-1ubuntu5_all.deb ...
146s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
146s Preparing to unpack .../3-systemd-timesyncd_255.4-1ubuntu5_s390x.deb ...
146s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
146s Preparing to unpack .../4-dbus-session-bus-common_1.14.10-4ubuntu2_all.deb ...
146s Unpacking dbus-session-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
146s Preparing to unpack .../5-libaudit-common_1%3a3.1.2-2.1_all.deb ...
146s Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ...
146s Setting up libaudit-common (1:3.1.2-2.1) ...
146s (Reading database ... 
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(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
146s Preparing to unpack .../libcap-ng0_0.8.4-2build1_s390x.deb ...
146s Unpacking libcap-ng0:s390x (0.8.4-2build1) over (0.8.4-2) ...
146s Setting up libcap-ng0:s390x (0.8.4-2build1) ...
146s (Reading database ... 
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(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
146s Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_s390x.deb ...
146s Unpacking libaudit1:s390x (1:3.1.2-2.1) over (1:3.1.2-2) ...
146s Setting up libaudit1:s390x (1:3.1.2-2.1) ...
146s (Reading database ... 
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(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
146s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_s390x.deb ...
146s Unpacking libpam0g:s390x (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
146s Setting up libpam0g:s390x (1.5.3-5ubuntu3) ...
146s (Reading database ... 
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
146s Preparing to unpack .../libselinux1_3.5-2ubuntu1_s390x.deb ...
146s Unpacking libselinux1:s390x (3.5-2ubuntu1) over (3.5-2build1) ...
146s Setting up libselinux1:s390x (3.5-2ubuntu1) ...
146s dpkg: libcurl4:s390x: dependency problems, but removing anyway as you requested:
146s  s390-tools depends on libcurl4 (>= 7.16.2).
146s  curl depends on libcurl4 (= 8.5.0-2ubuntu2).
146s 
146s (Reading database ... 
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52167 files and directories currently installed.)
146s Removing libcurl4:s390x (8.5.0-2ubuntu2) ...
146s Selecting previously unselected package libcurl4t64:s390x.
146s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52162 files and directories currently installed.)
146s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu8_s390x.deb ...
146s Unpacking libcurl4t64:s390x (8.5.0-2ubuntu8) ...
146s Preparing to unpack .../curl_8.5.0-2ubuntu8_s390x.deb ...
146s Unpacking curl (8.5.0-2ubuntu8) over (8.5.0-2ubuntu2) ...
146s dpkg: libpsl5:s390x: dependency problems, but removing anyway as you requested:
146s  wget depends on libpsl5 (>= 0.16.0).
146s  libcurl3-gnutls:s390x depends on libpsl5 (>= 0.16.0).
146s 
146s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 52168 files and directories currently installed.)
146s Removing libpsl5:s390x (0.21.2-1build1) ...
146s Selecting previously unselected package libpsl5t64:s390x.
146s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 35%
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
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146s Preparing to unpack .../00-libpsl5t64_0.21.2-1.1_s390x.deb ...
146s Unpacking libpsl5t64:s390x (0.21.2-1.1) ...
146s Preparing to unpack .../01-wget_1.21.4-1ubuntu2_s390x.deb ...
146s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ...
146s Preparing to unpack .../02-tnftp_20230507-2build1_s390x.deb ...
146s Unpacking tnftp (20230507-2build1) over (20230507-2) ...
146s Preparing to unpack .../03-tcpdump_4.99.4-3ubuntu2_s390x.deb ...
146s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ...
146s Preparing to unpack .../04-libsystemd-shared_255.4-1ubuntu5_s390x.deb ...
146s Unpacking libsystemd-shared:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
146s Preparing to unpack .../05-systemd-resolved_255.4-1ubuntu5_s390x.deb ...
146s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
146s Preparing to unpack .../06-sudo_1.9.15p5-3ubuntu3_s390x.deb ...
146s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ...
146s Preparing to unpack .../07-rsync_3.2.7-1build1_s390x.deb ...
146s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ...
146s Preparing to unpack .../08-python3-cryptography_41.0.7-4build2_s390x.deb ...
146s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ...
147s Preparing to unpack .../09-openssl_3.0.13-0ubuntu2_s390x.deb ...
147s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
147s Preparing to unpack .../10-openssh-sftp-server_1%3a9.6p1-3ubuntu11_s390x.deb ...
147s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
147s Preparing to unpack .../11-openssh-client_1%3a9.6p1-3ubuntu11_s390x.deb ...
147s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
147s Preparing to unpack .../12-openssh-server_1%3a9.6p1-3ubuntu11_s390x.deb ...
147s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
147s Preparing to unpack .../13-libssh-4_0.10.6-2build1_s390x.deb ...
147s Unpacking libssh-4:s390x (0.10.6-2build1) over (0.10.6-2) ...
147s Preparing to unpack .../14-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_s390x.deb ...
147s Unpacking libsasl2-modules:s390x (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
147s Preparing to unpack .../15-python3.12_3.12.2-4build3_s390x.deb ...
147s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ...
147s Preparing to unpack .../16-python3.12-minimal_3.12.2-4build3_s390x.deb ...
147s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ...
147s Preparing to unpack .../17-libpython3.12-minimal_3.12.2-4build3_s390x.deb ...
147s Unpacking libpython3.12-minimal:s390x (3.12.2-4build3) over (3.12.2-1) ...
147s dpkg: libparted2:s390x: dependency problems, but removing anyway as you requested:
147s  parted depends on libparted2 (= 3.6-3).
147s 
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147s Removing libparted2:s390x (3.6-3) ...
147s Selecting previously unselected package libparted2t64:s390x.
147s (Reading database ... 
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147s Preparing to unpack .../00-libparted2t64_3.6-3.1build2_s390x.deb ...
147s Unpacking libparted2t64:s390x (3.6-3.1build2) ...
147s Preparing to unpack .../01-parted_3.6-3.1build2_s390x.deb ...
147s Unpacking parted (3.6-3.1build2) over (3.6-3) ...
147s Preparing to unpack .../02-python3.11_3.11.8-1build4_s390x.deb ...
147s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ...
147s Preparing to unpack .../03-python3.11-minimal_3.11.8-1build4_s390x.deb ...
147s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ...
147s Preparing to unpack .../04-libpython3.11-minimal_3.11.8-1build4_s390x.deb ...
147s Unpacking libpython3.11-minimal:s390x (3.11.8-1build4) over (3.11.8-1) ...
148s Preparing to unpack .../05-libpython3.11-stdlib_3.11.8-1build4_s390x.deb ...
148s Unpacking libpython3.11-stdlib:s390x (3.11.8-1build4) over (3.11.8-1) ...
148s Preparing to unpack .../06-shared-mime-info_2.4-1build1_s390x.deb ...
148s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ...
148s Preparing to unpack .../07-gir1.2-girepository-2.0_1.79.1-1ubuntu6_s390x.deb ...
148s Unpacking gir1.2-girepository-2.0:s390x (1.79.1-1ubuntu6) over (1.79.1-1) ...
148s Preparing to unpack .../08-gir1.2-glib-2.0_2.79.3-3ubuntu5_s390x.deb ...
148s Unpacking gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
148s Preparing to unpack .../09-libgirepository-1.0-1_1.79.1-1ubuntu6_s390x.deb ...
148s Unpacking libgirepository-1.0-1:s390x (1.79.1-1ubuntu6) over (1.79.1-1) ...
148s Preparing to unpack .../10-python3-gi_3.47.0-3build1_s390x.deb ...
148s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ...
148s Preparing to unpack .../11-python3-dbus_1.3.2-5build2_s390x.deb ...
148s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ...
148s Selecting previously unselected package libnetplan1:s390x.
148s Preparing to unpack .../12-libnetplan1_1.0-1_s390x.deb ...
148s Unpacking libnetplan1:s390x (1.0-1) ...
148s Preparing to unpack .../13-python3-netplan_1.0-1_s390x.deb ...
148s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ...
148s Preparing to unpack .../14-netplan-generator_1.0-1_s390x.deb ...
148s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
148s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ...
148s Preparing to unpack .../15-initramfs-tools-bin_0.142ubuntu23_s390x.deb ...
148s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ...
148s Preparing to unpack .../16-initramfs-tools-core_0.142ubuntu23_all.deb ...
148s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ...
148s Preparing to unpack .../17-initramfs-tools_0.142ubuntu23_all.deb ...
148s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ...
148s Preparing to unpack .../18-netplan.io_1.0-1_s390x.deb ...
148s Unpacking netplan.io (1.0-1) over (0.107.1-3) ...
148s Preparing to unpack .../19-libxmlb2_0.3.15-1build1_s390x.deb ...
148s Unpacking libxmlb2:s390x (0.3.15-1build1) over (0.3.15-1) ...
148s dpkg: libgpgme11:s390x: dependency problems, but removing anyway as you requested:
148s  libvolume-key1:s390x depends on libgpgme11 (>= 1.4.1).
148s  libjcat1:s390x depends on libgpgme11 (>= 1.2.0).
148s 
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148s Removing libgpgme11:s390x (1.18.0-4ubuntu1) ...
148s Selecting previously unselected package libgpgme11t64:s390x.
148s (Reading database ... 
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148s Preparing to unpack .../00-libgpgme11t64_1.18.0-4.1ubuntu3_s390x.deb ...
148s Unpacking libgpgme11t64:s390x (1.18.0-4.1ubuntu3) ...
148s Preparing to unpack .../01-libvolume-key1_0.3.12-7build1_s390x.deb ...
148s Unpacking libvolume-key1:s390x (0.3.12-7build1) over (0.3.12-5build2) ...
148s Preparing to unpack .../02-libqrtr-glib0_1.2.2-1ubuntu3_s390x.deb ...
148s Unpacking libqrtr-glib0:s390x (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ...
148s Preparing to unpack .../03-libqmi-glib5_1.35.2-0ubuntu1_s390x.deb ...
148s Unpacking libqmi-glib5:s390x (1.35.2-0ubuntu1) over (1.34.0-2) ...
148s Preparing to unpack .../04-libqmi-proxy_1.35.2-0ubuntu1_s390x.deb ...
148s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ...
148s Preparing to unpack .../05-libpolkit-agent-1-0_124-1ubuntu1_s390x.deb ...
148s Unpacking libpolkit-agent-1-0:s390x (124-1ubuntu1) over (124-1) ...
148s Preparing to unpack .../06-libpolkit-gobject-1-0_124-1ubuntu1_s390x.deb ...
148s Unpacking libpolkit-gobject-1-0:s390x (124-1ubuntu1) over (124-1) ...
148s Preparing to unpack .../07-libmm-glib0_1.23.4-0ubuntu1_s390x.deb ...
148s Unpacking libmm-glib0:s390x (1.23.4-0ubuntu1) over (1.22.0-3) ...
149s Preparing to unpack .../08-libmbim-glib4_1.31.2-0ubuntu2_s390x.deb ...
149s Unpacking libmbim-glib4:s390x (1.31.2-0ubuntu2) over (1.30.0-1) ...
149s Preparing to unpack .../09-libmbim-proxy_1.31.2-0ubuntu2_s390x.deb ...
149s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ...
149s Preparing to unpack .../10-libjson-glib-1.0-common_1.8.0-2build1_all.deb ...
149s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ...
149s Preparing to unpack .../11-libjson-glib-1.0-0_1.8.0-2build1_s390x.deb ...
149s Unpacking libjson-glib-1.0-0:s390x (1.8.0-2build1) over (1.8.0-2) ...
149s Preparing to unpack .../12-libgusb2_0.4.8-1build1_s390x.deb ...
149s Unpacking libgusb2:s390x (0.4.8-1build1) over (0.4.8-1) ...
149s Preparing to unpack .../13-libgudev-1.0-0_1%3a238-3ubuntu2_s390x.deb ...
149s Unpacking libgudev-1.0-0:s390x (1:238-3ubuntu2) over (1:238-3) ...
149s dpkg: libarchive13:s390x: dependency problems, but removing anyway as you requested:
149s  fwupd depends on libarchive13 (>= 3.2.1).
149s 
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149s Removing libarchive13:s390x (3.7.2-1ubuntu2) ...
149s Selecting previously unselected package libarchive13t64:s390x.
149s (Reading database ... 
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149s Preparing to unpack .../libarchive13t64_3.7.2-1.1ubuntu2_s390x.deb ...
149s Unpacking libarchive13t64:s390x (3.7.2-1.1ubuntu2) ...
149s Preparing to unpack .../fwupd_1.9.15-2_s390x.deb ...
149s Unpacking fwupd (1.9.15-2) over (1.9.14-1) ...
149s dpkg: libcurl3-gnutls:s390x: dependency problems, but removing anyway as you requested:
149s  libfwupd2:s390x depends on libcurl3-gnutls (>= 7.63.0).
149s 
149s (Reading database ... 
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149s Removing libcurl3-gnutls:s390x (8.5.0-2ubuntu2) ...
149s Selecting previously unselected package libcurl3t64-gnutls:s390x.
149s (Reading database ... 
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149s Preparing to unpack .../0-libcurl3t64-gnutls_8.5.0-2ubuntu8_s390x.deb ...
149s Unpacking libcurl3t64-gnutls:s390x (8.5.0-2ubuntu8) ...
149s Preparing to unpack .../1-libfwupd2_1.9.15-2_s390x.deb ...
149s Unpacking libfwupd2:s390x (1.9.15-2) over (1.9.14-1) ...
149s Preparing to unpack .../2-libblockdev3_3.1.0-1build1_s390x.deb ...
149s Unpacking libblockdev3:s390x (3.1.0-1build1) over (3.1.0-1) ...
149s Preparing to unpack .../3-libblockdev-utils3_3.1.0-1build1_s390x.deb ...
149s Unpacking libblockdev-utils3:s390x (3.1.0-1build1) over (3.1.0-1) ...
149s Preparing to unpack .../4-libblockdev-swap3_3.1.0-1build1_s390x.deb ...
149s Unpacking libblockdev-swap3:s390x (3.1.0-1build1) over (3.1.0-1) ...
149s Preparing to unpack .../5-libblockdev-part3_3.1.0-1build1_s390x.deb ...
149s Unpacking libblockdev-part3:s390x (3.1.0-1build1) over (3.1.0-1) ...
149s dpkg: libnvme1: dependency problems, but removing anyway as you requested:
149s  libblockdev-nvme3:s390x depends on libnvme1 (>= 1.7.1).
149s 
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149s Removing libnvme1 (1.8-2) ...
149s Selecting previously unselected package libnvme1t64.
149s (Reading database ... 
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149s Preparing to unpack .../0-libnvme1t64_1.8-3_s390x.deb ...
149s Unpacking libnvme1t64 (1.8-3) ...
149s Preparing to unpack .../1-libblockdev-nvme3_3.1.0-1build1_s390x.deb ...
149s Unpacking libblockdev-nvme3:s390x (3.1.0-1build1) over (3.1.0-1) ...
149s Preparing to unpack .../2-libblockdev-mdraid3_3.1.0-1build1_s390x.deb ...
149s Unpacking libblockdev-mdraid3:s390x (3.1.0-1build1) over (3.1.0-1) ...
149s Preparing to unpack .../3-libblockdev-loop3_3.1.0-1build1_s390x.deb ...
149s Unpacking libblockdev-loop3:s390x (3.1.0-1build1) over (3.1.0-1) ...
149s Preparing to unpack .../4-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ...
149s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
149s Preparing to unpack .../5-logsave_1.47.0-2.4~exp1ubuntu2_s390x.deb ...
149s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
149s dpkg: libext2fs2:s390x: dependency problems, but removing anyway as you requested:
149s  libblockdev-fs3:s390x depends on libext2fs2 (>= 1.42.11).
149s  e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1).
149s  btrfs-progs depends on libext2fs2 (>= 1.42).
149s 
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149s Removing libext2fs2:s390x (1.47.0-2ubuntu1) ...
149s Selecting previously unselected package libext2fs2t64:s390x.
149s (Reading database ... 
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149s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_s390x.deb ...
149s Adding 'diversion of /lib/s390x-linux-gnu/libe2p.so.2 to /lib/s390x-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64'
149s Adding 'diversion of /lib/s390x-linux-gnu/libe2p.so.2.3 to /lib/s390x-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64'
149s Adding 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2 to /lib/s390x-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64'
149s Adding 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2.4 to /lib/s390x-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64'
149s Unpacking libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu2) ...
149s Setting up libcom-err2:s390x (1.47.0-2.4~exp1ubuntu2) ...
149s Setting up libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu2) ...
149s (Reading database ... 
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149s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_s390x.deb ...
149s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
149s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested:
149s  btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27).
149s 
149s (Reading database ... 
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149s Removing libreiserfscore0 (1:3.6.27-7) ...
149s Selecting previously unselected package libreiserfscore0t64.
149s (Reading database ... 
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149s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_s390x.deb ...
149s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ...
149s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_s390x.deb ...
149s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ...
150s Preparing to unpack .../libblockdev-fs3_3.1.0-1build1_s390x.deb ...
150s Unpacking libblockdev-fs3:s390x (3.1.0-1build1) over (3.1.0-1) ...
150s Preparing to unpack .../libblockdev-crypto3_3.1.0-1build1_s390x.deb ...
150s Unpacking libblockdev-crypto3:s390x (3.1.0-1build1) over (3.1.0-1) ...
150s Preparing to unpack .../bolt_0.9.6-2build1_s390x.deb ...
150s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ...
150s dpkg: libglib2.0-0:s390x: dependency problems, but removing anyway as you requested:
150s  s390-tools depends on libglib2.0-0 (>= 2.77.0).
150s  libnetplan0:s390x depends on libglib2.0-0 (>= 2.75.3).
150s  libjcat1:s390x depends on libglib2.0-0 (>= 2.75.3).
150s 
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150s Removing libglib2.0-0:s390x (2.79.2-1~ubuntu1) ...
150s Selecting previously unselected package libglib2.0-0t64:s390x.
150s (Reading database ... 
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150s Preparing to unpack .../0-libglib2.0-0t64_2.79.3-3ubuntu5_s390x.deb ...
150s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:s390x.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
150s removed '/var/lib/dpkg/info/libglib2.0-0:s390x.postrm'
150s Unpacking libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ...
150s Preparing to unpack .../1-libjcat1_0.2.0-2build2_s390x.deb ...
150s Unpacking libjcat1:s390x (0.2.0-2build2) over (0.2.0-2) ...
150s Preparing to unpack .../2-libldap2_2.6.7+dfsg-1~exp1ubuntu6_s390x.deb ...
150s Unpacking libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
150s Preparing to unpack .../3-ubuntu-pro-client-l10n_31.2.2_s390x.deb ...
150s Unpacking ubuntu-pro-client-l10n (31.2.2) over (31.1) ...
150s Preparing to unpack .../4-ubuntu-pro-client_31.2.2_s390x.deb ...
150s Unpacking ubuntu-pro-client (31.2.2) over (31.1) ...
150s Preparing to unpack .../5-gnupg-utils_2.4.4-2ubuntu15_s390x.deb ...
150s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
150s Preparing to unpack .../6-keyboxd_2.4.4-2ubuntu15_s390x.deb ...
150s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
150s dpkg: libnpth0:s390x: dependency problems, but removing anyway as you requested:
150s  gpgv depends on libnpth0 (>= 0.90).
150s  gpgsm depends on libnpth0 (>= 0.90).
150s  gpg-agent depends on libnpth0 (>= 0.90).
150s  gpg depends on libnpth0 (>= 0.90).
150s  dirmngr depends on libnpth0 (>= 0.90).
150s 
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150s Removing libnpth0:s390x (1.6-3build2) ...
150s Selecting previously unselected package libnpth0t64:s390x.
150s (Reading database ... 
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150s Preparing to unpack .../libnpth0t64_1.6-3.1_s390x.deb ...
150s Unpacking libnpth0t64:s390x (1.6-3.1) ...
150s Setting up libnpth0t64:s390x (1.6-3.1) ...
150s (Reading database ... 
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150s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_s390x.deb ...
150s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
150s Setting up gpgv (2.4.4-2ubuntu15) ...
150s (Reading database ... 
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150s Preparing to unpack .../0-gpg-wks-client_2.4.4-2ubuntu15_s390x.deb ...
150s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
150s Preparing to unpack .../1-gpg-agent_2.4.4-2ubuntu15_s390x.deb ...
150s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
150s Preparing to unpack .../2-gpg_2.4.4-2ubuntu15_s390x.deb ...
150s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
150s Preparing to unpack .../3-dirmngr_2.4.4-2ubuntu15_s390x.deb ...
150s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
150s Preparing to unpack .../4-gnupg_2.4.4-2ubuntu15_all.deb ...
150s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
150s Preparing to unpack .../5-python3-apt_2.7.7_s390x.deb ...
150s Unpacking python3-apt (2.7.7) over (2.7.6) ...
150s Preparing to unpack .../6-apt-utils_2.7.14_s390x.deb ...
150s Unpacking apt-utils (2.7.14) over (2.7.12) ...
150s dpkg: libapt-pkg6.0:s390x: dependency problems, but removing anyway as you requested:
150s  apt depends on libapt-pkg6.0 (>= 2.7.12).
150s 
150s (Reading database ... 
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150s Removing libapt-pkg6.0:s390x (2.7.12) ...
150s dpkg: libnettle8:s390x: dependency problems, but removing anyway as you requested:
150s  libhogweed6:s390x depends on libnettle8.
150s  libgnutls30:s390x depends on libnettle8 (>= 3.9~).
150s 
150s Removing libnettle8:s390x (3.9.1-2) ...
150s Selecting previously unselected package libapt-pkg6.0t64:s390x.
150s (Reading database ... 
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150s Preparing to unpack .../libapt-pkg6.0t64_2.7.14_s390x.deb ...
150s Unpacking libapt-pkg6.0t64:s390x (2.7.14) ...
151s Setting up libapt-pkg6.0t64:s390x (2.7.14) ...
151s Selecting previously unselected package libnettle8t64:s390x.
151s (Reading database ... 
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151s Preparing to unpack .../libnettle8t64_3.9.1-2.2_s390x.deb ...
151s Unpacking libnettle8t64:s390x (3.9.1-2.2) ...
151s Setting up libnettle8t64:s390x (3.9.1-2.2) ...
151s dpkg: libhogweed6:s390x: dependency problems, but removing anyway as you requested:
151s  libgnutls30:s390x depends on libhogweed6 (>= 3.6).
151s 
151s (Reading database ... 
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151s Removing libhogweed6:s390x (3.9.1-2) ...
151s Selecting previously unselected package libhogweed6t64:s390x.
151s (Reading database ... 
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151s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_s390x.deb ...
151s Unpacking libhogweed6t64:s390x (3.9.1-2.2) ...
151s Setting up libhogweed6t64:s390x (3.9.1-2.2) ...
151s dpkg: libgnutls30:s390x: dependency problems, but removing anyway as you requested:
151s  apt depends on libgnutls30 (>= 3.8.1).
151s 
151s (Reading database ... 
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151s Removing libgnutls30:s390x (3.8.3-1ubuntu1) ...
151s Selecting previously unselected package libgnutls30t64:s390x.
151s (Reading database ... 
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151s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_s390x.deb ...
151s Unpacking libgnutls30t64:s390x (3.8.3-1.1ubuntu2) ...
151s Setting up libgnutls30t64:s390x (3.8.3-1.1ubuntu2) ...
151s (Reading database ... 
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151s Preparing to unpack .../archives/apt_2.7.14_s390x.deb ...
151s Unpacking apt (2.7.14) over (2.7.12) ...
151s Setting up apt (2.7.14) ...
151s (Reading database ... 
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151s Preparing to unpack .../gpgconf_2.4.4-2ubuntu15_s390x.deb ...
151s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
151s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_s390x.deb ...
151s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
152s dpkg: libreadline8:s390x: dependency problems, but removing anyway as you requested:
152s  libpython3.12-stdlib:s390x depends on libreadline8 (>= 7.0~beta).
152s  gawk depends on libreadline8 (>= 6.0).
152s  fdisk depends on libreadline8 (>= 6.0).
152s 
152s (Reading database ... 
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152s Removing libreadline8:s390x (8.2-3) ...
152s Selecting previously unselected package libreadline8t64:s390x.
152s (Reading database ... 
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152s Preparing to unpack .../libreadline8t64_8.2-4_s390x.deb ...
152s Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8 to /lib/s390x-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
152s Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8.2 to /lib/s390x-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
152s Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8 to /lib/s390x-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
152s Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8.2 to /lib/s390x-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
152s Unpacking libreadline8t64:s390x (8.2-4) ...
152s Setting up libreadline8t64:s390x (8.2-4) ...
152s (Reading database ... 
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152s Preparing to unpack .../gawk_1%3a5.2.1-2build2_s390x.deb ...
152s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ...
152s Preparing to unpack .../fdisk_2.39.3-9ubuntu2_s390x.deb ...
152s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
152s Preparing to unpack .../libpython3.12-stdlib_3.12.2-4build3_s390x.deb ...
152s Unpacking libpython3.12-stdlib:s390x (3.12.2-4build3) over (3.12.2-1) ...
152s Preparing to unpack .../perl-base_5.38.2-3.2_s390x.deb ...
152s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
152s Setting up perl-base (5.38.2-3.2) ...
152s (Reading database ... 
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152s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
152s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
152s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu1.1_s390x.deb ...
152s Unpacking python3-gdbm:s390x (3.12.2-3ubuntu1.1) over (3.11.5-1) ...
152s Preparing to unpack .../man-db_2.12.0-3build4_s390x.deb ...
152s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ...
152s dpkg: libgdbm-compat4:s390x: dependency problems, but removing anyway as you requested:
152s  libperl5.38:s390x depends on libgdbm-compat4 (>= 1.18-3).
152s 
153s (Reading database ... 
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153s Removing libgdbm-compat4:s390x (1.23-5) ...
153s dpkg: libgdbm6:s390x: dependency problems, but removing anyway as you requested:
153s  libperl5.38:s390x depends on libgdbm6 (>= 1.21).
153s 
153s Removing libgdbm6:s390x (1.23-5) ...
153s Selecting previously unselected package libgdbm6t64:s390x.
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153s Preparing to unpack .../libgdbm6t64_1.23-5.1_s390x.deb ...
153s Unpacking libgdbm6t64:s390x (1.23-5.1) ...
153s Selecting previously unselected package libgdbm-compat4t64:s390x.
153s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_s390x.deb ...
153s Unpacking libgdbm-compat4t64:s390x (1.23-5.1) ...
153s dpkg: libperl5.38:s390x: dependency problems, but removing anyway as you requested:
153s  perl depends on libperl5.38 (= 5.38.2-3).
153s 
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153s Removing libperl5.38:s390x (5.38.2-3) ...
153s Selecting previously unselected package libperl5.38t64:s390x.
153s (Reading database ... 
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153s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_s390x.deb ...
153s Unpacking libperl5.38t64:s390x (5.38.2-3.2) ...
153s Preparing to unpack .../perl_5.38.2-3.2_s390x.deb ...
153s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ...
153s dpkg: libdb5.3:s390x: dependency problems, but removing anyway as you requested:
153s  libsasl2-modules-db:s390x depends on libdb5.3.
153s  libpam-modules:s390x depends on libdb5.3.
153s  iproute2 depends on libdb5.3.
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153s Removing libdb5.3:s390x (5.3.28+dfsg2-4) ...
153s Selecting previously unselected package libdb5.3t64:s390x.
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153s Preparing to unpack .../0-libdb5.3t64_5.3.28+dfsg2-6_s390x.deb ...
153s Unpacking libdb5.3t64:s390x (5.3.28+dfsg2-6) ...
153s Preparing to unpack .../1-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_s390x.deb ...
153s Unpacking libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
153s Preparing to unpack .../2-libsasl2-2_2.1.28+dfsg1-5ubuntu1_s390x.deb ...
153s Unpacking libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
153s Preparing to unpack .../3-libfido2-1_1.14.0-1build1_s390x.deb ...
153s Unpacking libfido2-1:s390x (1.14.0-1build1) over (1.14.0-1) ...
153s Preparing to unpack .../4-libcryptsetup12_2%3a2.7.0-1ubuntu2_s390x.deb ...
153s Unpacking libcryptsetup12:s390x (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ...
153s Preparing to unpack .../5-dhcpcd-base_1%3a10.0.6-1ubuntu2_s390x.deb ...
153s Unpacking dhcpcd-base (1:10.0.6-1ubuntu2) over (1:10.0.6-1ubuntu1) ...
153s dpkg: libuv1:s390x: dependency problems, but removing anyway as you requested:
153s  bind9-libs:s390x depends on libuv1 (>= 1.40.0).
153s 
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153s Removing libuv1:s390x (1.48.0-1) ...
153s Selecting previously unselected package libuv1t64:s390x.
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153s Preparing to unpack .../libuv1t64_1.48.0-1.1_s390x.deb ...
153s Unpacking libuv1t64:s390x (1.48.0-1.1) ...
153s Preparing to unpack .../bind9-host_1%3a9.18.24-0ubuntu3_s390x.deb ...
153s Unpacking bind9-host (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ...
153s Preparing to unpack .../bind9-dnsutils_1%3a9.18.24-0ubuntu3_s390x.deb ...
153s Unpacking bind9-dnsutils (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ...
153s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_s390x.deb ...
153s Unpacking bind9-libs:s390x (1:9.18.24-0ubuntu3) over (1:9.18.21-0ubuntu1) ...
153s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested:
153s  systemd depends on libssl3 (>= 3.0.0).
153s  s390-tools depends on libssl3 (>= 3.0.0).
153s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
153s 
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153s Removing libssl3:s390x (3.0.10-1ubuntu4) ...
153s Selecting previously unselected package libssl3t64:s390x.
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153s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ...
153s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ...
153s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ...
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153s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_s390x.deb ...
153s Unpacking libnss-systemd:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
153s Preparing to unpack .../libudev1_255.4-1ubuntu5_s390x.deb ...
153s Unpacking libudev1:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
154s Setting up libudev1:s390x (255.4-1ubuntu5) ...
154s (Reading database ... 
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154s Preparing to unpack .../systemd_255.4-1ubuntu5_s390x.deb ...
154s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
154s Preparing to unpack .../udev_255.4-1ubuntu5_s390x.deb ...
154s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
154s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_s390x.deb ...
154s Unpacking libsystemd0:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
154s Setting up libsystemd0:s390x (255.4-1ubuntu5) ...
154s Setting up libcryptsetup12:s390x (2:2.7.0-1ubuntu2) ...
154s Setting up libkmod2:s390x (31+20240202-2ubuntu4) ...
154s Setting up libsystemd-shared:s390x (255.4-1ubuntu5) ...
154s Setting up systemd-dev (255.4-1ubuntu5) ...
154s Setting up systemd (255.4-1ubuntu5) ...
155s (Reading database ... 
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155s Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_s390x.deb ...
155s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
155s Preparing to unpack .../libpam-systemd_255.4-1ubuntu5_s390x.deb ...
155s Unpacking libpam-systemd:s390x (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
155s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_s390x.deb ...
155s Unpacking libpam-modules-bin (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
155s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ...
155s pam_namespace.service is a disabled or a static unit not running, not starting it.
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155s Preparing to unpack .../libpam-modules_1.5.3-5ubuntu3_s390x.deb ...
155s Unpacking libpam-modules:s390x (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
155s Setting up libpam-modules:s390x (1.5.3-5ubuntu3) ...
155s Installing new version of config file /etc/security/namespace.init ...
155s (Reading database ... 
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155s Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu3_all.deb ...
155s Unpacking libpam-runtime (1.5.3-5ubuntu3) over (1.5.2-9.1ubuntu3) ...
155s Setting up libpam-runtime (1.5.3-5ubuntu3) ...
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155s Preparing to unpack .../0-dbus-user-session_1.14.10-4ubuntu2_s390x.deb ...
155s Unpacking dbus-user-session (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
155s Preparing to unpack .../1-libapparmor1_4.0.0-beta3-0ubuntu2_s390x.deb ...
155s Unpacking libapparmor1:s390x (4.0.0-beta3-0ubuntu2) over (4.0.0~alpha4-0ubuntu1) ...
155s Preparing to unpack .../2-libexpat1_2.6.1-2_s390x.deb ...
155s Unpacking libexpat1:s390x (2.6.1-2) over (2.6.0-1) ...
155s Preparing to unpack .../3-dbus-system-bus-common_1.14.10-4ubuntu2_all.deb ...
155s Unpacking dbus-system-bus-common (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
155s Preparing to unpack .../4-dbus-bin_1.14.10-4ubuntu2_s390x.deb ...
155s Unpacking dbus-bin (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
155s Preparing to unpack .../5-dbus_1.14.10-4ubuntu2_s390x.deb ...
155s Unpacking dbus (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
155s Preparing to unpack .../6-dbus-daemon_1.14.10-4ubuntu2_s390x.deb ...
155s Unpacking dbus-daemon (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
155s Preparing to unpack .../7-libdbus-1-3_1.14.10-4ubuntu2_s390x.deb ...
155s Unpacking libdbus-1-3:s390x (1.14.10-4ubuntu2) over (1.14.10-4ubuntu1) ...
155s Preparing to unpack .../8-libmount1_2.39.3-9ubuntu2_s390x.deb ...
155s Unpacking libmount1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
155s Setting up libmount1:s390x (2.39.3-9ubuntu2) ...
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155s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu2_s390x.deb ...
155s Unpacking libseccomp2:s390x (2.5.5-1ubuntu2) over (2.5.5-1ubuntu1) ...
156s Setting up libseccomp2:s390x (2.5.5-1ubuntu2) ...
156s (Reading database ... 
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156s Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu2_s390x.deb ...
156s Unpacking libdevmapper1.02.1:s390x (2:1.02.185-3ubuntu2) over (2:1.02.185-3ubuntu1) ...
156s Preparing to unpack .../libuuid1_2.39.3-9ubuntu2_s390x.deb ...
156s Unpacking libuuid1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
156s Setting up libuuid1:s390x (2.39.3-9ubuntu2) ...
156s (Reading database ... 
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156s Preparing to unpack .../libfdisk1_2.39.3-9ubuntu2_s390x.deb ...
156s Unpacking libfdisk1:s390x (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
156s Preparing to unpack .../mount_2.39.3-9ubuntu2_s390x.deb ...
156s Unpacking mount (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
156s Preparing to unpack .../libsqlite3-0_3.45.1-1ubuntu1_s390x.deb ...
156s Unpacking libsqlite3-0:s390x (3.45.1-1ubuntu1) over (3.45.1-1) ...
156s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_s390x.deb ...
156s Unpacking gcc-14-base:s390x (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
156s Setting up gcc-14-base:s390x (14-20240315-1ubuntu1) ...
156s (Reading database ... 
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156s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_s390x.deb ...
156s Unpacking libgcc-s1:s390x (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
156s Setting up libgcc-s1:s390x (14-20240315-1ubuntu1) ...
156s (Reading database ... 
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156s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_s390x.deb ...
156s Unpacking libstdc++6:s390x (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ...
156s Setting up libstdc++6:s390x (14-20240315-1ubuntu1) ...
156s (Reading database ... 
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156s Preparing to unpack .../dpkg_1.22.6ubuntu5_s390x.deb ...
156s Unpacking dpkg (1.22.6ubuntu5) over (1.22.4ubuntu5) ...
156s Setting up dpkg (1.22.6ubuntu5) ...
157s Setting up libpython3.12-minimal:s390x (3.12.2-4build3) ...
157s Setting up libexpat1:s390x (2.6.1-2) ...
157s Setting up python3.12-minimal (3.12.2-4build3) ...
158s (Reading database ... 
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158s dpkg: libelf1:s390x: dependency problems, but removing anyway as you requested:
158s  linux-headers-6.8.0-11-generic depends on libelf1 (>= 0.144).
158s  iproute2 depends on libelf1 (>= 0.131).
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158s dpkg: libtirpc3:s390x: dependency problems, but removing anyway as you requested:
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158s Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.1_s390x.deb ...
158s Adding 'diversion of /lib/s390x-linux-gnu/libtirpc.so.3 to /lib/s390x-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
158s Adding 'diversion of /lib/s390x-linux-gnu/libtirpc.so.3.0.0 to /lib/s390x-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
158s Unpacking libtirpc3t64:s390x (1.3.4+ds-1.1) ...
158s Preparing to unpack .../1-iproute2_6.1.0-1ubuntu5_s390x.deb ...
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160s fstrim.service is a disabled or a static unit not running, not starting it.
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160s dpkg: liburcu8:s390x: dependency problems, but removing anyway as you requested:
160s  xfsprogs depends on liburcu8 (>= 0.13.0).
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162s Preparing to unpack .../019-inetutils-telnet_2%3a2.5-3ubuntu3_s390x.deb ...
162s Unpacking inetutils-telnet (2:2.5-3ubuntu3) over (2:2.5-3ubuntu1) ...
162s Preparing to unpack .../020-info_7.1-3build1_s390x.deb ...
162s Unpacking info (7.1-3build1) over (7.1-3) ...
162s Preparing to unpack .../021-libxmuu1_2%3a1.1.3-3build1_s390x.deb ...
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162s Preparing to unpack .../022-lshw_02.19.git.2021.06.19.996aaad9c7-2build2_s390x.deb ...
162s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2build2) over (02.19.git.2021.06.19.996aaad9c7-2build1) ...
162s Selecting previously unselected package manpages.
162s Preparing to unpack .../023-manpages_6.05.01-1_all.deb ...
162s Unpacking manpages (6.05.01-1) ...
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162s Unpacking mtr-tiny (0.95-1.1build1) over (0.95-1.1) ...
162s Preparing to unpack .../025-plymouth-theme-ubuntu-text_24.004.60-1ubuntu6_s390x.deb ...
162s Unpacking plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ...
162s Preparing to unpack .../026-plymouth_24.004.60-1ubuntu6_s390x.deb ...
162s Unpacking plymouth (24.004.60-1ubuntu6) over (24.004.60-1ubuntu3) ...
162s Preparing to unpack .../027-telnet_0.17+2.5-3ubuntu3_all.deb ...
162s Unpacking telnet (0.17+2.5-3ubuntu3) over (0.17+2.5-3ubuntu1) ...
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162s Unpacking usb.ids (2024.03.18-1) over (2024.01.30-1) ...
162s Preparing to unpack .../029-xz-utils_5.6.0-0.2_s390x.deb ...
162s Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ...
162s Preparing to unpack .../030-libctf0_2.42-4ubuntu1_s390x.deb ...
162s Unpacking libctf0:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
162s Preparing to unpack .../031-libctf-nobfd0_2.42-4ubuntu1_s390x.deb ...
162s Unpacking libctf-nobfd0:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
162s Preparing to unpack .../032-binutils-s390x-linux-gnu_2.42-4ubuntu1_s390x.deb ...
162s Unpacking binutils-s390x-linux-gnu (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
162s Preparing to unpack .../033-libbinutils_2.42-4ubuntu1_s390x.deb ...
162s Unpacking libbinutils:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
162s Preparing to unpack .../034-binutils_2.42-4ubuntu1_s390x.deb ...
162s Unpacking binutils (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
162s Preparing to unpack .../035-binutils-common_2.42-4ubuntu1_s390x.deb ...
162s Unpacking binutils-common:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
162s Preparing to unpack .../036-libsframe1_2.42-4ubuntu1_s390x.deb ...
162s Unpacking libsframe1:s390x (2.42-4ubuntu1) over (2.42-3ubuntu1) ...
162s Selecting previously unselected package libllvm18:s390x.
162s Preparing to unpack .../037-libllvm18_1%3a18.1.2-1ubuntu2_s390x.deb ...
162s Unpacking libllvm18:s390x (1:18.1.2-1ubuntu2) ...
163s Selecting previously unselected package libclang-cpp18.
163s Preparing to unpack .../038-libclang-cpp18_1%3a18.1.2-1ubuntu2_s390x.deb ...
163s Unpacking libclang-cpp18 (1:18.1.2-1ubuntu2) ...
164s Selecting previously unselected package libbpfcc:s390x.
164s Preparing to unpack .../039-libbpfcc_0.29.1+ds-1ubuntu4_s390x.deb ...
164s Unpacking libbpfcc:s390x (0.29.1+ds-1ubuntu4) ...
164s Selecting previously unselected package python3-bpfcc.
164s Preparing to unpack .../040-python3-bpfcc_0.29.1+ds-1ubuntu4_all.deb ...
164s Unpacking python3-bpfcc (0.29.1+ds-1ubuntu4) ...
164s Selecting previously unselected package ieee-data.
164s Preparing to unpack .../041-ieee-data_20220827.1_all.deb ...
164s Unpacking ieee-data (20220827.1) ...
164s Selecting previously unselected package python3-netaddr.
164s Preparing to unpack .../042-python3-netaddr_0.8.0-2ubuntu1_all.deb ...
164s Unpacking python3-netaddr (0.8.0-2ubuntu1) ...
164s Selecting previously unselected package bpfcc-tools.
164s Preparing to unpack .../043-bpfcc-tools_0.29.1+ds-1ubuntu4_all.deb ...
164s Unpacking bpfcc-tools (0.29.1+ds-1ubuntu4) ...
164s Selecting previously unselected package libclang1-18.
164s Preparing to unpack .../044-libclang1-18_1%3a18.1.2-1ubuntu2_s390x.deb ...
164s Unpacking libclang1-18 (1:18.1.2-1ubuntu2) ...
164s Selecting previously unselected package libdw1t64:s390x.
164s Preparing to unpack .../045-libdw1t64_0.190-1.1build2_s390x.deb ...
164s Unpacking libdw1t64:s390x (0.190-1.1build2) ...
164s Selecting previously unselected package bpftrace.
164s Preparing to unpack .../046-bpftrace_0.20.2-1ubuntu1_s390x.deb ...
164s Unpacking bpftrace (0.20.2-1ubuntu1) ...
164s Preparing to unpack .../047-cryptsetup-bin_2%3a2.7.0-1ubuntu2_s390x.deb ...
164s Unpacking cryptsetup-bin (2:2.7.0-1ubuntu2) over (2:2.7.0-1ubuntu1) ...
165s Preparing to unpack .../048-dpkg-dev_1.22.6ubuntu5_all.deb ...
165s Unpacking dpkg-dev (1.22.6ubuntu5) over (1.22.4ubuntu5) ...
165s Preparing to unpack .../049-libdpkg-perl_1.22.6ubuntu5_all.deb ...
165s Unpacking libdpkg-perl (1.22.6ubuntu5) over (1.22.4ubuntu5) ...
165s Selecting previously unselected package fonts-dejavu-mono.
165s Preparing to unpack .../050-fonts-dejavu-mono_2.37-8_all.deb ...
165s Unpacking fonts-dejavu-mono (2.37-8) ...
165s Selecting previously unselected package fonts-dejavu-core.
165s Preparing to unpack .../051-fonts-dejavu-core_2.37-8_all.deb ...
165s Unpacking fonts-dejavu-core (2.37-8) ...
165s Selecting previously unselected package fontconfig-config.
165s Preparing to unpack .../052-fontconfig-config_2.15.0-1.1ubuntu1_s390x.deb ...
165s Unpacking fontconfig-config (2.15.0-1.1ubuntu1) ...
165s Preparing to unpack .../053-gnupg-l10n_2.4.4-2ubuntu15_all.deb ...
165s Unpacking gnupg-l10n (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
165s Selecting previously unselected package hwdata.
165s Preparing to unpack .../054-hwdata_0.379-1_all.deb ...
165s Unpacking hwdata (0.379-1) ...
165s Preparing to unpack .../055-libibverbs1_50.0-2build1_s390x.deb ...
165s Unpacking libibverbs1:s390x (50.0-2build1) over (50.0-2) ...
165s Preparing to unpack .../056-ibverbs-providers_50.0-2build1_s390x.deb ...
165s Unpacking ibverbs-providers:s390x (50.0-2build1) over (50.0-2) ...
165s Preparing to unpack .../057-jq_1.7.1-3_s390x.deb ...
165s Unpacking jq (1.7.1-3) over (1.7.1-2) ...
165s Preparing to unpack .../058-libjq1_1.7.1-3_s390x.deb ...
165s Unpacking libjq1:s390x (1.7.1-3) over (1.7.1-2) ...
165s Selecting previously unselected package libaio1t64:s390x.
165s Preparing to unpack .../059-libaio1t64_0.3.113-6_s390x.deb ...
165s Unpacking libaio1t64:s390x (0.3.113-6) ...
165s Selecting previously unselected package libatm1t64:s390x.
165s Preparing to unpack .../060-libatm1t64_1%3a2.5.1-5.1_s390x.deb ...
165s Unpacking libatm1t64:s390x (1:2.5.1-5.1) ...
165s Selecting previously unselected package libc-dev-bin.
165s Preparing to unpack .../061-libc-dev-bin_2.39-0ubuntu6_s390x.deb ...
165s Unpacking libc-dev-bin (2.39-0ubuntu6) ...
165s Selecting previously unselected package libfreetype6:s390x.
165s Preparing to unpack .../062-libfreetype6_2.13.2+dfsg-1build2_s390x.deb ...
165s Unpacking libfreetype6:s390x (2.13.2+dfsg-1build2) ...
165s Selecting previously unselected package libfontconfig1:s390x.
165s Preparing to unpack .../063-libfontconfig1_2.15.0-1.1ubuntu1_s390x.deb ...
165s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu1) ...
165s Selecting previously unselected package libjpeg-turbo8:s390x.
165s Preparing to unpack .../064-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ...
165s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ...
165s Selecting previously unselected package libjpeg8:s390x.
165s Preparing to unpack .../065-libjpeg8_8c-2ubuntu11_s390x.deb ...
165s Unpacking libjpeg8:s390x (8c-2ubuntu11) ...
165s Selecting previously unselected package libdeflate0:s390x.
165s Preparing to unpack .../066-libdeflate0_1.19-1_s390x.deb ...
165s Unpacking libdeflate0:s390x (1.19-1) ...
165s Selecting previously unselected package libjbig0:s390x.
165s Preparing to unpack .../067-libjbig0_2.1-6.1ubuntu1_s390x.deb ...
165s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ...
165s Selecting previously unselected package libsharpyuv0:s390x.
165s Preparing to unpack .../068-libsharpyuv0_1.3.2-0.4build2_s390x.deb ...
165s Unpacking libsharpyuv0:s390x (1.3.2-0.4build2) ...
165s Selecting previously unselected package libwebp7:s390x.
165s Preparing to unpack .../069-libwebp7_1.3.2-0.4build2_s390x.deb ...
165s Unpacking libwebp7:s390x (1.3.2-0.4build2) ...
165s Selecting previously unselected package libtiff6:s390x.
165s Preparing to unpack .../070-libtiff6_4.5.1+git230720-4ubuntu1_s390x.deb ...
165s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu1) ...
165s Selecting previously unselected package libxpm4:s390x.
165s Preparing to unpack .../071-libxpm4_1%3a3.5.17-1build1_s390x.deb ...
165s Unpacking libxpm4:s390x (1:3.5.17-1build1) ...
165s Selecting previously unselected package libgd3:s390x.
165s Preparing to unpack .../072-libgd3_2.3.3-9ubuntu3_s390x.deb ...
165s Unpacking libgd3:s390x (2.3.3-9ubuntu3) ...
165s Selecting previously unselected package libc-devtools.
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165s Unpacking libc-devtools (2.39-0ubuntu6) ...
165s Selecting previously unselected package linux-libc-dev:s390x.
165s Preparing to unpack .../074-linux-libc-dev_6.8.0-20.20_s390x.deb ...
165s Unpacking linux-libc-dev:s390x (6.8.0-20.20) ...
165s Selecting previously unselected package libcrypt-dev:s390x.
165s Preparing to unpack .../075-libcrypt-dev_1%3a4.4.36-4_s390x.deb ...
165s Unpacking libcrypt-dev:s390x (1:4.4.36-4) ...
165s Selecting previously unselected package rpcsvc-proto.
165s Preparing to unpack .../076-rpcsvc-proto_1.4.2-0ubuntu6_s390x.deb ...
165s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
165s Selecting previously unselected package libc6-dev:s390x.
165s Preparing to unpack .../077-libc6-dev_2.39-0ubuntu6_s390x.deb ...
165s Unpacking libc6-dev:s390x (2.39-0ubuntu6) ...
166s Preparing to unpack .../078-libevent-core-2.1-7_2.1.12-stable-9build1_s390x.deb ...
166s Unpacking libevent-core-2.1-7:s390x (2.1.12-stable-9build1) over (2.1.12-stable-9) ...
166s Preparing to unpack .../079-libftdi1-2_1.5-6build4_s390x.deb ...
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166s Preparing to unpack .../080-libldap-common_2.6.7+dfsg-1~exp1ubuntu6_all.deb ...
166s Unpacking libldap-common (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
166s Selecting previously unselected package linux-modules-6.8.0-20-generic.
166s Preparing to unpack .../081-linux-modules-6.8.0-20-generic_6.8.0-20.20_s390x.deb ...
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166s Selecting previously unselected package linux-image-6.8.0-20-generic.
166s Preparing to unpack .../082-linux-image-6.8.0-20-generic_6.8.0-20.20_s390x.deb ...
166s Unpacking linux-image-6.8.0-20-generic (6.8.0-20.20) ...
166s Selecting previously unselected package linux-modules-extra-6.8.0-20-generic.
166s Preparing to unpack .../083-linux-modules-extra-6.8.0-20-generic_6.8.0-20.20_s390x.deb ...
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166s Selecting previously unselected package linux-headers-6.8.0-20.
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168s Selecting previously unselected package linux-headers-6.8.0-20-generic.
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169s Selecting previously unselected package linux-tools-common.
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169s Selecting previously unselected package ubuntu-kernel-accessories.
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170s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ...
170s Setting up pinentry-curses (1.2.1-3ubuntu4) ...
170s Setting up motd-news-config (13ubuntu8) ...
170s Setting up libtext-iconv-perl:s390x (1.7-8build2) ...
170s Setting up libtext-charwidth-perl:s390x (0.04-11build2) ...
170s Setting up libsharpyuv0:s390x (1.3.2-0.4build2) ...
170s Setting up liburcu8t64:s390x (0.14.0-3.1) ...
170s Setting up tcpdump (4.99.4-3ubuntu2) ...
170s Setting up libibverbs1:s390x (50.0-2build1) ...
170s Setting up systemd-sysv (255.4-1ubuntu5) ...
170s Setting up ubuntu-kernel-accessories (1.536build1) ...
170s Setting up libapparmor1:s390x (4.0.0-beta3-0ubuntu2) ...
170s Setting up libatm1t64:s390x (1:2.5.1-5.1) ...
170s Setting up libgdbm6t64:s390x (1.23-5.1) ...
170s Setting up bsdextrautils (2.39.3-9ubuntu2) ...
170s Setting up libxpm4:s390x (1:3.5.17-1build1) ...
170s Setting up libgdbm-compat4t64:s390x (1.23-5.1) ...
170s Setting up xdg-user-dirs (0.18-1) ...
170s Setting up ibverbs-providers:s390x (50.0-2build1) ...
170s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ...
170s Setting up libmagic-mgc (1:5.45-3) ...
170s Setting up gawk (1:5.2.1-2build2) ...
170s Setting up libjq1:s390x (1.7.1-3) ...
170s Setting up manpages (6.05.01-1) ...
170s Setting up libtirpc-common (1.3.4+ds-1.1) ...
170s Setting up libbrotli1:s390x (1.1.0-2build1) ...
170s Setting up libsqlite3-0:s390x (3.45.1-1ubuntu1) ...
170s Setting up libsasl2-modules:s390x (2.1.28+dfsg1-5ubuntu1) ...
170s Setting up libuv1t64:s390x (1.48.0-1.1) ...
170s Setting up libmagic1t64:s390x (1:5.45-3) ...
170s Setting up rsyslog (8.2312.0-3ubuntu7) ...
170s info: The user `syslog' is already a member of `adm'.
171s Setting up binutils-common:s390x (2.42-4ubuntu1) ...
171s Setting up libpsl5t64:s390x (0.21.2-1.1) ...
171s Setting up libnghttp2-14:s390x (1.59.0-1build1) ...
171s Setting up libdeflate0:s390x (1.19-1) ...
171s Setting up linux-libc-dev:s390x (6.8.0-20.20) ...
171s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ...
171s Setting up libctf-nobfd0:s390x (2.42-4ubuntu1) ...
171s Setting up libnss-systemd:s390x (255.4-1ubuntu5) ...
171s Setting up krb5-locales (1.20.1-6ubuntu1) ...
171s Setting up file (1:5.45-3) ...
171s Setting up kmod (31+20240202-2ubuntu4) ...
171s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ...
171s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ...
171s Setting up libprotobuf-c1:s390x (1.4.1-1ubuntu3) ...
171s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ...
171s Setting up xxd (2:9.1.0016-1ubuntu6) ...
171s Setting up libsframe1:s390x (2.42-4ubuntu1) ...
171s Setting up libelf1t64:s390x (0.190-1.1build2) ...
171s Setting up libkrb5support0:s390x (1.20.1-6ubuntu1) ...
171s Setting up libdw1t64:s390x (0.190-1.1build2) ...
171s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ...
171s Setting up eject (2.39.3-9ubuntu2) ...
171s Setting up apparmor (4.0.0-beta3-0ubuntu2) ...
171s Installing new version of config file /etc/apparmor.d/abstractions/authentication ...
171s Installing new version of config file /etc/apparmor.d/abstractions/crypto ...
171s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ...
171s Installing new version of config file /etc/apparmor.d/abstractions/openssl ...
171s Installing new version of config file /etc/apparmor.d/code ...
171s Installing new version of config file /etc/apparmor.d/firefox ...
172s Reloading AppArmor profiles 
173s Setting up libglib2.0-0t64:s390x (2.79.3-3ubuntu5) ...
173s No schema files found: doing nothing.
173s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
173s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
173s Setting up vim-common (2:9.1.0016-1ubuntu6) ...
173s Setting up gcc-13-base:s390x (13.2.0-21ubuntu1) ...
173s Setting up libqrtr-glib0:s390x (1.2.2-1ubuntu3) ...
173s Setting up libslang2:s390x (2.3.3-3build1) ...
173s Setting up libnvme1t64 (1.8-3) ...
173s Setting up mtr-tiny (0.95-1.1build1) ...
173s Setting up gnupg-l10n (2.4.4-2ubuntu15) ...
173s Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build6) ...
173s Setting up libdbus-1-3:s390x (1.14.10-4ubuntu2) ...
173s Setting up xz-utils (5.6.0-0.2) ...
173s Setting up perl-modules-5.38 (5.38.2-3.2) ...
173s Setting up libproc2-0:s390x (2:4.0.4-4ubuntu2) ...
173s Setting up libblockdev-utils3:s390x (3.1.0-1build1) ...
173s Setting up fonts-dejavu-mono (2.37-8) ...
173s Setting up libpng16-16t64:s390x (1.6.43-3) ...
173s Setting up systemd-timesyncd (255.4-1ubuntu5) ...
173s Setting up libevent-core-2.1-7:s390x (2.1.12-stable-9build1) ...
173s Setting up udev (255.4-1ubuntu5) ...
174s Setting up libss2:s390x (1.47.0-2.4~exp1ubuntu2) ...
174s Setting up usb.ids (2024.03.18-1) ...
174s Setting up sudo (1.9.15p5-3ubuntu3) ...
174s Setting up fonts-dejavu-core (2.37-8) ...
174s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ...
174s Setting up gir1.2-glib-2.0:s390x (2.79.3-3ubuntu5) ...
174s Setting up libk5crypto3:s390x (1.20.1-6ubuntu1) ...
174s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ...
174s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ...
174s Setting up libwebp7:s390x (1.3.2-0.4build2) ...
174s Setting up libfdisk1:s390x (2.39.3-9ubuntu2) ...
174s Setting up libdb5.3t64:s390x (5.3.28+dfsg2-6) ...
174s Setting up libblockdev-nvme3:s390x (3.1.0-1build1) ...
174s Setting up libdevmapper1.02.1:s390x (2:1.02.185-3ubuntu2) ...
174s Setting up libblockdev-fs3:s390x (3.1.0-1build1) ...
174s Setting up libaio1t64:s390x (0.3.113-6) ...
174s Setting up python-apt-common (2.7.7) ...
174s Setting up mount (2.39.3-9ubuntu2) ...
174s Setting up dmsetup (2:1.02.185-3ubuntu2) ...
174s Setting up uuid-runtime (2.39.3-9ubuntu2) ...
175s uuidd.service is a disabled or a static unit not running, not starting it.
175s Setting up libmm-glib0:s390x (1.23.4-0ubuntu1) ...
175s Setting up groff-base (1.23.0-3build1) ...
175s Setting up libcrypt-dev:s390x (1:4.4.36-4) ...
175s Setting up libplymouth5:s390x (24.004.60-1ubuntu6) ...
175s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ...
175s Setting up kpartx (0.9.4-5ubuntu6) ...
175s Setting up jq (1.7.1-3) ...
175s Setting up procps (2:4.0.4-4ubuntu2) ...
175s Setting up gpgconf (2.4.4-2ubuntu15) ...
175s Setting up libgirepository-1.0-1:s390x (1.79.1-1ubuntu6) ...
175s Setting up libjson-glib-1.0-common (1.8.0-2build1) ...
175s Setting up libkrb5-3:s390x (1.20.1-6ubuntu1) ...
175s Setting up libpython3.11-minimal:s390x (3.11.8-1build4) ...
175s Setting up libusb-1.0-0:s390x (2:1.0.27-1) ...
175s Setting up libperl5.38t64:s390x (5.38.2-3.2) ...
175s Setting up tnftp (20230507-2build1) ...
175s Setting up libbinutils:s390x (2.42-4ubuntu1) ...
175s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ...
175s Setting up libfido2-1:s390x (1.14.0-1build1) ...
175s Setting up libc-dev-bin (2.39-0ubuntu6) ...
175s Setting up openssl (3.0.13-0ubuntu2) ...
175s Setting up linux-modules-6.8.0-20-generic (6.8.0-20.20) ...
175s Setting up readline-common (8.2-4) ...
175s Setting up libxml2:s390x (2.9.14+dfsg-1.3ubuntu2) ...
175s Setting up libxmuu1:s390x (2:1.1.3-3build1) ...
175s Setting up dbus-bin (1.14.10-4ubuntu2) ...
175s Setting up info (7.1-3build1) ...
175s Setting up liblocale-gettext-perl (1.07-6ubuntu4) ...
175s Setting up gpg (2.4.4-2ubuntu15) ...
175s Setting up libgudev-1.0-0:s390x (1:238-3ubuntu2) ...
175s Setting up libpolkit-gobject-1-0:s390x (124-1ubuntu1) ...
175s Setting up libbpf1:s390x (1:1.3.0-2build1) ...
175s Setting up libmbim-glib4:s390x (1.31.2-0ubuntu2) ...
176s Setting up rsync (3.2.7-1build1) ...
176s rsync.service is a disabled or a static unit not running, not starting it.
176s Setting up libudisks2-0:s390x (2.10.1-6) ...
176s Setting up bolt (0.9.6-2build1) ...
177s bolt.service is a disabled or a static unit not running, not starting it.
177s Setting up s390-tools-data (2.31.0-0ubuntu3) ...
177s Setting up libllvm18:s390x (1:18.1.2-1ubuntu2) ...
177s Setting up gnupg-utils (2.4.4-2ubuntu15) ...
177s Setting up initramfs-tools-bin (0.142ubuntu23) ...
177s Setting up libctf0:s390x (2.42-4ubuntu1) ...
177s Setting up libjpeg8:s390x (8c-2ubuntu11) ...
177s Setting up python3.11-minimal (3.11.8-1build4) ...
178s Setting up libclang1-18 (1:18.1.2-1ubuntu2) ...
178s Setting up manpages-dev (6.05.01-1) ...
178s Setting up linux-modules-extra-6.8.0-20-generic (6.8.0-20.20) ...
178s Setting up apt-utils (2.7.14) ...
178s Setting up binutils-s390x-linux-gnu (2.42-4ubuntu1) ...
178s Setting up gpg-agent (2.4.4-2ubuntu15) ...
179s Setting up libpython3.12-stdlib:s390x (3.12.2-4build3) ...
179s Setting up libblockdev-mdraid3:s390x (3.1.0-1build1) ...
179s Setting up wget (1.21.4-1ubuntu2) ...
179s Setting up linux-image-6.8.0-20-generic (6.8.0-20.20) ...
179s I: /boot/vmlinuz is now a symlink to vmlinuz-6.8.0-20-generic
179s I: /boot/initrd.img is now a symlink to initrd.img-6.8.0-20-generic
179s Setting up libblockdev-swap3:s390x (3.1.0-1build1) ...
179s Setting up plymouth (24.004.60-1ubuntu6) ...
179s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic
179s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
183s Not invoking zipl: initrd doesn't exist yet
183s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
183s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
183s Setting up fontconfig-config (2.15.0-1.1ubuntu1) ...
183s Setting up libxmlb2:s390x (0.3.15-1build1) ...
183s Setting up btrfs-progs (6.6.3-1.1build1) ...
183s Setting up libpython3.11-stdlib:s390x (3.11.8-1build4) ...
183s Setting up python3.12 (3.12.2-4build3) ...
185s Setting up libblockdev-loop3:s390x (3.1.0-1build1) ...
185s Setting up gpgsm (2.4.4-2ubuntu15) ...
185s Setting up inetutils-telnet (2:2.5-3ubuntu3) ...
185s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ...
185s update-initramfs: deferring update (trigger activated)
185s e2scrub_all.service is a disabled or a static unit not running, not starting it.
186s Setting up libparted2t64:s390x (3.6-3.1build2) ...
186s Setting up linux-headers-generic (6.8.0-20.20+1) ...
186s Setting up dbus-daemon (1.14.10-4ubuntu2) ...
186s Setting up binutils (2.42-4ubuntu1) ...
186s Setting up libmbim-proxy (1.31.2-0ubuntu2) ...
186s Setting up vim-tiny (2:9.1.0016-1ubuntu6) ...
186s Setting up libnetplan1:s390x (1.0-1) ...
186s Setting up man-db (2.12.0-3build4) ...
186s Updating database of manual pages ...
188s man-db.service is a disabled or a static unit not running, not starting it.
188s Setting up libblockdev3:s390x (3.1.0-1build1) ...
188s Setting up fdisk (2.39.3-9ubuntu2) ...
188s Setting up multipath-tools (0.9.4-5ubuntu6) ...
189s Setting up libjson-glib-1.0-0:s390x (1.8.0-2build1) ...
189s Setting up libblockdev-part3:s390x (3.1.0-1build1) ...
189s Setting up libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu1) ...
189s Setting up hwdata (0.379-1) ...
189s Setting up libftdi1-2:s390x (1.5-6build4) ...
189s Setting up perl (5.38.2-3.2) ...
189s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ...
189s update-initramfs: deferring update (trigger activated)
189s Setting up libfreetype6:s390x (2.13.2+dfsg-1build2) ...
189s Setting up gir1.2-girepository-2.0:s390x (1.79.1-1ubuntu6) ...
189s Setting up dbus (1.14.10-4ubuntu2) ...
189s A reboot is required to replace the running dbus-daemon.
189s Please reboot the system when convenient.
189s Setting up shared-mime-info (2.4-1build1) ...
189s Setting up libgssapi-krb5-2:s390x (1.20.1-6ubuntu1) ...
189s Setting up ftp (20230507-2build1) ...
189s Setting up keyboxd (2.4.4-2ubuntu15) ...
189s Setting up libdpkg-perl (1.22.6ubuntu5) ...
189s Setting up libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu1) ...
189s Setting up libssh-4:s390x (0.10.6-2build1) ...
189s Setting up ieee-data (20220827.1) ...
189s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu1) ...
189s Setting up libpam-systemd:s390x (255.4-1ubuntu5) ...
189s Setting up libpolkit-agent-1-0:s390x (124-1ubuntu1) ...
189s Setting up libc6-dev:s390x (2.39-0ubuntu6) ...
189s Setting up libgpgme11t64:s390x (1.18.0-4.1ubuntu3) ...
189s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu1) ...
189s Setting up linux-image-virtual (6.8.0-20.20+1) ...
189s Setting up netplan-generator (1.0-1) ...
190s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
190s Setting up initramfs-tools-core (0.142ubuntu23) ...
190s Setting up libclang-cpp18 (1:18.1.2-1ubuntu2) ...
190s Setting up libbpfcc:s390x (0.29.1+ds-1ubuntu4) ...
190s Setting up linux-tools-common (6.8.0-20.20) ...
190s Setting up libarchive13t64:s390x (3.7.2-1.1ubuntu2) ...
190s Setting up libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu6) ...
190s Setting up libpython3-stdlib:s390x (3.12.2-0ubuntu1) ...
190s Setting up systemd-resolved (255.4-1ubuntu5) ...
190s Setting up python3.11 (3.11.8-1build4) ...
191s Setting up linux-image-generic (6.8.0-20.20+1) ...
191s Setting up telnet (0.17+2.5-3ubuntu3) ...
191s Setting up initramfs-tools (0.142ubuntu23) ...
191s update-initramfs: deferring update (trigger activated)
191s Setting up linux-headers-virtual (6.8.0-20.20+1) ...
191s Setting up linux-generic (6.8.0-20.20+1) ...
191s Setting up libcurl4t64:s390x (8.5.0-2ubuntu8) ...
191s Setting up bpftrace (0.20.2-1ubuntu1) ...
191s Setting up bind9-libs:s390x (1:9.18.24-0ubuntu3) ...
191s Setting up libtirpc3t64:s390x (1.3.4+ds-1.1) ...
191s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ...
191s Setting up iproute2 (6.1.0-1ubuntu5) ...
191s Setting up openssh-client (1:9.6p1-3ubuntu11) ...
191s Setting up libgusb2:s390x (0.4.8-1build1) ...
191s Setting up libcurl3t64-gnutls:s390x (8.5.0-2ubuntu8) ...
191s Setting up parted (3.6-3.1build2) ...
191s Setting up libqmi-glib5:s390x (1.35.2-0ubuntu1) ...
191s Setting up linux-tools-6.8.0-20 (6.8.0-20.20) ...
191s Setting up python3 (3.12.2-0ubuntu1) ...
191s Setting up libjcat1:s390x (0.2.0-2build2) ...
191s Setting up dpkg-dev (1.22.6ubuntu5) ...
191s Setting up linux-virtual (6.8.0-20.20+1) ...
191s Setting up dirmngr (2.4.4-2ubuntu15) ...
192s Setting up dbus-user-session (1.14.10-4ubuntu2) ...
192s Setting up linux-tools-6.8.0-20-generic (6.8.0-20.20) ...
192s Setting up python3-cryptography (41.0.7-4build2) ...
192s Setting up python3-gi (3.47.0-3build1) ...
192s Setting up libgd3:s390x (2.3.3-9ubuntu3) ...
192s Setting up python3-typing-extensions (4.10.0-1) ...
192s Setting up lsof (4.95.0-1build2) ...
192s Setting up python3-pyrsistent:s390x (0.20.0-1build1) ...
192s Setting up python3-netaddr (0.8.0-2ubuntu1) ...
193s Setting up libnsl2:s390x (1.3.0-3build2) ...
193s Setting up gnupg (2.4.4-2ubuntu15) ...
193s Setting up python3-netplan (1.0-1) ...
193s Setting up curl (8.5.0-2ubuntu8) ...
193s Setting up libvolume-key1:s390x (0.3.12-7build1) ...
193s Setting up bind9-host (1:9.18.24-0ubuntu3) ...
193s Setting up python3-lib2to3 (3.12.2-3ubuntu1.1) ...
193s Setting up python3-bpfcc (0.29.1+ds-1ubuntu4) ...
193s Setting up libc-devtools (2.39-0ubuntu6) ...
193s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ...
193s Setting up python3-distutils (3.12.2-3ubuntu1.1) ...
193s python3.12: can't get files for byte-compilation
193s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ...
193s Setting up python3-dbus (1.3.2-5build2) ...
194s Setting up python3-setuptools (68.1.2-2ubuntu1) ...
194s Setting up gpg-wks-client (2.4.4-2ubuntu15) ...
194s Setting up openssh-server (1:9.6p1-3ubuntu11) ...
194s Replacing config file /etc/ssh/sshd_config with new version
196s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket.

197s Setting up libblockdev-crypto3:s390x (3.1.0-1build1) ...
197s Setting up python3-gdbm:s390x (3.12.2-3ubuntu1.1) ...
197s Setting up python3-apt (2.7.7) ...
197s Setting up libfwupd2:s390x (1.9.15-2) ...
197s Setting up python3-yaml (6.0.1-2build1) ...
197s Setting up libqmi-proxy (1.35.2-0ubuntu1) ...
197s Setting up netplan.io (1.0-1) ...
197s Setting up bpfcc-tools (0.29.1+ds-1ubuntu4) ...
197s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ...
197s Setting up ubuntu-pro-client (31.2.2) ...
199s Setting up fwupd (1.9.15-2) ...
199s fwupd-offline-update.service is a disabled or a static unit not running, not starting it.
199s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
199s Setting up ubuntu-pro-client-l10n (31.2.2) ...
199s Setting up udisks2 (2.10.1-6) ...
200s Processing triggers for ufw (0.36.2-5) ...
200s Processing triggers for debianutils (5.17) ...
200s Processing triggers for install-info (7.1-3build1) ...
200s Processing triggers for libc-bin (2.39-0ubuntu6) ...
200s Processing triggers for linux-image-6.8.0-20-generic (6.8.0-20.20) ...
200s /etc/kernel/postinst.d/initramfs-tools:
200s update-initramfs: Generating /boot/initrd.img-6.8.0-20-generic
200s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
204s Using config file '/etc/zipl.conf'
204s Building bootmap in '/boot'
204s Adding IPL section 'ubuntu' (default)
204s Preparing boot device for LD-IPL: vda (0000).
204s Done.
204s /etc/kernel/postinst.d/zz-zipl:
204s Using config file '/etc/zipl.conf'
204s Building bootmap in '/boot'
204s Adding IPL section 'ubuntu' (default)
204s Preparing boot device for LD-IPL: vda (0000).
204s Done.
204s Processing triggers for initramfs-tools (0.142ubuntu23) ...
204s update-initramfs: Generating /boot/initrd.img-6.8.0-20-generic
204s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
208s Using config file '/etc/zipl.conf'
208s Building bootmap in '/boot'
208s Adding IPL section 'ubuntu' (default)
208s Preparing boot device for LD-IPL: vda (0000).
208s Done.
209s Reading package lists...
209s Building dependency tree...
209s Reading state information...
209s The following packages will be REMOVED:
209s   libaio1* libnetplan0* python3-distutils* python3-lib2to3*
210s 0 upgraded, 0 newly installed, 4 to remove and 1 not upgraded.
210s After this operation, 1445 kB disk space will be freed.
210s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81786 files and directories currently installed.)
210s Removing libaio1:s390x (0.3.113-5) ...
210s Removing libnetplan0:s390x (0.107.1-3) ...
210s Removing python3-distutils (3.12.2-3ubuntu1.1) ...
210s Removing python3-lib2to3 (3.12.2-3ubuntu1.1) ...
210s Processing triggers for libc-bin (2.39-0ubuntu6) ...
210s autopkgtest [22:19:17]: rebooting testbed after setup commands that affected boot
246s autopkgtest [22:19:53]: testbed running kernel: Linux 6.8.0-20-generic #20-Ubuntu SMP Mon Mar 18 10:49:25 UTC 2024
249s autopkgtest [22:19:56]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo
255s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B]
255s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB]
255s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B]
256s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC
256s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
256s gpgv:                issuer "tille@debian.org"
256s gpgv: Can't check signature: No public key
256s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found
256s autopkgtest [22:20:03]: testing package tombo version 1.5.1-6
256s autopkgtest [22:20:03]: build not needed
263s autopkgtest [22:20:10]: test run-unit-test: preparing testbed
264s Reading package lists...
264s Building dependency tree...
264s Reading state information...
264s Starting pkgProblemResolver with broken count: 0
264s Starting 2 pkgProblemResolver with broken count: 0
264s Done
265s The following additional packages will be installed:
265s   fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5
265s   libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax
265s   libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2
265s   python3-decorator python3-h5py python3-h5py-serial python3-mappy
265s   python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo
265s   tombo-doc
265s Suggested packages:
265s   fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc
265s   gfortran python3-dev python3-pytest python-scipy-doc
265s Recommended packages:
265s   javascript-common g++ | c++-compiler python3-pil python3-pyfaidx
265s   python3-rpy2
265s The following NEW packages will be installed:
265s   autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0
265s   libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery
265s   libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1
265s   libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy
265s   python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo
265s   tombo-doc
265s 0 upgraded, 27 newly installed, 0 to remove and 1 not upgraded.
265s Need to get 65.9 MB/65.9 MB of archives.
265s After this operation, 229 MB of additional disk space will be used.
265s Get:1 /tmp/autopkgtest.ZrneC5/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B]
265s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fonts-lato all 2.015-1 [2781 kB]
269s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
269s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
271s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libaec0 s390x 1.1.2-1 [25.7 kB]
271s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB]
271s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgfortran5 s390x 14-20240315-1ubuntu1 [600 kB]
272s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libsz2 s390x 1.1.2-1 [5346 B]
272s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-3.1ubuntu3 [1436 kB]
273s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-3.1ubuntu3 [58.2 kB]
273s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
273s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
273s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjs-sphinxdoc all 7.2.6-6 [149 kB]
273s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB]
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276s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB]
277s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x python3-scipy s390x 1.11.4-6 [20.1 MB]
280s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x tombo s390x 1.5.1-6 [502 kB]
280s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
280s Get:27 http://ftpmaster.internal/ubuntu noble/universe s390x tombo-doc all 1.5.1-6 [21.7 MB]
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293s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d'
293s   CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])')
294s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|'
294s   '`conda list | grep "r-base\|rpy2"` (last columns should match).')
294s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+'
294s   re.match('\+', fastq_rec[2]) is None):
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298s autopkgtest [22:20:45]: test run-unit-test: [-----------------------
298s ********* Testing help commands **********
298s usage: tombo [-h] [-v]
298s              {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot}
298s              ...
298s 
298s ********** Tombo *********
298s 
298s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.
298s 
298s Tombo also provides tools for the analysis and visualization of raw nanopore signal.
298s 
298s Tombo command groups (additional help available within each command group):
298s 	resquiggle               Re-annotate raw signal with genomic alignment from existing basecalls.
298s 	preprocess               Pre-process nanopore reads for Tombo processing.
298s 	filter                   Apply filter to Tombo index file for specified criterion.
298s 	detect_modifications     Perform statistical testing to detect non-standard nucleotides.
298s 	text_output              Output Tombo results in text files.
298s 	build_model              Create canonical and alternative base Tombo models.
298s 	plot                     Save plots to visualize raw nanopore signal or testing results.
298s 
298s options:
298s   -h, --help            show this help message and exit
298s   -v, --version         show Tombo version and exit.
298s usage: tombo resquiggle [--dna] [--rna]
298s                         [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]]
298s                         [--q-score Q_SCORE]
298s                         [--signal-matching-score SIGNAL_MATCHING_SCORE]
298s                         [--processes PROCESSES]
298s                         [--corrected-group CORRECTED_GROUP]
298s                         [--basecall-group BASECALL_GROUP]
298s                         [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
298s                         [--overwrite]
298s                         [--failed-reads-filename FAILED_READS_FILENAME]
298s                         [--num-most-common-errors NUM_MOST_COMMON_ERRORS]
298s                         [--print-advanced-arguments] [--quiet] [--help]
298s                         fast5s_basedir reference
298s 
298s Required Arguments:
298s   fast5s_basedir        Directory containing fast5 files. All files ending in
298s                         "fast5" found recursively within this base directory
298s                         will be processed.
298s   reference             Reference genome/transcriptome FASTA file or minimap2
298s                         index (with "map-ont" preset) for mapping.
298s 
298s Model Parameters:
298s   --dna                 Explicitly select canonical DNA model. Default:
298s                         Automatically determine from FAST5s
298s   --rna                 Explicitly select canonical RNA model. Default:
298s                         Automatically determine from FAST5s
298s 
298s Read Filtering Argument:
298s   --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]
298s                         Filter reads based on observations per base percentile
298s                         thresholds. Format thresholds as "percentile:thresh
298s                         [pctl2:thresh2 ...]". For example to filter reads with
298s                         99th pctl > 200 obs/base or max > 5k obs/base use
298s                         "99:200 100:5000".
298s   --q-score Q_SCORE     Q-score threshold for filtering low quality reads.
298s                         Default: 0.000000
298s   --signal-matching-score SIGNAL_MATCHING_SCORE
298s                         Observed to expected signal matching score (higher
298s                         score indicates poor matching). Sample type defaults:
298s                         RNA : 2 || DNA : 1.1
298s 
298s Multiprocessing Arguments:
298s   --processes PROCESSES
298s                         Number of processes. Default: 1
298s 
298s FAST5 Data Arguments:
298s   --corrected-group CORRECTED_GROUP
298s                         FAST5 group created by resquiggle command. Default:
298s                         RawGenomeCorrected_000
298s   --basecall-group BASECALL_GROUP
298s                         FAST5 group obtain original basecalls (under Analyses
298s                         group). Default: Basecall_1D_000
298s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
298s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
298s                         group]/) containing basecalls and created within
298s                         [--corrected-group] containing re-squiggle results.
298s                         Default: ['BaseCalled_template']
298s   --overwrite           Overwrite previous corrected group in FAST5 files.
298s                         Note: only effects --corrected-group or --new-
298s                         corrected-group.
298s 
298s Input/Output Arguments:
298s   --failed-reads-filename FAILED_READS_FILENAME
298s                         Output failed read filenames with assoicated error.
298s                         Default: Do not store failed reads.
298s   --num-most-common-errors NUM_MOST_COMMON_ERRORS
298s                         Dynamically show this many most common errors so far
298s                         through run. Default: 0; Just show progress
298s 
298s Advanced Arguments:
298s   --print-advanced-arguments
298s                         Print advanced re-squiggle arguments and exit.
298s 
298s Miscellaneous Arguments:
298s   --quiet, -q           Don't print status information.
298s   --help, -h            Print this help message and exit
298s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR
298s                                                  --fastq-filenames
298s                                                  FASTQ_FILENAMES
298s                                                  [FASTQ_FILENAMES ...]
298s                                                  [--basecall-group BASECALL_GROUP]
298s                                                  [--basecall-subgroup BASECALL_SUBGROUP]
298s                                                  [--overwrite]
298s                                                  [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]]
298s                                                  [--processes PROCESSES]
298s                                                  [--quiet] [--help]
298s 
298s Required Arguments:
298s   --fast5-basedir FAST5_BASEDIR
298s                         Directory containing fast5 files.
298s   --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...]
298s                         FASTQ filenames containing basecalls to be added to
298s                         raw FAST5 files.
298s 
298s FAST5 Data Arguments:
298s   --basecall-group BASECALL_GROUP
298s                         FAST5 group obtain original basecalls (under Analyses
298s                         group). Default: Basecall_1D_000
298s   --basecall-subgroup BASECALL_SUBGROUP
298s                         FAST5 subgroup (under /Analyses/[--basecall-group]/)
298s                         under which to store basecalls from FASTQs. Default:
298s                         BaseCalled_template
298s   --overwrite           Overwrite previous corrected group in FAST5 files.
298s                         Note: only effects --corrected-group or --new-
298s                         corrected-group.
298s 
298s Sequencing Summary Argument:
298s   --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]
298s                         Sequencing summary filenames produced by albacore.
298s                         These can make annotation of raw FAST5 files with
298s                         FASTQ sequence much faster.
298s 
298s Multiprocessing Argument:
298s   --processes PROCESSES
298s                         Number of processes. Default: 1
298s 
298s Miscellaneous Arguments:
298s   --quiet, -q           Don't print status information.
298s   --help, -h            Print this help message and exit
298s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS
298s                                   [FAST5_BASEDIRS ...]
298s                                   [--corrected-group CORRECTED_GROUP]
298s                                   [--quiet] [--help]
298s 
298s Required Argument:
298s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
298s                         Directories containing fast5 files.
298s 
298s FAST5 Data Argument:
298s   --corrected-group CORRECTED_GROUP
298s                         FAST5 group created by resquiggle command. Default:
298s                         RawGenomeCorrected_000
298s 
298s Miscellaneous Arguments:
298s   --quiet, -q           Don't print status information.
298s   --help, -h            Print this help message and exit
298s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
298s                           [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]]
298s                           [--corrected-group CORRECTED_GROUP] [--quiet]
298s                           [--help]
298s 
298s Required Argument:
298s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
298s                         Directories containing fast5 files.
298s 
298s Read Filtering Argument:
298s   --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]
298s                         Filter reads based on observations per base percentile
298s                         thresholds. Format thresholds as "percentile:thresh
298s                         [pctl2:thresh2 ...]". For example to filter reads with
298s                         99th pctl > 200 obs/base or max > 5k obs/base use
298s                         "99:200 100:5000".
298s 
298s FAST5 Data Argument:
298s   --corrected-group CORRECTED_GROUP
298s                         FAST5 group created by resquiggle command. Default:
298s                         RawGenomeCorrected_000
298s 
298s Miscellaneous Arguments:
298s   --quiet, -q           Don't print status information.
298s   --help, -h            Print this help message and exit
298s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS
298s                                    [FAST5_BASEDIRS ...]
298s                                    [--percent-to-filter PERCENT_TO_FILTER]
298s                                    [--corrected-group CORRECTED_GROUP]
298s                                    [--quiet] [--help]
298s 
298s Required Arguments:
298s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
298s                         Directories containing fast5 files.
298s 
298s Read Filtering Argument:
298s   --percent-to-filter PERCENT_TO_FILTER
298s                         Percentage of all reads to filter. Reads are randomly
298s                         selected weighted according to the approximate
298s                         coverage at the mapped genomic location. This can be
298s                         useful in modeling and testing. Default: 10.000000
298s 
298s FAST5 Data Arguments:
298s   --corrected-group CORRECTED_GROUP
298s                         FAST5 group created by resquiggle command. Default:
298s                         RawGenomeCorrected_000
298s 
298s Miscellaneous Arguments:
298s   --quiet, -q           Don't print status information.
298s   --help, -h            Print this help message and exit
298s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS
298s                             [FAST5_BASEDIRS ...] [--q-score Q_SCORE]
298s                             [--corrected-group CORRECTED_GROUP]
298s                             [--basecall-group BASECALL_GROUP] [--quiet]
298s                             [--help]
298s 
298s Required Arguments:
298s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
298s                         Directories containing fast5 files.
298s 
298s Read Filtering Argument:
298s   --q-score Q_SCORE     Q-score threshold for filtering low quality reads.
298s                         Default: 7.000000
298s 
298s FAST5 Data Arguments:
298s   --corrected-group CORRECTED_GROUP
298s                         FAST5 group created by resquiggle command. Default:
298s                         RawGenomeCorrected_000
298s   --basecall-group BASECALL_GROUP
298s                         FAST5 group obtain original basecalls (under Analyses
298s                         group). Default: Basecall_1D_000
298s 
298s Miscellaneous Arguments:
298s   --quiet, -q           Don't print status information.
298s   --help, -h            Print this help message and exit
298s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS
298s                                         [FAST5_BASEDIRS ...]
298s                                         --signal-matching-score
298s                                         SIGNAL_MATCHING_SCORE
298s                                         [--corrected-group CORRECTED_GROUP]
298s                                         [--quiet] [--help]
298s 
298s Required Arguments:
298s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
298s                         Directories containing fast5 files.
298s   --signal-matching-score SIGNAL_MATCHING_SCORE
298s                         Observed to expected signal matching score (higher
298s                         score indicates poor matching). Sample type defaults:
298s                         RNA : 2 || DNA : 1.1
298s 
298s FAST5 Data Arguments:
298s   --corrected-group CORRECTED_GROUP
298s                         FAST5 group created by resquiggle command. Default:
298s                         RawGenomeCorrected_000
298s 
298s Miscellaneous Arguments:
298s   --quiet, -q           Don't print status information.
298s   --help, -h            Print this help message and exit
299s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS
299s                                      [FAST5_BASEDIRS ...]
299s                                      [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]]
299s                                      [--include-partial-overlap]
299s                                      [--corrected-group CORRECTED_GROUP]
299s                                      [--quiet] [--help]
299s 
299s Required Arguments:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s   --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]
299s                         Filter out reads not falling completely within include
299s                         regions. Omit start and end coordinates to include an
299s                         entire chromosome/sequence record. Format regions as
299s                         "chrm[:start-end] [chrm2[:start2-end2] ...]".
299s 
299s Filter Argument:
299s   --include-partial-overlap
299s                         Include reads that partially overlap the specified
299s                         region. Default: Only include reads completely
299s                         contained in a specified region
299s 
299s FAST5 Data Argument:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS
299s                                           [FAST5_BASEDIRS ...]
299s                                           --statistics-file-basename
299s                                           STATISTICS_FILE_BASENAME [--dna]
299s                                           [--rna]
299s                                           [--fishers-method-context FISHERS_METHOD_CONTEXT]
299s                                           [--minimum-test-reads MINIMUM_TEST_READS]
299s                                           [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]]
299s                                           [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
299s                                           [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME]
299s                                           [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
299s                                           [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
299s                                           [--processes PROCESSES]
299s                                           [--corrected-group CORRECTED_GROUP]
299s                                           [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                           [--quiet] [--help]
299s 
299s Required Argument:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s   --statistics-file-basename STATISTICS_FILE_BASENAME
299s                         File base name to save base by base statistics from
299s                         testing. Filenames will be [--statistics-file-
299s                         basename].[--alternate-bases]?.tombo.stats
299s 
299s Comparison Model Arguments:
299s   --dna                 Explicitly select canonical DNA model. Default:
299s                         Automatically determine from FAST5s
299s   --rna                 Explicitly select canonical RNA model. Default:
299s                         Automatically determine from FAST5s
299s 
299s Significance Test Arguments:
299s   --fishers-method-context FISHERS_METHOD_CONTEXT
299s                         Number of context bases up and downstream over which
299s                         to compute Fisher's method combined p-values. Note:
299s                         Not applicable for alternative model likelihood ratio
299s                         tests. Default: 1.
299s   --minimum-test-reads MINIMUM_TEST_READS
299s                         Number of reads required at a position to perform
299s                         significance testing or contribute to model
299s                         estimation. Default: 1
299s   --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]
299s                         P-value threshold when computing fraction of
299s                         significant reads at each genomic position. If two
299s                         values are provided, statistics between these values
299s                         are not considered. Default thresholds: DNA:0.15-0.5 ,
299s                         RNA:0.05-0.4
299s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
299s                         Dampen fraction modified estimates for low coverage
299s                         sites. Two parameters are unmodified and modified
299s                         pseudo read counts. This is equivalent to a beta prior
299s                         on the fraction estimate. Set to "0 0" to disable
299s                         dampened fraction estimation. Default: [2, 0]
299s 
299s Output Argument:
299s   --per-read-statistics-basename PER_READ_STATISTICS_BASENAME
299s                         Base for binary files containing per-read statistics
299s                         from statistical testing. Filenames will be [--per-
299s                         read-statistics-basename].[--alternate-
299s                         bases]?.tombo.per_read_stats
299s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
299s                         Number of the most significant sites to store for
299s                         faster access. If a longer list of most significant
299s                         sites is required the list must be re-computed from
299s                         all batches. Very large values can increase RAM usage.
299s                         Default: 100000
299s 
299s Multiprocessing Arguments:
299s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
299s                         Size of regions over which to multiprocesses statistic
299s                         computation. For very deep samples a smaller value is
299s                         recommmended in order to control memory consumption.
299s                         Default: 10000
299s   --processes PROCESSES
299s                         Number of processes. Default: 1
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo detect_modifications alternative_model
299s                                                     [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
299s                                                     [--statistics-file-basename STATISTICS_FILE_BASENAME]
299s                                                     [--alternate-bases {dam,5mC,6mA,CpG,dcm} [{dam,5mC,6mA,CpG,dcm} ...]]
299s                                                     [--print-available-models]
299s                                                     [--dna] [--rna]
299s                                                     [--minimum-test-reads MINIMUM_TEST_READS]
299s                                                     [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]]
299s                                                     [--standard-log-likelihood-ratio]
299s                                                     [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
299s                                                     [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME]
299s                                                     [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
299s                                                     [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
299s                                                     [--processes PROCESSES]
299s                                                     [--corrected-group CORRECTED_GROUP]
299s                                                     [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                                     [--quiet] [--help]
299s 
299s Required Argument:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s   --statistics-file-basename STATISTICS_FILE_BASENAME
299s                         File base name to save base by base statistics from
299s                         testing. Filenames will be [--statistics-file-
299s                         basename].[--alternate-bases]?.tombo.stats
299s   --alternate-bases {dam,5mC,6mA,CpG,dcm} [{dam,5mC,6mA,CpG,dcm} ...]
299s                         Default non-standard base model for testing (not
299s                         required if user created --alternate-model-filenames
299s                         is provided).
299s 
299s Comparison Arguments:
299s   --print-available-models
299s                         Print available alternative models and exit.
299s   --dna                 Explicitly select canonical DNA model. Default:
299s                         Automatically determine from FAST5s
299s   --rna                 Explicitly select canonical RNA model. Default:
299s                         Automatically determine from FAST5s
299s 
299s Significance Test Arguments:
299s   --minimum-test-reads MINIMUM_TEST_READS
299s                         Number of reads required at a position to perform
299s                         significance testing or contribute to model
299s                         estimation. Default: 1
299s   --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]
299s                         Log likelihood ratio threshold when computing fraction
299s                         of significant reads at each genomic position. If two
299s                         values are provided, statistics between these values
299s                         are not considered. Default thresholds: DNA:-1.5-2.5 ,
299s                         RNA:-2.5-2.5
299s   --standard-log-likelihood-ratio
299s                         Use a standard log likelihood ratio (LLR) statistic.
299s                         Default is to use an outlier-robust LLR-like
299s                         statistic. Detail in full online documentation.
299s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
299s                         Dampen fraction modified estimates for low coverage
299s                         sites. Two parameters are unmodified and modified
299s                         pseudo read counts. This is equivalent to a beta prior
299s                         on the fraction estimate. Set to "0 0" to disable
299s                         dampened fraction estimation. Default: [2, 0]
299s 
299s Output Argument:
299s   --per-read-statistics-basename PER_READ_STATISTICS_BASENAME
299s                         Base for binary files containing per-read statistics
299s                         from statistical testing. Filenames will be [--per-
299s                         read-statistics-basename].[--alternate-
299s                         bases]?.tombo.per_read_stats
299s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
299s                         Number of the most significant sites to store for
299s                         faster access. If a longer list of most significant
299s                         sites is required the list must be re-computed from
299s                         all batches. Very large values can increase RAM usage.
299s                         Default: 100000
299s 
299s Multiprocessing Arguments:
299s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
299s                         Size of regions over which to multiprocesses statistic
299s                         computation. For very deep samples a smaller value is
299s                         recommmended in order to control memory consumption.
299s                         Default: 10000
299s   --processes PROCESSES
299s                         Number of processes. Default: 1
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo detect_modifications model_sample_compare --fast5-basedirs
299s                                                        FAST5_BASEDIRS
299s                                                        [FAST5_BASEDIRS ...]
299s                                                        --statistics-file-basename
299s                                                        STATISTICS_FILE_BASENAME
299s                                                        --control-fast5-basedirs
299s                                                        CONTROL_FAST5_BASEDIRS
299s                                                        [CONTROL_FAST5_BASEDIRS ...]
299s                                                        [--sample-only-estimates]
299s                                                        [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS]
299s                                                        [--dna] [--rna]
299s                                                        [--fishers-method-context FISHERS_METHOD_CONTEXT]
299s                                                        [--minimum-test-reads MINIMUM_TEST_READS]
299s                                                        [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]]
299s                                                        [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
299s                                                        [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME]
299s                                                        [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
299s                                                        [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
299s                                                        [--processes PROCESSES]
299s                                                        [--corrected-group CORRECTED_GROUP]
299s                                                        [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                                        [--quiet] [--help]
299s 
299s Required Argument:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s   --statistics-file-basename STATISTICS_FILE_BASENAME
299s                         File base name to save base by base statistics from
299s                         testing. Filenames will be [--statistics-file-
299s                         basename].[--alternate-bases]?.tombo.stats
299s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
299s                         Set of directories containing fast5 files for control
299s                         reads, containing only canonical nucleotides.
299s 
299s Model Prior Arguments:
299s   --sample-only-estimates
299s                         Only use canonical sample to estimate expected signal
299s                         level and spread. Default: Use canonical model to
299s                         improve estimtates (esp. for low coverage regions)
299s                         using baysian posterior estimates.
299s   --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS
299s                         Prior weights (one each for mean and spread) applied
299s                         to canonical base model for estimating posterior model
299s                         parameters for sample comparison. Default: [5, 40]
299s   --dna                 Explicitly select canonical DNA model. Default:
299s                         Automatically determine from FAST5s
299s   --rna                 Explicitly select canonical RNA model. Default:
299s                         Automatically determine from FAST5s
299s 
299s Significance Test Arguments:
299s   --fishers-method-context FISHERS_METHOD_CONTEXT
299s                         Number of context bases up and downstream over which
299s                         to compute Fisher's method combined p-values. Note:
299s                         Not applicable for alternative model likelihood ratio
299s                         tests. Default: 1.
299s   --minimum-test-reads MINIMUM_TEST_READS
299s                         Number of reads required at a position to perform
299s                         significance testing or contribute to model
299s                         estimation. Default: 1
299s   --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]
299s                         P-value threshold when computing fraction of
299s                         significant reads at each genomic position. If two
299s                         values are provided, statistics between these values
299s                         are not considered. Default thresholds: DNA:0.15-0.5 ,
299s                         RNA:0.05-0.4
299s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
299s                         Dampen fraction modified estimates for low coverage
299s                         sites. Two parameters are unmodified and modified
299s                         pseudo read counts. This is equivalent to a beta prior
299s                         on the fraction estimate. Set to "0 0" to disable
299s                         dampened fraction estimation. Default: [2, 0]
299s 
299s Output Argument:
299s   --per-read-statistics-basename PER_READ_STATISTICS_BASENAME
299s                         Base for binary files containing per-read statistics
299s                         from statistical testing. Filenames will be [--per-
299s                         read-statistics-basename].[--alternate-
299s                         bases]?.tombo.per_read_stats
299s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
299s                         Number of the most significant sites to store for
299s                         faster access. If a longer list of most significant
299s                         sites is required the list must be re-computed from
299s                         all batches. Very large values can increase RAM usage.
299s                         Default: 100000
299s 
299s Multiprocessing Arguments:
299s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
299s                         Size of regions over which to multiprocesses statistic
299s                         computation. For very deep samples a smaller value is
299s                         recommmended in order to control memory consumption.
299s                         Default: 10000
299s   --processes PROCESSES
299s                         Number of processes. Default: 1
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo detect_modifications level_sample_compare --fast5-basedirs
299s                                                        FAST5_BASEDIRS
299s                                                        [FAST5_BASEDIRS ...]
299s                                                        --statistics-file-basename
299s                                                        STATISTICS_FILE_BASENAME
299s                                                        --alternate-fast5-basedirs
299s                                                        ALTERNATE_FAST5_BASEDIRS
299s                                                        [ALTERNATE_FAST5_BASEDIRS ...]
299s                                                        [--fishers-method-context FISHERS_METHOD_CONTEXT]
299s                                                        [--minimum-test-reads MINIMUM_TEST_READS]
299s                                                        [--statistic-type {ks,u,t}]
299s                                                        [--store-p-value]
299s                                                        [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
299s                                                        [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
299s                                                        [--processes PROCESSES]
299s                                                        [--corrected-group CORRECTED_GROUP]
299s                                                        [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                                        [--quiet] [--help]
299s 
299s Required Argument:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s   --statistics-file-basename STATISTICS_FILE_BASENAME
299s                         File base name to save base by base statistics from
299s                         testing. Filenames will be [--statistics-file-
299s                         basename].[--alternate-bases]?.tombo.stats
299s   --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...]
299s                         Set of directories containing fast5 files for
299s                         alternate set of reads.
299s 
299s Significance Test Arguments:
299s   --fishers-method-context FISHERS_METHOD_CONTEXT
299s                         Number of context bases up and downstream over which
299s                         to compute Fisher's method combined p-values. Note:
299s                         Not applicable for alternative model likelihood ratio
299s                         tests. Default: 1.
299s   --minimum-test-reads MINIMUM_TEST_READS
299s                         Number of reads required at a position to perform
299s                         significance testing or contribute to model
299s                         estimation. Default: 50
299s   --statistic-type {ks,u,t}
299s                         Type of statistical test to apply. Default: "ks"
299s   --store-p-value       Store p-value instead of effect-size statistic.
299s                         Statistics are D-statistic (KS-test), deviation from
299s                         even common language effect size (u-test), and Cohen's
299s                         D (t-test).
299s 
299s Output Argument:
299s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
299s                         Number of the most significant sites to store for
299s                         faster access. If a longer list of most significant
299s                         sites is required the list must be re-computed from
299s                         all batches. Very large values can increase RAM usage.
299s                         Default: 100000
299s 
299s Multiprocessing Arguments:
299s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
299s                         Size of regions over which to multiprocesses statistic
299s                         computation. For very deep samples a smaller value is
299s                         recommmended in order to control memory consumption.
299s                         Default: 10000
299s   --processes PROCESSES
299s                         Number of processes. Default: 1
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo detect_modifications aggregate_per_read_stats
299s                                                            --per-read-statistics-filename
299s                                                            PER_READ_STATISTICS_FILENAME
299s                                                            --statistics-filename
299s                                                            STATISTICS_FILENAME
299s                                                            --single-read-threshold
299s                                                            SINGLE_READ_THRESHOLD
299s                                                            [SINGLE_READ_THRESHOLD ...]
299s                                                            [--minimum-test-reads MINIMUM_TEST_READS]
299s                                                            [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
299s                                                            [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
299s                                                            [--processes PROCESSES]
299s                                                            [--corrected-group CORRECTED_GROUP]
299s                                                            [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                                            [--quiet] [--help]
299s 
299s Required Argument:
299s   --per-read-statistics-filename PER_READ_STATISTICS_FILENAME
299s                         Binary file containing per-read statistics from
299s                         statistical testing.
299s   --statistics-filename STATISTICS_FILENAME
299s                         File to save/load genomic base anchored statistics.
299s   --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]
299s                         P-value or log likelihood ratio threshold when
299s                         computing fraction of significant reads at each
299s                         genomic position. If two values are provided,
299s                         statistics between these values are not considered.
299s 
299s Significance Test Arguments:
299s   --minimum-test-reads MINIMUM_TEST_READS
299s                         Number of reads required at a position to perform
299s                         significance testing or contribute to model
299s                         estimation. Default: 1
299s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
299s                         Dampen fraction modified estimates for low coverage
299s                         sites. Two parameters are unmodified and modified
299s                         pseudo read counts. This is equivalent to a beta prior
299s                         on the fraction estimate. Set to "0 0" to disable
299s                         dampened fraction estimation. Default: [2, 0]
299s 
299s Output Argument:
299s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
299s                         Number of the most significant sites to store for
299s                         faster access. If a longer list of most significant
299s                         sites is required the list must be re-computed from
299s                         all batches. Very large values can increase RAM usage.
299s                         Default: 100000
299s 
299s Multiprocessing Arguments:
299s   --processes PROCESSES
299s                         Number of processes. Default: 1
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo text_output browser_files
299s                                        [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
299s                                        [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
299s                                        [--statistics-filename STATISTICS_FILENAME]
299s                                        [--genome-fasta GENOME_FASTA]
299s                                        [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]]
299s                                        [--browser-file-basename BROWSER_FILE_BASENAME]
299s                                        [--file-types {coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} [{coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} ...]]
299s                                        [--corrected-group CORRECTED_GROUP]
299s                                        [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                        [--quiet] [--help]
299s 
299s Data Arguments:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
299s                         Set of directories containing fast5 files for control
299s                         reads, containing only canonical nucleotides.
299s   --statistics-filename STATISTICS_FILENAME
299s                         File to save/load genomic base anchored statistics.
299s 
299s Statistic Motif Filter Arguments:
299s   --genome-fasta GENOME_FASTA
299s                         FASTA file used to re-squiggle. For faster sequence
299s                         access.
299s   --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]
299s                         Ground truth, motif centered, modified base
299s                         descriptions for output filtering. Format descriptions
299s                         as: "motif:mod_pos:name". The mod_pos indicates the
299s                         modified base within the motif (1-based index).
299s                         Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter
299s                         output for identification of E. coli dam and dcm
299s                         methylation.
299s 
299s Output Arguments:
299s   --browser-file-basename BROWSER_FILE_BASENAME
299s                         Basename for output browser files. Two files (plus and
299s                         minus strand) will be produced for each --file-types
299s                         supplied. Filenames formatted as "[browser-file-
299s                         basename].[file-
299s                         type].[sample|control]?.[plus|minus].[wig|bedgraph]".
299s                         Default: tombo_results
299s   --file-types {coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} [{coverage,valid_coverage,fraction,dampened_fraction,signal,signal_sd,dwell,difference,statistic} ...]
299s                         Data types of genome browser files to produce.
299s                         Produced coverage files are in bedGraph format, while
299s                         all other file types will be in wiggle format
299s                         (https://genome.ucsc.edu/goldenpath/help/wiggle.html).
299s                         Default: "coverage"
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo text_output signif_sequence_context --statistics-filename
299s                                                  STATISTICS_FILENAME
299s                                                  [--genome-fasta GENOME_FASTA]
299s                                                  [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
299s                                                  [--num-regions NUM_REGIONS]
299s                                                  [--num-bases NUM_BASES]
299s                                                  [--sequences-filename SEQUENCES_FILENAME]
299s                                                  [--corrected-group CORRECTED_GROUP]
299s                                                  [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                                  [--quiet] [--help]
299s 
299s Required Argument:
299s   --statistics-filename STATISTICS_FILENAME
299s                         File to save/load genomic base anchored statistics.
299s 
299s Sequence Arguments (Provide either FAST5s dir or genome FASTA):
299s   --genome-fasta GENOME_FASTA
299s                         FASTA file used to re-squiggle. For faster sequence
299s                         access.
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s 
299s Region Selection Arguments:
299s   --num-regions NUM_REGIONS
299s                         Number of regions to plot. Default: 100
299s   --num-bases NUM_BASES
299s                         Number of bases to plot/output. Default: 15
299s 
299s Output Arguments:
299s   --sequences-filename SEQUENCES_FILENAME
299s                         File for sequences from selected regions. Sequences
299s                         will be stored in FASTA format. Default:
299s                         tombo_results.significant_regions.fasta.
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS
299s                                [FAST5_BASEDIRS ...]
299s                                [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
299s                                [--plot-standard-model]
299s                                [--plot-alternate-model {CpG,dam,5mC,6mA,dcm}]
299s                                [--overplot-threshold OVERPLOT_THRESHOLD]
299s                                [--overplot-type {Downsample,Boxplot,Quantile,Density}]
299s                                [--num-regions NUM_REGIONS]
299s                                [--num-bases NUM_BASES]
299s                                [--pdf-filename PDF_FILENAME]
299s                                [--corrected-group CORRECTED_GROUP]
299s                                [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                [--quiet] [--help]
299s 
299s Required Argument:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s 
299s Comparison Arguments:
299s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
299s                         Set of directories containing fast5 files for control
299s                         reads, containing only canonical nucleotides.
299s   --plot-standard-model
299s                         Add default standard model distribution to the plot.
299s   --plot-alternate-model {CpG,dam,5mC,6mA,dcm}
299s                         Add alternative model distribution to the plot.
299s 
299s Overplotting Arguments:
299s   --overplot-threshold OVERPLOT_THRESHOLD
299s                         Coverage level to trigger alternative plot type
299s                         instead of raw signal. Default: 50
299s   --overplot-type {Downsample,Boxplot,Quantile,Density}
299s                         Plot type for regions with higher coverage. Default:
299s                         Downsample
299s 
299s Plotting Region Arguments:
299s   --num-regions NUM_REGIONS
299s                         Number of regions to plot. Default: 10
299s   --num-bases NUM_BASES
299s                         Number of bases to plot/output. Default: 21
299s 
299s Output Argument:
299s   --pdf-filename PDF_FILENAME
299s                         PDF filename to store plot(s). Default:
299s                         tombo_results.max_coverage.pdf
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS
299s                                    [FAST5_BASEDIRS ...] --genome-locations
299s                                    GENOME_LOCATIONS [GENOME_LOCATIONS ...]
299s                                    [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
299s                                    [--plot-standard-model]
299s                                    [--plot-alternate-model {dcm,5mC,dam,6mA,CpG}]
299s                                    [--overplot-threshold OVERPLOT_THRESHOLD]
299s                                    [--overplot-type {Downsample,Boxplot,Quantile,Density}]
299s                                    [--num-bases NUM_BASES]
299s                                    [--pdf-filename PDF_FILENAME]
299s                                    [--corrected-group CORRECTED_GROUP]
299s                                    [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                    [--quiet] [--help]
299s 
299s Required Arguments:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s   --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...]
299s                         Genomic locations at which to plot signal. Format
299s                         locations as "chrm:position[:strand]
299s                         [chrm2:position2[:strand2] ...]" (strand not
299s                         applicable for all applications)
299s 
299s Comparison Arguments:
299s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
299s                         Set of directories containing fast5 files for control
299s                         reads, containing only canonical nucleotides.
299s   --plot-standard-model
299s                         Add default standard model distribution to the plot.
299s   --plot-alternate-model {dcm,5mC,dam,6mA,CpG}
299s                         Add alternative model distribution to the plot.
299s 
299s Overplotting Arguments:
299s   --overplot-threshold OVERPLOT_THRESHOLD
299s                         Coverage level to trigger alternative plot type
299s                         instead of raw signal. Default: 50
299s   --overplot-type {Downsample,Boxplot,Quantile,Density}
299s                         Plot type for regions with higher coverage. Default:
299s                         Downsample
299s 
299s Plotting Region Argument:
299s   --num-bases NUM_BASES
299s                         Number of bases to plot/output. Default: 21
299s 
299s Output Argument:
299s   --pdf-filename PDF_FILENAME
299s                         PDF filename to store plot(s). Default:
299s                         tombo_results.genome_locations.pdf
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
299s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS
299s                                  [FAST5_BASEDIRS ...] --motif MOTIF
299s                                  --genome-fasta GENOME_FASTA
299s                                  [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
299s                                  [--plot-standard-model]
299s                                  [--plot-alternate-model {6mA,5mC,CpG,dam,dcm}]
299s                                  [--overplot-threshold OVERPLOT_THRESHOLD]
299s                                  [--overplot-type {Downsample,Boxplot,Quantile,Density}]
299s                                  [--num-regions NUM_REGIONS]
299s                                  [--num-bases NUM_BASES] [--deepest-coverage]
299s                                  [--pdf-filename PDF_FILENAME]
299s                                  [--corrected-group CORRECTED_GROUP]
299s                                  [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
299s                                  [--quiet] [--help]
299s 
299s Required Arguments:
299s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
299s                         Directories containing fast5 files.
299s   --motif MOTIF         Motif of interest at which to plot signal and
299s                         statsitics. Supports IUPAC single letter codes (use T
299s                         for RNA).
299s   --genome-fasta GENOME_FASTA
299s                         FASTA file used to re-squiggle. For faster sequence
299s                         access.
299s 
299s Comparison Arguments:
299s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
299s                         Set of directories containing fast5 files for control
299s                         reads, containing only canonical nucleotides.
299s   --plot-standard-model
299s                         Add default standard model distribution to the plot.
299s   --plot-alternate-model {6mA,5mC,CpG,dam,dcm}
299s                         Add alternative model distribution to the plot.
299s 
299s Overplotting Arguments:
299s   --overplot-threshold OVERPLOT_THRESHOLD
299s                         Coverage level to trigger alternative plot type
299s                         instead of raw signal. Default: 50
299s   --overplot-type {Downsample,Boxplot,Quantile,Density}
299s                         Plot type for regions with higher coverage. Default:
299s                         Downsample
299s 
299s Plotting Region Arguments:
299s   --num-regions NUM_REGIONS
299s                         Number of regions to plot. Default: 10
299s   --num-bases NUM_BASES
299s                         Number of bases to plot/output. Default: 21
299s   --deepest-coverage    Plot the deepest coverage regions.
299s 
299s Output Argument:
299s   --pdf-filename PDF_FILENAME
299s                         PDF filename to store plot(s). Default:
299s                         tombo_results.motif_centered.pdf
299s 
299s FAST5 Data Arguments:
299s   --corrected-group CORRECTED_GROUP
299s                         FAST5 group created by resquiggle command. Default:
299s                         RawGenomeCorrected_000
299s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
299s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
299s                         group]/) containing basecalls and created within
299s                         [--corrected-group] containing re-squiggle results.
299s                         Default: ['BaseCalled_template']
299s 
299s Miscellaneous Arguments:
299s   --quiet, -q           Don't print status information.
299s   --help, -h            Print this help message and exit
300s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS
300s                                  [FAST5_BASEDIRS ...] --control-fast5-basedirs
300s                                  CONTROL_FAST5_BASEDIRS
300s                                  [CONTROL_FAST5_BASEDIRS ...]
300s                                  [--overplot-threshold OVERPLOT_THRESHOLD]
300s                                  [--overplot-type {Downsample,Boxplot,Quantile,Density}]
300s                                  [--num-regions NUM_REGIONS]
300s                                  [--num-bases NUM_BASES]
300s                                  [--pdf-filename PDF_FILENAME]
300s                                  [--sequences-filename SEQUENCES_FILENAME]
300s                                  [--corrected-group CORRECTED_GROUP]
300s                                  [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
300s                                  [--quiet] [--help]
300s 
300s Required Arguments:
300s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
300s                         Directories containing fast5 files.
300s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
300s                         Set of directories containing fast5 files for control
300s                         reads, containing only canonical nucleotides.
300s 
300s Overplotting Arguments:
300s   --overplot-threshold OVERPLOT_THRESHOLD
300s                         Coverage level to trigger alternative plot type
300s                         instead of raw signal. Default: 50
300s   --overplot-type {Downsample,Boxplot,Quantile,Density}
300s                         Plot type for regions with higher coverage. Default:
300s                         Downsample
300s 
300s Plotting Region Arguments:
300s   --num-regions NUM_REGIONS
300s                         Number of regions to plot. Default: 10
300s   --num-bases NUM_BASES
300s                         Number of bases to plot/output. Default: 21
300s 
300s Output Arguments:
300s   --pdf-filename PDF_FILENAME
300s                         PDF filename to store plot(s). Default:
300s                         tombo_results.max_difference.pdf
300s   --sequences-filename SEQUENCES_FILENAME
300s                         File for sequences from selected regions. Sequences
300s                         will be stored in FASTA format. Default: None.
300s 
300s FAST5 Data Arguments:
300s   --corrected-group CORRECTED_GROUP
300s                         FAST5 group created by resquiggle command. Default:
300s                         RawGenomeCorrected_000
300s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
300s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
300s                         group]/) containing basecalls and created within
300s                         [--corrected-group] containing re-squiggle results.
300s                         Default: ['BaseCalled_template']
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS
300s                                    [FAST5_BASEDIRS ...] --statistics-filename
300s                                    STATISTICS_FILENAME
300s                                    [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
300s                                    [--plot-standard-model]
300s                                    [--plot-alternate-model {5mC,6mA,CpG,dam,dcm}]
300s                                    [--overplot-threshold OVERPLOT_THRESHOLD]
300s                                    [--overplot-type {Downsample,Boxplot,Quantile,Density}]
300s                                    [--num-regions NUM_REGIONS]
300s                                    [--num-bases NUM_BASES]
300s                                    [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
300s                                    [--pdf-filename PDF_FILENAME]
300s                                    [--sequences-filename SEQUENCES_FILENAME]
300s                                    [--corrected-group CORRECTED_GROUP]
300s                                    [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
300s                                    [--quiet] [--help]
300s 
300s Required Arguments:
300s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
300s                         Directories containing fast5 files.
300s   --statistics-filename STATISTICS_FILENAME
300s                         File to save/load genomic base anchored statistics.
300s 
300s Comparison Arguments:
300s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
300s                         Set of directories containing fast5 files for control
300s                         reads, containing only canonical nucleotides.
300s   --plot-standard-model
300s                         Add default standard model distribution to the plot.
300s   --plot-alternate-model {5mC,6mA,CpG,dam,dcm}
300s                         Add alternative model distribution to the plot.
300s 
300s Overplotting Arguments:
300s   --overplot-threshold OVERPLOT_THRESHOLD
300s                         Coverage level to trigger alternative plot type
300s                         instead of raw signal. Default: 50
300s   --overplot-type {Downsample,Boxplot,Quantile,Density}
300s                         Plot type for regions with higher coverage. Default:
300s                         Downsample
300s 
300s Plotting Region Arguments:
300s   --num-regions NUM_REGIONS
300s                         Number of regions to plot. Default: 10
300s   --num-bases NUM_BASES
300s                         Number of bases to plot/output. Default: 21
300s 
300s Statistical Argument:
300s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
300s                         Dampen fraction modified estimates for low coverage
300s                         sites. Two parameters are unmodified and modified
300s                         pseudo read counts. This is equivalent to a beta prior
300s                         on the fraction estimate. Set to "0 0" to disable
300s                         dampened fraction estimation. Default: [2, 0]
300s 
300s Output Arguments:
300s   --pdf-filename PDF_FILENAME
300s                         PDF filename to store plot(s). Default:
300s                         tombo_results.significant_difference.pdf
300s   --sequences-filename SEQUENCES_FILENAME
300s                         File for sequences from selected regions. Sequences
300s                         will be stored in FASTA format. Default: None.
300s 
300s FAST5 Data Arguments:
300s   --corrected-group CORRECTED_GROUP
300s                         FAST5 group created by resquiggle command. Default:
300s                         RawGenomeCorrected_000
300s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
300s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
300s                         group]/) containing basecalls and created within
300s                         [--corrected-group] containing re-squiggle results.
300s                         Default: ['BaseCalled_template']
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS
300s                                    [FAST5_BASEDIRS ...] --motif MOTIF
300s                                    --statistics-filename STATISTICS_FILENAME
300s                                    --genome-fasta GENOME_FASTA
300s                                    [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
300s                                    [--plot-standard-model]
300s                                    [--plot-alternate-model {dcm,CpG,6mA,5mC,dam}]
300s                                    [--overplot-threshold OVERPLOT_THRESHOLD]
300s                                    [--num-regions NUM_REGIONS]
300s                                    [--num-context NUM_CONTEXT]
300s                                    [--num-statistics NUM_STATISTICS]
300s                                    [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
300s                                    [--pdf-filename PDF_FILENAME]
300s                                    [--corrected-group CORRECTED_GROUP]
300s                                    [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
300s                                    [--quiet] [--help]
300s 
300s Required Arguments:
300s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
300s                         Directories containing fast5 files.
300s   --motif MOTIF         Motif of interest at which to plot signal and
300s                         statsitics. Supports IUPAC single letter codes (use T
300s                         for RNA).
300s   --statistics-filename STATISTICS_FILENAME
300s                         File to save/load genomic base anchored statistics.
300s   --genome-fasta GENOME_FASTA
300s                         FASTA file used to re-squiggle. For faster sequence
300s                         access.
300s 
300s Comparison Arguments:
300s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
300s                         Set of directories containing fast5 files for control
300s                         reads, containing only canonical nucleotides.
300s   --plot-standard-model
300s                         Add default standard model distribution to the plot.
300s   --plot-alternate-model {dcm,CpG,6mA,5mC,dam}
300s                         Add alternative model distribution to the plot.
300s 
300s Overplotting Argument:
300s   --overplot-threshold OVERPLOT_THRESHOLD
300s                         Coverage level to trigger alternative plot type
300s                         instead of raw signal. Default: 50
300s 
300s Plotting Region Arguments:
300s   --num-regions NUM_REGIONS
300s                         Number of regions to plot. Default: 3
300s   --num-context NUM_CONTEXT
300s                         Number of context bases around motif. Default: 5
300s   --num-statistics NUM_STATISTICS
300s                         Number of motif centered regions to include in
300s                         statistic distributions. Default: 200
300s 
300s Statistical Argument:
300s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
300s                         Dampen fraction modified estimates for low coverage
300s                         sites. Two parameters are unmodified and modified
300s                         pseudo read counts. This is equivalent to a beta prior
300s                         on the fraction estimate. Set to "0 0" to disable
300s                         dampened fraction estimation. Default: [2, 0]
300s 
300s Output Argument:
300s   --pdf-filename PDF_FILENAME
300s                         PDF filename to store plot(s). Default:
300s                         tombo_results.motif_statistics.pdf
300s 
300s FAST5 Data Arguments:
300s   --corrected-group CORRECTED_GROUP
300s                         FAST5 group created by resquiggle command. Default:
300s                         RawGenomeCorrected_000
300s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
300s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
300s                         group]/) containing basecalls and created within
300s                         [--corrected-group] containing re-squiggle results.
300s                         Default: ['BaseCalled_template']
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS
300s                            [GENOME_LOCATIONS ...]
300s                            --per-read-statistics-filename
300s                            PER_READ_STATISTICS_FILENAME
300s                            [--genome-fasta GENOME_FASTA]
300s                            [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
300s                            [--num-reads NUM_READS] [--num-bases NUM_BASES]
300s                            [--box-center] [--pdf-filename PDF_FILENAME]
300s                            [--corrected-group CORRECTED_GROUP]
300s                            [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
300s                            [--quiet] [--help]
300s 
300s Required Arguments:
300s   --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...]
300s                         Genomic locations at which to plot signal. Format
300s                         locations as "chrm:position[:strand]
300s                         [chrm2:position2[:strand2] ...]" (strand not
300s                         applicable for all applications)
300s   --per-read-statistics-filename PER_READ_STATISTICS_FILENAME
300s                         Binary file containing per-read statistics from
300s                         statistical testing.
300s 
300s Sequence Arguments (Provide either FAST5s dir or genome FASTA):
300s   --genome-fasta GENOME_FASTA
300s                         FASTA file used to re-squiggle. For faster sequence
300s                         access.
300s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
300s                         Directories containing fast5 files.
300s 
300s Plotting Region Arguments:
300s   --num-reads NUM_READS
300s                         Number of reads to plot. Default: 100
300s   --num-bases NUM_BASES
300s                         Number of bases to plot/output. Default: 51
300s   --box-center          Plot a box around the central base.
300s 
300s Output Argument:
300s   --pdf-filename PDF_FILENAME
300s                         PDF filename to store plot(s). Default:
300s                         tombo_results.per_read_stats.pdf
300s 
300s FAST5 Data Arguments:
300s   --corrected-group CORRECTED_GROUP
300s                         FAST5 group created by resquiggle command. Default:
300s                         RawGenomeCorrected_000
300s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
300s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
300s                         group]/) containing basecalls and created within
300s                         [--corrected-group] containing re-squiggle results.
300s                         Default: ['BaseCalled_template']
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES
300s                       [STATISTICS_FILENAMES ...]
300s                       [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]]
300s                       [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]]
300s                       [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]]
300s                       [--genome-fasta GENOME_FASTA]
300s                       [--pdf-filename PDF_FILENAME]
300s                       [--statistics-per-block STATISTICS_PER_BLOCK]
300s                       [--total-statistics-limit TOTAL_STATISTICS_LIMIT]
300s                       [--quiet] [--help]
300s 
300s Required Argument:
300s   --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...]
300s                         Files to load genomic base anchored statistics.
300s 
300s Ground Truth Arguments (provide bed files or motifs):
300s   --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]
300s                         Modification description and bed format files
300s                         containing single base locations of ground truth
300s                         modified sites. Bed files should contain 6 fields
300s                         including strand. Format descriptions as
300s                         "mod_name:locs.bed". Example: "CpG
300s                         bisulfite":bisulfite_locs.bed
300s   --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]
300s                         Bed format files containing single base locations of
300s                         ground truth unmodified sites. Bed files should
300s                         contain 6 fields including strand.
300s   --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]
300s                         Ground truth, motif centered, modified base
300s                         descriptions for computing ROC and PR curves. Each
300s                         statistics file is associated with a set of motif
300s                         descriptions. Format descriptions as:
300s                         "motif:mod_pos:name[::motif2:mod_pos2:name2...]".
300s                         mod_pos indicates the alternate-base within the motif
300s                         (1-based index). Example: CCWGG:2:"dcm
300s                         5mC"::GATC:2:"dam 6mA" would assess the performance of
300s                         a single Tombo statistics file for identification of
300s                         E. coli dam and dcm methylation.
300s   --genome-fasta GENOME_FASTA
300s                         FASTA file used to re-squiggle. For faster sequence
300s                         access.
300s 
300s Output Arguments:
300s   --pdf-filename PDF_FILENAME
300s                         PDF filename to store plot(s). Default:
300s                         tombo_results.roc.pdf
300s 
300s Down-sampling Arguments:
300s   --statistics-per-block STATISTICS_PER_BLOCK
300s                         Number of randomly selected per-read, per-base
300s                         statistics to extract from each genomic block for
300s                         plotting. Default: Include all stats
300s   --total-statistics-limit TOTAL_STATISTICS_LIMIT
300s                         Total per-read statistics to be extracted for
300s                         plotting. Avoids memory overflow for large runs.
300s                         Default: 5000000
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo plot per_read_roc --per-read-statistics-filenames
300s                                PER_READ_STATISTICS_FILENAMES
300s                                [PER_READ_STATISTICS_FILENAMES ...]
300s                                [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]]
300s                                [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]]
300s                                [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]]
300s                                [--genome-fasta GENOME_FASTA]
300s                                [--statistics-per-block STATISTICS_PER_BLOCK]
300s                                [--total-statistics-limit TOTAL_STATISTICS_LIMIT]
300s                                [--pdf-filename PDF_FILENAME] [--quiet]
300s                                [--help]
300s 
300s Required Argument:
300s   --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...]
300s                         Binary files containing per-read statistics from
300s                         statistical testing.
300s 
300s Ground Truth Arguments (provide bed files or motifs):
300s   --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]
300s                         Modification description and bed format files
300s                         containing single base locations of ground truth
300s                         modified sites. Bed files should contain 6 fields
300s                         including strand. Format descriptions as
300s                         "mod_name:locs.bed". Example: "CpG
300s                         bisulfite":bisulfite_locs.bed
300s   --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]
300s                         Bed format files containing single base locations of
300s                         ground truth unmodified sites. Bed files should
300s                         contain 6 fields including strand.
300s   --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]
300s                         Ground truth, motif centered, modified base
300s                         descriptions for computing ROC and PR curves. Each
300s                         statistics file is associated with a set of motif
300s                         descriptions. Format descriptions as:
300s                         "motif:mod_pos:name[::motif2:mod_pos2:name2...]".
300s                         mod_pos indicates the alternate-base within the motif
300s                         (1-based index). Example: CCWGG:2:"dcm
300s                         5mC"::GATC:2:"dam 6mA" would assess the performance of
300s                         a single Tombo statistics file for identification of
300s                         E. coli dam and dcm methylation.
300s   --genome-fasta GENOME_FASTA
300s                         FASTA file used to re-squiggle. For faster sequence
300s                         access.
300s 
300s Down-sampling Arguments:
300s   --statistics-per-block STATISTICS_PER_BLOCK
300s                         Number of randomly selected per-read, per-base
300s                         statistics to extract from each genomic block for
300s                         plotting. Default: 100000
300s   --total-statistics-limit TOTAL_STATISTICS_LIMIT
300s                         Total per-read statistics to be extracted for
300s                         plotting. Avoids memory overflow for large runs.
300s                         Default: 5000000
300s 
300s Output Arguments:
300s   --pdf-filename PDF_FILENAME
300s                         PDF filename to store plot(s). Default:
300s                         tombo_results.per_reads_roc.pdf
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
300s                        [--upstream-bases {0,1,2,3,4}]
300s                        [--downstream-bases {0,1,2,3,4}] [--read-mean]
300s                        [--num-kmer-threshold NUM_KMER_THRESHOLD]
300s                        [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME]
300s                        [--r-data-filename R_DATA_FILENAME] [--dont-plot]
300s                        [--corrected-group CORRECTED_GROUP]
300s                        [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
300s                        [--quiet] [--help]
300s 
300s Required Argument:
300s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
300s                         Directories containing fast5 files.
300s 
300s Data Processing Arguments:
300s   --upstream-bases {0,1,2,3,4}
300s                         Upstream bases in k-mer. Default: 1
300s   --downstream-bases {0,1,2,3,4}
300s                         Downstream bases in k-mer. Default: 2
300s   --read-mean           Plot k-mer means across whole reads as opposed to
300s                         individual k-mer event levels.
300s   --num-kmer-threshold NUM_KMER_THRESHOLD
300s                         Observations of each k-mer required to include a read
300s                         in read level averages. Default: 1
300s 
300s Plotting Region Arguments:
300s   --num-reads NUM_READS
300s                         Number of reads to plot. Default: 100
300s 
300s Output Arguments:
300s   --pdf-filename PDF_FILENAME
300s                         PDF filename to store plot(s). Default:
300s                         tombo_results.kmer_distribution.pdf
300s   --r-data-filename R_DATA_FILENAME
300s                         Filename to save R data structure. Default: Don't save
300s   --dont-plot           Don't plot result. Useful to produce only R data file.
300s 
300s FAST5 Data Arguments:
300s   --corrected-group CORRECTED_GROUP
300s                         FAST5 group created by resquiggle command. Default:
300s                         RawGenomeCorrected_000
300s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
300s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
300s                         group]/) containing basecalls and created within
300s                         [--corrected-group] containing re-squiggle results.
300s                         Default: ['BaseCalled_template']
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS
300s                                            [FAST5_BASEDIRS ...]
300s                                            --control-fast5-basedirs
300s                                            CONTROL_FAST5_BASEDIRS
300s                                            [CONTROL_FAST5_BASEDIRS ...]
300s                                            --statistics-filename
300s                                            STATISTICS_FILENAME
300s                                            [--genome-fasta GENOME_FASTA]
300s                                            [--processes PROCESSES]
300s                                            [--num-regions NUM_REGIONS]
300s                                            [--num-bases NUM_BASES]
300s                                            [--slide-span SLIDE_SPAN]
300s                                            [--pdf-filename PDF_FILENAME]
300s                                            [--r-data-filename R_DATA_FILENAME]
300s                                            [--corrected-group CORRECTED_GROUP]
300s                                            [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
300s                                            [--quiet] [--help]
300s 
300s Required Arguments:
300s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
300s                         Directories containing fast5 files.
300s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
300s                         Set of directories containing fast5 files for control
300s                         reads, containing only canonical nucleotides.
300s   --statistics-filename STATISTICS_FILENAME
300s                         File to save/load genomic base anchored statistics.
300s 
300s FASTA Sequence Argument:
300s   --genome-fasta GENOME_FASTA
300s                         FASTA file used to re-squiggle. For faster sequence
300s                         access.
300s 
300s Multiprocessing Argument:
300s   --processes PROCESSES
300s                         Number of processes. Default: 1
300s 
300s Plotting Region Arguments:
300s   --num-regions NUM_REGIONS
300s                         Number of regions to plot. Default: 10
300s   --num-bases NUM_BASES
300s                         Number of bases to plot/output. Default: 21
300s   --slide-span SLIDE_SPAN
300s                         Number of bases offset over which to search when
300s                         computing distances for signal cluster plotting.
300s                         Default: 0 (exact position)
300s 
300s Output Arguments:
300s   --pdf-filename PDF_FILENAME
300s                         PDF filename to store plot(s). Default:
300s                         tombo_results.signal_clusters.pdf
300s   --r-data-filename R_DATA_FILENAME
300s                         Filename to save R data structure. Default: Don't save
300s 
300s FAST5 Data Arguments:
300s   --corrected-group CORRECTED_GROUP
300s                         FAST5 group created by resquiggle command. Default:
300s                         RawGenomeCorrected_000
300s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
300s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
300s                         group]/) containing basecalls and created within
300s                         [--corrected-group] containing re-squiggle results.
300s                         Default: ['BaseCalled_template']
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir
300s 
300s Required Arguments:
300s   fast5s_basedir  Directory containing fast5 files. All files ending in
300s                   "fast5" found recursively within this base directory will be
300s                   processed.
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q     Don't print status information.
300s   --help, -h      Print this help message and exit
300s usage: tombo build_model event_resquiggle
300s                                           [--minimap2-executable MINIMAP2_EXECUTABLE]
300s                                           [--minimap2-index MINIMAP2_INDEX]
300s                                           [--bwa-mem-executable BWA_MEM_EXECUTABLE]
300s                                           [--graphmap-executable GRAPHMAP_EXECUTABLE]
300s                                           [--alignment-batch-size ALIGNMENT_BATCH_SIZE]
300s                                           [--normalization-type {median,pA,pA_raw,none}]
300s                                           [--pore-model-filename PORE_MODEL_FILENAME]
300s                                           [--outlier-threshold OUTLIER_THRESHOLD]
300s                                           [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS]
300s                                           [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]]
300s                                           [--timeout TIMEOUT]
300s                                           [--cpts-limit CPTS_LIMIT]
300s                                           [--skip-index] [--overwrite]
300s                                           [--failed-reads-filename FAILED_READS_FILENAME]
300s                                           [--include-event-stdev]
300s                                           [--corrected-group CORRECTED_GROUP]
300s                                           [--basecall-group BASECALL_GROUP]
300s                                           [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
300s                                           [--processes PROCESSES]
300s                                           [--align-processes ALIGN_PROCESSES]
300s                                           [--align-threads-per-process ALIGN_THREADS_PER_PROCESS]
300s                                           [--resquiggle-processes RESQUIGGLE_PROCESSES]
300s                                           [--quiet] [--help]
300s                                           fast5s_basedir reference_fasta
300s 
300s Required Arguments:
300s   fast5s_basedir        Directory containing fast5 files. All files ending in
300s                         "fast5" found recursively within this base directory
300s                         will be processed.
300s   reference_fasta       Reference genome/transcriptome FASTA file for mapping.
300s 
300s Mapper Arguments (One mapper is required):
300s   --minimap2-executable MINIMAP2_EXECUTABLE
300s                         Path to minimap2 executable.
300s   --minimap2-index MINIMAP2_INDEX
300s                         Path to minimap2 index (with map-ont preset) file
300s                         corresponding to the [genome_fasta] provided.
300s   --bwa-mem-executable BWA_MEM_EXECUTABLE
300s                         Path to bwa-mem executable.
300s   --graphmap-executable GRAPHMAP_EXECUTABLE
300s                         Path to graphmap executable.
300s   --alignment-batch-size ALIGNMENT_BATCH_SIZE
300s                         Number of reads included in each alignment call. Note:
300s                         A new system mapping call is made for each batch
300s                         (including loading of the genome), so it is advised to
300s                         use larger values for larger genomes. Default: 1000
300s 
300s Signal Processing Arguments:
300s   --normalization-type {median,pA,pA_raw,none}
300s                         Choices: "none": raw 16-bit DAQ values, "pA_raw": pA
300s                         as in the ONT events (using offset, range and
300s                         digitization), "pA": k-mer-based correction for pA
300s                         drift as in nanopolish (requires [--pore-model-
300s                         filename]), "median": median and MAD from raw signal.
300s                         Default: median
300s   --pore-model-filename PORE_MODEL_FILENAME
300s                         File containing kmer model parameters (level_mean and
300s                         level_stdv) used in order to compute kmer-based
300s                         corrected pA values. E.g. https://github.com/jts/nanop
300s                         olish/blob/master/etc/r9-
300s                         models/template_median68pA.5mers.model
300s   --outlier-threshold OUTLIER_THRESHOLD
300s                         Windosrize the signal at this number of scale values.
300s                         Negative value disables outlier clipping. Default:
300s                         5.000000
300s   --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS
300s                         Specify the 2 parameters for segmentation 1) running
300s                         neighboring windows width 2) minimum raw observations
300s                         per genomic base. Sample type defaults: RNA : 12 6 ||
300s                         DNA : 5 3
300s 
300s Read Filtering Arguments:
300s   --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]
300s                         Filter reads based on observations per base percentile
300s                         thresholds. Format thresholds as "percentile:thresh
300s                         [pctl2:thresh2 ...]". For example to filter reads with
300s                         99th pctl > 200 obs/base or max > 5k obs/base use
300s                         "99:200 100:5000".
300s   --timeout TIMEOUT     Timeout in seconds for processing a single read.
300s                         Default: No timeout.
300s   --cpts-limit CPTS_LIMIT
300s                         Maximum number of changepoints to find within a single
300s                         indel group. Default: No limit.
300s 
300s Input/Output Arguments:
300s   --skip-index          Skip creation of tombo index. This drastically slows
300s                         downstream tombo commands. Default stores tombo index
300s                         named ".[--fast5-basedir].[--corrected-
300s                         group].tombo.index" to be loaded automatically for
300s                         downstream commands.
300s   --overwrite           Overwrite previous corrected group in FAST5 files.
300s                         Note: only effects --corrected-group or --new-
300s                         corrected-group.
300s   --failed-reads-filename FAILED_READS_FILENAME
300s                         Output failed read filenames with assoicated error.
300s                         Default: Do not store failed reads.
300s   --include-event-stdev
300s                         Include corrected event standard deviation in output
300s                         FAST5 data.
300s 
300s FAST5 Data Arguments:
300s   --corrected-group CORRECTED_GROUP
300s                         FAST5 group created by resquiggle command. Default:
300s                         RawGenomeCorrected_000
300s   --basecall-group BASECALL_GROUP
300s                         FAST5 group obtain original basecalls (under Analyses
300s                         group). Default: Basecall_1D_000
300s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
300s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
300s                         group]/) containing basecalls and created within
300s                         [--corrected-group] containing re-squiggle results.
300s                         Default: ['BaseCalled_template']
300s 
300s Multiprocessing Arguments:
300s   --processes PROCESSES
300s                         Number of processes. Default: 2
300s   --align-processes ALIGN_PROCESSES
300s                         Number of processes to use for parsing and aligning
300s                         original basecalls. Each process will independently
300s                         load the genome into memory, so use caution with
300s                         larger genomes (e.g. human). Default: 1
300s   --align-threads-per-process ALIGN_THREADS_PER_PROCESS
300s                         Number of threads to use for aligner system call.
300s                         Default: [--processes] / (2 * [--align-processes)]
300s   --resquiggle-processes RESQUIGGLE_PROCESSES
300s                         Number of processes to use for resquiggle algorithm.
300s                         Default: [--processes] / 2
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
300s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS
300s                                             [FAST5_BASEDIRS ...]
300s                                             --tombo-model-filename
300s                                             TOMBO_MODEL_FILENAME
300s                                             [--estimate-mean]
300s                                             [--kmer-specific-sd]
300s                                             [--upstream-bases {0,1,2,3,4}]
300s                                             [--downstream-bases {0,1,2,3,4}]
300s                                             [--minimum-test-reads MINIMUM_TEST_READS]
300s                                             [--coverage-threshold COVERAGE_THRESHOLD]
300s                                             [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS]
300s                                             [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
300s                                             [--processes PROCESSES]
300s                                             [--corrected-group CORRECTED_GROUP]
300s                                             [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
300s                                             [--quiet] [--help]
300s 
300s Required Arguments:
300s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
300s                         Directories containing fast5 files.
300s   --tombo-model-filename TOMBO_MODEL_FILENAME
300s                         Filename to save Tombo model.
300s 
300s Modeling Arguments:
300s   --estimate-mean       Use the mean instead of median for model level
300s                         estimation. Note: This can cause poor fits due to
300s                         outliers
300s   --kmer-specific-sd    Estimate standard deviation for each k-mers
300s                         individually.
300s   --upstream-bases {0,1,2,3,4}
300s                         Upstream bases in k-mer. Default: 1
300s   --downstream-bases {0,1,2,3,4}
300s                         Downstream bases in k-mer. Default: 2
300s 
300s Filtering Arguments:
300s   --minimum-test-reads MINIMUM_TEST_READS
300s                         Number of reads required at a position to perform
300s                         significance testing or contribute to model
300s                         estimation. Default: 10
300s   --coverage-threshold COVERAGE_THRESHOLD
300s                         Maximum mean coverage per region when estimating k-mer
300s                         model (limits compute time for deep samples). Default:
300s                         100
300s   --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS
300s                         Number of each k-mer observations required in order to
300s                         produce a reference (genomic locations for standard
300s                         reference and per-read for alternative reference).
300s                         Default: 5
300s 
300s Multiprocessing Arguments:
300s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
300s                         Size of regions over which to multiprocesses statistic
300s                         computation. For very deep samples a smaller value is
300s                         recommmended in order to control memory consumption.
300s                         Default: 10000
300s   --processes PROCESSES
300s                         Number of processes. Default: 1
300s 
300s FAST5 Data Arguments:
300s   --corrected-group CORRECTED_GROUP
300s                         FAST5 group created by resquiggle command. Default:
300s                         RawGenomeCorrected_000
300s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
300s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
300s                         group]/) containing basecalls and created within
300s                         [--corrected-group] containing re-squiggle results.
300s                         Default: ['BaseCalled_template']
300s 
300s Miscellaneous Arguments:
300s   --quiet, -q           Don't print status information.
300s   --help, -h            Print this help message and exit
301s usage: tombo build_model estimate_alt_reference --alternate-model-filename
301s                                                 ALTERNATE_MODEL_FILENAME
301s                                                 --alternate-model-name
301s                                                 ALTERNATE_MODEL_NAME
301s                                                 --alternate-model-base
301s                                                 {A,C,G,T}
301s                                                 [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
301s                                                 [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
301s                                                 [--alternate-density-filename ALTERNATE_DENSITY_FILENAME]
301s                                                 [--control-density-filename CONTROL_DENSITY_FILENAME]
301s                                                 [--dna] [--rna]
301s                                                 [--tombo-model-filename TOMBO_MODEL_FILENAME]
301s                                                 [--alt-fraction-percentile ALT_FRACTION_PERCENTILE]
301s                                                 [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH]
301s                                                 [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS]
301s                                                 [--save-density-basename SAVE_DENSITY_BASENAME]
301s                                                 [--processes PROCESSES]
301s                                                 [--corrected-group CORRECTED_GROUP]
301s                                                 [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
301s                                                 [--quiet] [--help]
301s 
301s Required Arguments:
301s   --alternate-model-filename ALTERNATE_MODEL_FILENAME
301s                         Tombo model for alternative likelihood ratio
301s                         significance testing.
301s   --alternate-model-name ALTERNATE_MODEL_NAME
301s                         A short name to associate with this alternate model
301s                         (e.g. 5mC, 6mA, etc.). This text will be included in
301s                         output filenames when this model is used for testing.
301s   --alternate-model-base {A,C,G,T}
301s                         Non-standard base is an alternative to this base.
301s 
301s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates):
301s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
301s                         Directories containing fast5 files.
301s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
301s                         Set of directories containing fast5 files for control
301s                         reads, containing only canonical nucleotides.
301s   --alternate-density-filename ALTERNATE_DENSITY_FILENAME
301s                         File containing k-mer level kernel density estimates
301s                         for the alternative sample saved using --save-density-
301s                         basename.
301s   --control-density-filename CONTROL_DENSITY_FILENAME
301s                         File containing k-mer level kernel density estimates
301s                         for the control sample saved using --save-density-
301s                         basename.
301s 
301s Standard Model Arguments:
301s   --dna                 Explicitly select canonical DNA model. Default:
301s                         Automatically determine from FAST5s
301s   --rna                 Explicitly select canonical RNA model. Default:
301s                         Automatically determine from FAST5s
301s   --tombo-model-filename TOMBO_MODEL_FILENAME
301s                         Tombo model filename. If no file is provided, the
301s                         default DNA or RNA Tombo model will be used.
301s 
301s Model Fitting Arguments:
301s   --alt-fraction-percentile ALT_FRACTION_PERCENTILE
301s                         When esitmating the alternative base incorporation
301s                         rate, this percent of k-mers are assumed to have
301s                         significantly shifted signal so the alternative
301s                         distribution minimally overlaps the standard base
301s                         distribution. Default: 5.000000
301s   --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH
301s                         Bandwidth applied when performing Gaussian kernal
301s                         density esitmation on standard and alternative base
301s                         signal distributions. Default: 0.050000
301s 
301s Filtering Argument:
301s   --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS
301s                         Number of each k-mer observations required in order to
301s                         produce a reference (genomic locations for standard
301s                         reference and per-read for alternative reference).
301s                         Default: 1000
301s 
301s Output Argument:
301s   --save-density-basename SAVE_DENSITY_BASENAME
301s                         Basename to save alternative model estimation density
301s                         estimation information. See scripts/debug_est_alt.R
301s                         for info use example. Default: Don't save.
301s 
301s Multiprocessing Arguments:
301s   --processes PROCESSES
301s                         Number of processes. Default: 1
301s 
301s FAST5 Data Arguments:
301s   --corrected-group CORRECTED_GROUP
301s                         FAST5 group created by resquiggle command. Default:
301s                         RawGenomeCorrected_000
301s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
301s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
301s                         group]/) containing basecalls and created within
301s                         [--corrected-group] containing re-squiggle results.
301s                         Default: ['BaseCalled_template']
301s 
301s Miscellaneous Arguments:
301s   --quiet, -q           Don't print status information.
301s   --help, -h            Print this help message and exit
301s This test only tests the help system
301s There is an extensive test in 
301s 
301s   tombo/tests/shell_tests.sh
301s 
301s but this requires to download larger data
301s sets which is not done for the moment.
301s autopkgtest [22:20:48]: test run-unit-test: -----------------------]
301s autopkgtest [22:20:48]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
301s run-unit-test        PASS
302s autopkgtest [22:20:49]: @@@@@@@@@@@@@@@@@@@@ summary
302s run-unit-test        PASS
338s Creating nova instance adt-noble-s390x-tombo-20240326-221547-juju-7f2275-prod-proposed-migration-environment-2-fd4e7b60-569b-44c6-85fe-f2350e325dc0 from image adt/ubuntu-noble-s390x-server-20240326.img (UUID c527e0e4-2e65-4e86-ad63-05d7f665f2fb)...