0s autopkgtest [02:08:49]: starting date and time: 2024-03-27 02:08:49+0000
  0s autopkgtest [02:08:49]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [02:08:49]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mgpeqbsy/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=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-ppc64el-15.secgroup --name adt-noble-ppc64el-tombo-20240327-020849-juju-7f2275-prod-proposed-migration-environment-2-26efedcb-8433-4892-98ca-fba585653f5b --image adt/ubuntu-noble-ppc64el-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/
118s autopkgtest [02:10:47]: testbed dpkg architecture: ppc64el
118s autopkgtest [02:10:47]: testbed apt version: 2.7.12
118s autopkgtest [02:10:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup
119s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
119s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [55.4 kB]
119s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B]
119s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB]
121s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
121s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [702 kB]
122s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
122s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
122s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
122s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4219 kB]
123s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
123s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [62.2 kB]
123s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
126s Fetched 9658 kB in 5s (1888 kB/s)
126s Reading package lists...
128s Reading package lists...
128s Building dependency tree...
128s Reading state information...
129s Calculating upgrade...
129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
129s Reading package lists...
129s Building dependency tree...
129s Reading state information...
129s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded.
130s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
130s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
130s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
130s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
131s Reading package lists...
131s Reading package lists...
131s Building dependency tree...
131s Reading state information...
132s Calculating upgrade...
132s The following packages were automatically installed and are no longer required:
132s   libaio1 libnetplan0 python3-distutils python3-lib2to3
132s Use 'sudo apt autoremove' to remove them.
132s The following packages will be REMOVED:
132s   libapt-pkg6.0 libarchive13 libatm1 libcurl3-gnutls libcurl4 libdb5.3 libelf1
132s   libext2fs2 libgdbm-compat4 libgdbm6 libglib2.0-0 libgnutls30 libgpgme11
132s   libhogweed6 libmagic1 libnettle8 libnpth0 libnvme1 libparted2 libperl5.38
132s   libpng16-16 libpsl5 libreadline8 libreiserfscore0 libssl3 libtirpc3 liburcu8
132s   libuv1
132s The following NEW packages will be installed:
132s   bpfcc-tools bpftrace fontconfig-config fonts-dejavu-core fonts-dejavu-mono
132s   ieee-data libaio1t64 libapt-pkg6.0t64 libarchive13t64 libatm1t64 libbpfcc
132s   libc-dev-bin libc-devtools libc6-dev libclang-cpp18 libclang1-18
132s   libcrypt-dev libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libdeflate0
132s   libdw1t64 libelf1t64 libext2fs2t64 libfontconfig1 libgd3 libgdbm-compat4t64
132s   libgdbm6t64 libglib2.0-0t64 libgnutls30t64 libgpgme11t64 libhogweed6t64
132s   libjbig0 libjpeg-turbo8 libjpeg8 liblerc4 libllvm18 libmagic1t64 libnetplan1
132s   libnettle8t64 libnpth0t64 libnvme1t64 libparted2t64 libperl5.38t64
132s   libpng16-16t64 libpsl5t64 libreadline8t64 libreiserfscore0t64 libsharpyuv0
132s   libssl3t64 libtiff6 libtirpc3t64 libunwind8 liburcu8t64 libuv1t64 libwebp7
132s   libxpm4 linux-headers-6.8.0-20 linux-headers-6.8.0-20-generic
132s   linux-image-6.8.0-20-generic linux-libc-dev linux-modules-6.8.0-20-generic
132s   linux-modules-extra-6.8.0-20-generic linux-tools-6.8.0-20
132s   linux-tools-6.8.0-20-generic linux-tools-common manpages manpages-dev
132s   python3-bpfcc python3-netaddr rpcsvc-proto ubuntu-kernel-accessories
132s   xdg-user-dirs
132s The following packages will be upgraded:
132s   apparmor apt apt-utils base-files bash bc bind9-dnsutils bind9-host
132s   bind9-libs binutils binutils-common binutils-powerpc64le-linux-gnu bolt
132s   bsdextrautils bsdutils btrfs-progs coreutils cryptsetup-bin curl dbus
132s   dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common
132s   dbus-user-session dhcpcd-base dirmngr dmsetup dpkg dpkg-dev e2fsprogs
132s   e2fsprogs-l10n eject fdisk file ftp fwupd gawk gcc-13-base gcc-14-base
132s   gir1.2-girepository-2.0 gir1.2-glib-2.0 gnupg gnupg-l10n gnupg-utils gpg
132s   gpg-agent gpg-wks-client gpgconf gpgsm gpgv groff-base grub-common
132s   grub-ieee1275 grub-ieee1275-bin grub2-common ibverbs-providers
132s   inetutils-telnet info initramfs-tools initramfs-tools-bin
132s   initramfs-tools-core install-info iproute2 jq keyboxd kmod kpartx
132s   krb5-locales libapparmor1 libaudit-common libaudit1 libbinutils libblkid1
132s   libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3
132s   libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3
132s   libblockdev3 libbpf1 libbrotli1 libcap-ng0 libcom-err2 libcryptsetup12
132s   libctf-nobfd0 libctf0 libdbus-1-3 libdebconfclient0 libdevmapper1.02.1
132s   libdpkg-perl libevent-core-2.1-7 libexpat1 libfdisk1 libfido2-1 libfreetype6
132s   libftdi1-2 libfwupd2 libgcc-s1 libgirepository-1.0-1 libglib2.0-data
132s   libgssapi-krb5-2 libgudev-1.0-0 libgusb2 libibverbs1 libjcat1 libjq1
132s   libjson-glib-1.0-0 libjson-glib-1.0-common libk5crypto3 libkmod2 libkrb5-3
132s   libkrb5support0 libldap-common libldap2 liblocale-gettext-perl liblzma5
132s   libmagic-mgc libmbim-glib4 libmbim-proxy libmm-glib0 libmount1 libnghttp2-14
132s   libnsl2 libnss-systemd libpam-modules libpam-modules-bin libpam-runtime
132s   libpam-systemd libpam0g libplymouth5 libpolkit-agent-1-0
132s   libpolkit-gobject-1-0 libproc2-0 libprotobuf-c1 libpython3-stdlib
132s   libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal
132s   libpython3.12-stdlib libqmi-glib5 libqmi-proxy libqrtr-glib0 librtmp1
132s   libsasl2-2 libsasl2-modules libsasl2-modules-db libseccomp2 libselinux1
132s   libsemanage-common libsemanage2 libsframe1 libslang2 libsmartcols1
132s   libsqlite3-0 libss2 libssh-4 libstdc++6 libsystemd-shared libsystemd0
132s   libtext-charwidth-perl libtext-iconv-perl libtirpc-common libudev1
132s   libudisks2-0 libusb-1.0-0 libuuid1 libvolume-key1 libxml2 libxmlb2 libxmuu1
132s   linux-generic linux-headers-generic linux-headers-virtual
132s   linux-image-generic linux-image-virtual linux-virtual logsave lshw lsof
132s   man-db motd-news-config mount mtr-tiny multipath-tools netplan-generator
132s   netplan.io openssh-client openssh-server openssh-sftp-server openssl parted
132s   perl perl-base perl-modules-5.38 pinentry-curses plymouth
132s   plymouth-theme-ubuntu-text procps python-apt-common python3 python3-apt
132s   python3-cryptography python3-dbus python3-distutils python3-gdbm python3-gi
132s   python3-lib2to3 python3-minimal python3-netplan python3-pkg-resources
132s   python3-pyrsistent python3-setuptools python3-typing-extensions python3-yaml
132s   python3.11 python3.11-minimal python3.12 python3.12-minimal readline-common
132s   rsync rsyslog shared-mime-info sudo systemd systemd-dev systemd-resolved
132s   systemd-sysv systemd-timesyncd tcpdump telnet tnftp ubuntu-pro-client
132s   ubuntu-pro-client-l10n udev udisks2 usb.ids util-linux uuid-runtime
132s   vim-common vim-tiny wget xxd xz-utils zlib1g
132s 248 upgraded, 73 newly installed, 28 to remove and 0 not upgraded.
132s Need to get 390 MB of archives.
132s After this operation, 640 MB of additional disk space will be used.
132s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el motd-news-config all 13ubuntu8 [5098 B]
132s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el base-files ppc64el 13ubuntu8 [74.5 kB]
132s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bash ppc64el 5.2.21-2ubuntu3 [977 kB]
133s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdutils ppc64el 1:2.39.3-9ubuntu2 [98.3 kB]
133s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el coreutils ppc64el 9.4-3ubuntu3 [1523 kB]
133s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libudisks2-0 ppc64el 2.10.1-6 [182 kB]
133s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el udisks2 ppc64el 2.10.1-6 [344 kB]
133s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el shared-mime-info ppc64el 2.4-1build1 [481 kB]
133s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gir1.2-girepository-2.0 ppc64el 1.79.1-1ubuntu6 [24.8 kB]
133s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gir1.2-glib-2.0 ppc64el 2.79.3-3ubuntu5 [182 kB]
133s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgirepository-1.0-1 ppc64el 1.79.1-1ubuntu6 [93.8 kB]
133s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-gi ppc64el 3.47.0-3build1 [261 kB]
133s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-dbus ppc64el 1.3.2-5build2 [107 kB]
133s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnetplan1 ppc64el 1.0-1 [136 kB]
134s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-netplan ppc64el 1.0-1 [21.8 kB]
134s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el netplan-generator ppc64el 1.0-1 [59.2 kB]
134s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el initramfs-tools-bin ppc64el 0.142ubuntu23 [21.0 kB]
134s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el initramfs-tools-core all 0.142ubuntu23 [50.1 kB]
134s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el initramfs-tools all 0.142ubuntu23 [9058 B]
134s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el netplan.io ppc64el 1.0-1 [66.2 kB]
134s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxmlb2 ppc64el 0.3.15-1build1 [82.6 kB]
134s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgpgme11t64 ppc64el 1.18.0-4.1ubuntu3 [173 kB]
134s Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libvolume-key1 ppc64el 0.3.12-7build1 [47.9 kB]
134s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libqrtr-glib0 ppc64el 1.2.2-1ubuntu3 [18.3 kB]
134s Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libqmi-glib5 ppc64el 1.35.2-0ubuntu1 [966 kB]
134s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libqmi-proxy ppc64el 1.35.2-0ubuntu1 [6208 B]
134s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpolkit-agent-1-0 ppc64el 124-1ubuntu1 [18.8 kB]
134s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpolkit-gobject-1-0 ppc64el 124-1ubuntu1 [52.7 kB]
134s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmm-glib0 ppc64el 1.23.4-0ubuntu1 [282 kB]
134s Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmbim-glib4 ppc64el 1.31.2-0ubuntu2 [253 kB]
134s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmbim-proxy ppc64el 1.31.2-0ubuntu2 [6274 B]
134s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjson-glib-1.0-common all 1.8.0-2build1 [4210 B]
134s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjson-glib-1.0-0 ppc64el 1.8.0-2build1 [73.6 kB]
134s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgusb2 ppc64el 0.4.8-1build1 [43.0 kB]
134s Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgudev-1.0-0 ppc64el 1:238-3ubuntu2 [15.8 kB]
134s Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el tnftp ppc64el 20230507-2build1 [116 kB]
134s Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el tcpdump ppc64el 4.99.4-3ubuntu2 [543 kB]
134s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsystemd0 ppc64el 255.4-1ubuntu5 [526 kB]
134s Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-dev all 255.4-1ubuntu5 [103 kB]
134s Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnss-systemd ppc64el 255.4-1ubuntu5 [208 kB]
134s Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libudev1 ppc64el 255.4-1ubuntu5 [200 kB]
134s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB]
134s Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd ppc64el 255.4-1ubuntu5 [3771 kB]
135s Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el udev ppc64el 255.4-1ubuntu5 [2038 kB]
135s Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-sysv ppc64el 255.4-1ubuntu5 [11.9 kB]
135s Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-systemd ppc64el 255.4-1ubuntu5 [304 kB]
135s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-timesyncd ppc64el 255.4-1ubuntu5 [37.9 kB]
135s Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsystemd-shared ppc64el 255.4-1ubuntu5 [2351 kB]
135s Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-resolved ppc64el 255.4-1ubuntu5 [346 kB]
135s Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el sudo ppc64el 1.9.15p5-3ubuntu3 [1005 kB]
135s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el rsync ppc64el 3.2.7-1build1 [487 kB]
136s Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-cryptography ppc64el 41.0.7-4build2 [860 kB]
136s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB]
136s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssh-sftp-server ppc64el 1:9.6p1-3ubuntu11 [43.7 kB]
136s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssh-client ppc64el 1:9.6p1-3ubuntu11 [1112 kB]
136s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssh-server ppc64el 1:9.6p1-3ubuntu11 [627 kB]
136s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssh-4 ppc64el 0.10.6-2build1 [234 kB]
136s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-modules ppc64el 2.1.28+dfsg1-5ubuntu1 [83.1 kB]
136s Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.12 ppc64el 3.12.2-4build3 [645 kB]
136s Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.12-minimal ppc64el 3.12.2-4build3 [2447 kB]
136s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.12-minimal ppc64el 3.12.2-4build3 [836 kB]
136s Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el grub-ieee1275 ppc64el 2.12-1ubuntu5 [63.1 kB]
136s Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el grub2-common ppc64el 2.12-1ubuntu5 [752 kB]
136s Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el grub-common ppc64el 2.12-1ubuntu5 [2356 kB]
137s Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el grub-ieee1275-bin ppc64el 2.12-1ubuntu5 [687 kB]
137s Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libparted2t64 ppc64el 3.6-3.1build2 [184 kB]
137s Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el parted ppc64el 3.6-3.1build2 [58.9 kB]
137s Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.11 ppc64el 3.11.8-1build4 [589 kB]
137s Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3.11-minimal ppc64el 3.11.8-1build4 [2292 kB]
137s Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.11-minimal ppc64el 3.11.8-1build4 [846 kB]
137s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.11-stdlib ppc64el 3.11.8-1build4 [1977 kB]
137s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gnupg-utils ppc64el 2.4.4-2ubuntu15 [123 kB]
138s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg-agent ppc64el 2.4.4-2ubuntu15 [275 kB]
138s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg-wks-client ppc64el 2.4.4-2ubuntu15 [85.0 kB]
138s Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg ppc64el 2.4.4-2ubuntu15 [706 kB]
138s Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el libnpth0t64 ppc64el 1.6-3.1 [8864 B]
138s Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgv ppc64el 2.4.4-2ubuntu15 [198 kB]
138s Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dirmngr ppc64el 2.4.4-2ubuntu15 [391 kB]
138s Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gnupg all 2.4.4-2ubuntu15 [359 kB]
138s Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el keyboxd ppc64el 2.4.4-2ubuntu15 [94.3 kB]
138s Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgconf ppc64el 2.4.4-2ubuntu15 [115 kB]
138s Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgsm ppc64el 2.4.4-2ubuntu15 [292 kB]
138s Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libreadline8t64 ppc64el 8.2-4 [182 kB]
138s Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gawk ppc64el 1:5.2.1-2build2 [528 kB]
139s Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el fdisk ppc64el 2.39.3-9ubuntu2 [132 kB]
139s Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bc ppc64el 1.07.1-3ubuntu2 [93.2 kB]
139s Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3.12-stdlib ppc64el 3.12.2-4build3 [2082 kB]
139s Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-base ppc64el 5.38.2-3.2 [1916 kB]
139s Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
140s Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-gdbm ppc64el 3.12.2-3ubuntu1.1 [19.8 kB]
140s Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el man-db ppc64el 2.12.0-3build4 [1274 kB]
140s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm6t64 ppc64el 1.23-5.1 [41.9 kB]
140s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm-compat4t64 ppc64el 1.23-5.1 [6972 B]
140s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libperl5.38t64 ppc64el 5.38.2-3.2 [4957 kB]
140s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl ppc64el 5.38.2-3.2 [231 kB]
140s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdb5.3t64 ppc64el 5.3.28+dfsg2-6 [875 kB]
141s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-modules-db ppc64el 2.1.28+dfsg1-5ubuntu1 [23.4 kB]
141s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-2 ppc64el 2.1.28+dfsg1-5ubuntu1 [68.0 kB]
141s Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnvme1t64 ppc64el 1.8-3 [98.2 kB]
141s Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el wget ppc64el 1.21.4-1ubuntu2 [382 kB]
141s Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl4t64 ppc64el 8.5.0-2ubuntu8 [428 kB]
141s Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el curl ppc64el 8.5.0-2ubuntu8 [234 kB]
141s Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpsl5t64 ppc64el 0.21.2-1.1 [59.0 kB]
141s Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libarchive13t64 ppc64el 3.7.2-1.1ubuntu2 [518 kB]
141s Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el fwupd ppc64el 1.9.15-2 [4634 kB]
142s Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl3t64-gnutls ppc64el 8.5.0-2ubuntu8 [419 kB]
142s Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfwupd2 ppc64el 1.9.15-2 [136 kB]
142s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev3 ppc64el 3.1.0-1build1 [55.2 kB]
142s Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-utils3 ppc64el 3.1.0-1build1 [20.3 kB]
142s Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-swap3 ppc64el 3.1.0-1build1 [8616 B]
142s Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-part3 ppc64el 3.1.0-1build1 [17.5 kB]
142s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-nvme3 ppc64el 3.1.0-1build1 [20.1 kB]
142s Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-mdraid3 ppc64el 3.1.0-1build1 [14.3 kB]
142s Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-loop3 ppc64el 3.1.0-1build1 [7742 B]
142s Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el e2fsprogs-l10n all 1.47.0-2.4~exp1ubuntu2 [5996 B]
142s Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el logsave ppc64el 1.47.0-2.4~exp1ubuntu2 [22.9 kB]
142s Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libext2fs2t64 ppc64el 1.47.0-2.4~exp1ubuntu2 [270 kB]
143s Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el e2fsprogs ppc64el 1.47.0-2.4~exp1ubuntu2 [663 kB]
143s Get:119 http://ftpmaster.internal/ubuntu noble/main ppc64el libreiserfscore0t64 ppc64el 1:3.6.27-7.1 [92.7 kB]
143s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el btrfs-progs ppc64el 6.6.3-1.1build1 [1352 kB]
143s Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-fs3 ppc64el 3.1.0-1build1 [41.2 kB]
143s Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblockdev-crypto3 ppc64el 3.1.0-1build1 [22.5 kB]
143s Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bolt ppc64el 0.9.6-2build1 [171 kB]
144s Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-0t64 ppc64el 2.79.3-3ubuntu5 [1773 kB]
144s Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjcat1 ppc64el 0.2.0-2build2 [40.0 kB]
144s Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libldap2 ppc64el 2.6.7+dfsg-1~exp1ubuntu6 [233 kB]
144s Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ubuntu-pro-client-l10n ppc64el 31.2.2 [19.4 kB]
144s Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ubuntu-pro-client ppc64el 31.2.2 [215 kB]
144s Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-apt ppc64el 2.7.7 [181 kB]
144s Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el apt-utils ppc64el 2.7.14 [226 kB]
144s Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapt-pkg6.0t64 ppc64el 2.7.14 [1063 kB]
144s Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnettle8t64 ppc64el 3.9.1-2.2 [226 kB]
145s Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libhogweed6t64 ppc64el 3.9.1-2.2 [208 kB]
145s Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgnutls30t64 ppc64el 3.8.3-1.1ubuntu2 [1154 kB]
145s Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el apt ppc64el 2.7.14 [1401 kB]
145s Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build6 [64.4 kB]
145s Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblzma5 ppc64el 5.6.0-0.2 [156 kB]
145s Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblkid1 ppc64el 2.39.3-9ubuntu2 [155 kB]
145s Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el kmod ppc64el 31+20240202-2ubuntu4 [122 kB]
145s Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkmod2 ppc64el 31+20240202-2ubuntu4 [64.4 kB]
145s Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libselinux1 ppc64el 3.5-2ubuntu1 [101 kB]
146s Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libaudit-common all 1:3.1.2-2.1 [5674 B]
146s Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcap-ng0 ppc64el 0.8.4-2build1 [16.2 kB]
146s Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libaudit1 ppc64el 1:3.1.2-2.1 [52.8 kB]
146s Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam0g ppc64el 1.5.3-5ubuntu3 [75.7 kB]
146s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules-bin ppc64el 1.5.3-5ubuntu3 [57.9 kB]
146s Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules ppc64el 1.5.3-5ubuntu3 [320 kB]
146s Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB]
146s Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-session-bus-common all 1.14.10-4ubuntu2 [80.3 kB]
146s Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-user-session ppc64el 1.14.10-4ubuntu2 [9960 B]
146s Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapparmor1 ppc64el 4.0.0-beta3-0ubuntu2 [55.0 kB]
146s Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libexpat1 ppc64el 2.6.1-2 [101 kB]
146s Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-system-bus-common all 1.14.10-4ubuntu2 [81.5 kB]
146s Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-bin ppc64el 1.14.10-4ubuntu2 [48.1 kB]
146s Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus ppc64el 1.14.10-4ubuntu2 [26.9 kB]
147s Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dbus-daemon ppc64el 1.14.10-4ubuntu2 [136 kB]
147s Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdbus-1-3 ppc64el 1.14.10-4ubuntu2 [244 kB]
147s Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.185-3ubuntu2 [182 kB]
147s Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libuuid1 ppc64el 2.39.3-9ubuntu2 [39.3 kB]
147s Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcryptsetup12 ppc64el 2:2.7.0-1ubuntu2 [376 kB]
147s Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfdisk1 ppc64el 2.39.3-9ubuntu2 [171 kB]
147s Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libseccomp2 ppc64el 2.5.5-1ubuntu2 [62.5 kB]
147s Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el mount ppc64el 2.39.3-9ubuntu2 [125 kB]
147s Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmount1 ppc64el 2.39.3-9ubuntu2 [169 kB]
147s Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el zlib1g ppc64el 1:1.3.dfsg-3.1ubuntu1 [72.8 kB]
148s Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-minimal ppc64el 3.12.2-0ubuntu1 [27.1 kB]
148s Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3 ppc64el 3.12.2-0ubuntu1 [24.1 kB]
148s Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libplymouth5 ppc64el 24.004.60-1ubuntu6 [166 kB]
148s Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpng16-16t64 ppc64el 1.6.43-3 [242 kB]
148s Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbrotli1 ppc64el 1.1.0-2build1 [410 kB]
148s Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfreetype6 ppc64el 2.13.2+dfsg-1build2 [545 kB]
148s Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsqlite3-0 ppc64el 3.45.1-1ubuntu1 [804 kB]
148s Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el pinentry-curses ppc64el 1.2.1-3ubuntu4 [38.7 kB]
148s Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-14-base ppc64el 14-20240315-1ubuntu1 [47.0 kB]
148s Get:175 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgcc-s1 ppc64el 14-20240315-1ubuntu1 [39.2 kB]
149s Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libstdc++6 ppc64el 14-20240315-1ubuntu1 [897 kB]
149s Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python-apt-common all 2.7.7 [19.8 kB]
149s Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsmartcols1 ppc64el 2.39.3-9ubuntu2 [79.0 kB]
149s Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el readline-common all 8.2-4 [56.4 kB]
149s Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdextrautils ppc64el 2.39.3-9ubuntu2 [78.6 kB]
149s Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el groff-base ppc64el 1.23.0-3build1 [1112 kB]
149s Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.2-0ubuntu1 [9798 B]
149s Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfido2-1 ppc64el 1.14.0-1build1 [111 kB]
149s Get:184 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-6ubuntu1 [185 kB]
149s Get:185 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5-3 ppc64el 1.20.1-6ubuntu1 [432 kB]
150s Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5support0 ppc64el 1.20.1-6ubuntu1 [38.5 kB]
150s Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libk5crypto3 ppc64el 1.20.1-6ubuntu1 [108 kB]
150s Get:188 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcom-err2 ppc64el 1.47.0-2.4~exp1ubuntu2 [22.9 kB]
150s Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libproc2-0 ppc64el 2:4.0.4-4ubuntu2 [68.8 kB]
150s Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el procps ppc64el 2:4.0.4-4ubuntu2 [736 kB]
150s Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnghttp2-14 ppc64el 1.59.0-1build1 [89.0 kB]
150s Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg ppc64el 1.22.6ubuntu5 [1343 kB]
150s Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el util-linux ppc64el 2.39.3-9ubuntu2 [1195 kB]
150s Get:194 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.3ubuntu2 [840 kB]
150s Get:195 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbpf1 ppc64el 1:1.3.0-2build1 [216 kB]
151s Get:196 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el iproute2 ppc64el 6.1.0-1ubuntu5 [1384 kB]
151s Get:197 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libelf1t64 ppc64el 0.190-1.1build2 [69.3 kB]
151s Get:198 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dhcpcd-base ppc64el 1:10.0.6-1ubuntu2 [276 kB]
151s Get:199 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el file ppc64el 1:5.45-3 [22.7 kB]
151s Get:200 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmagic-mgc ppc64el 1:5.45-3 [307 kB]
151s Get:201 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmagic1t64 ppc64el 1:5.45-3 [106 kB]
151s Get:202 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc-common all 1.3.4+ds-1.1 [8018 B]
151s Get:203 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el lsof ppc64el 4.95.0-1build2 [256 kB]
151s Get:204 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnsl2 ppc64el 1.3.0-3build2 [48.9 kB]
151s Get:205 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc3t64 ppc64el 1.3.4+ds-1.1 [102 kB]
152s Get:206 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el multipath-tools ppc64el 0.9.4-5ubuntu6 [341 kB]
152s Get:207 http://ftpmaster.internal/ubuntu noble/main ppc64el liburcu8t64 ppc64el 0.14.0-3.1 [73.6 kB]
152s Get:208 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bind9-host ppc64el 1:9.18.24-0ubuntu3 [54.5 kB]
152s Get:209 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bind9-dnsutils ppc64el 1:9.18.24-0ubuntu3 [167 kB]
152s Get:210 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bind9-libs ppc64el 1:9.18.24-0ubuntu3 [1436 kB]
152s Get:211 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libuv1t64 ppc64el 1.48.0-1.1 [117 kB]
152s Get:212 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblocale-gettext-perl ppc64el 1.07-6ubuntu4 [16.1 kB]
152s Get:213 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el uuid-runtime ppc64el 2.39.3-9ubuntu2 [33.8 kB]
152s Get:214 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdebconfclient0 ppc64el 0.271ubuntu2 [11.2 kB]
152s Get:215 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsemanage-common all 3.5-1build4 [10.1 kB]
152s Get:216 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsemanage2 ppc64el 3.5-1build4 [115 kB]
153s Get:217 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el install-info ppc64el 7.1-3build1 [64.5 kB]
153s Get:218 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13-base ppc64el 13.2.0-21ubuntu1 [48.3 kB]
153s Get:219 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libss2 ppc64el 1.47.0-2.4~exp1ubuntu2 [18.0 kB]
153s Get:220 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dmsetup ppc64el 2:1.02.185-3ubuntu2 [91.8 kB]
153s Get:221 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el eject ppc64el 2.39.3-9ubuntu2 [28.2 kB]
154s Get:222 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el krb5-locales all 1.20.1-6ubuntu1 [13.8 kB]
154s Get:223 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
154s Get:224 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libslang2 ppc64el 2.3.3-3build1 [501 kB]
154s Get:225 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-charwidth-perl ppc64el 0.04-11build2 [9506 B]
154s Get:226 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-iconv-perl ppc64el 1.7-8build2 [13.7 kB]
154s Get:227 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-yaml ppc64el 6.0.1-2build1 [123 kB]
154s Get:228 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-setuptools all 68.1.2-2ubuntu1 [396 kB]
154s Get:229 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB]
154s Get:230 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el rsyslog ppc64el 8.2312.0-3ubuntu7 [629 kB]
154s Get:231 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el vim-tiny ppc64el 2:9.1.0016-1ubuntu6 [1042 kB]
154s Get:232 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el vim-common all 2:9.1.0016-1ubuntu6 [385 kB]
155s Get:233 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-user-dirs ppc64el 0.18-1 [20.0 kB]
155s Get:234 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el xxd ppc64el 2:9.1.0016-1ubuntu6 [63.7 kB]
155s Get:235 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el apparmor ppc64el 4.0.0-beta3-0ubuntu2 [747 kB]
155s Get:236 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ftp all 20230507-2build1 [4724 B]
155s Get:237 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el inetutils-telnet ppc64el 2:2.5-3ubuntu3 [115 kB]
155s Get:238 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el info ppc64el 7.1-3build1 [188 kB]
156s Get:239 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libusb-1.0-0 ppc64el 2:1.0.27-1 [64.0 kB]
156s Get:240 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxmuu1 ppc64el 2:1.1.3-3build1 [9488 B]
156s Get:241 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el lshw ppc64el 02.19.git.2021.06.19.996aaad9c7-2build2 [334 kB]
156s Get:242 http://ftpmaster.internal/ubuntu noble/main ppc64el manpages all 6.05.01-1 [1340 kB]
157s Get:243 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el mtr-tiny ppc64el 0.95-1.1build1 [62.8 kB]
157s Get:244 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el plymouth-theme-ubuntu-text ppc64el 24.004.60-1ubuntu6 [11.1 kB]
157s Get:245 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el plymouth ppc64el 24.004.60-1ubuntu6 [155 kB]
157s Get:246 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el telnet all 0.17+2.5-3ubuntu3 [3682 B]
157s Get:247 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el usb.ids all 2024.03.18-1 [223 kB]
157s Get:248 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el xz-utils ppc64el 5.6.0-0.2 [281 kB]
157s Get:249 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libctf0 ppc64el 2.42-4ubuntu1 [112 kB]
158s Get:250 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libctf-nobfd0 ppc64el 2.42-4ubuntu1 [112 kB]
158s Get:251 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.42-4ubuntu1 [2473 kB]
159s Get:252 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbinutils ppc64el 2.42-4ubuntu1 [699 kB]
159s Get:253 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el binutils ppc64el 2.42-4ubuntu1 [3078 B]
159s Get:254 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el binutils-common ppc64el 2.42-4ubuntu1 [217 kB]
159s Get:255 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsframe1 ppc64el 2.42-4ubuntu1 [16.0 kB]
160s Get:256 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libllvm18 ppc64el 1:18.1.2-1ubuntu2 [28.9 MB]
169s Get:257 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libclang-cpp18 ppc64el 1:18.1.2-1ubuntu2 [14.6 MB]
174s Get:258 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libbpfcc ppc64el 0.29.1+ds-1ubuntu4 [707 kB]
174s Get:259 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-bpfcc all 0.29.1+ds-1ubuntu4 [40.2 kB]
174s Get:260 http://ftpmaster.internal/ubuntu noble/main ppc64el ieee-data all 20220827.1 [2113 kB]
174s Get:261 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-netaddr all 0.8.0-2ubuntu1 [319 kB]
174s Get:262 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el bpfcc-tools all 0.29.1+ds-1ubuntu4 [687 kB]
174s Get:263 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libclang1-18 ppc64el 1:18.1.2-1ubuntu2 [8725 kB]
175s Get:264 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdw1t64 ppc64el 0.190-1.1build2 [301 kB]
175s Get:265 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el bpftrace ppc64el 0.20.2-1ubuntu1 [1058 kB]
176s Get:266 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el cryptsetup-bin ppc64el 2:2.7.0-1ubuntu2 [227 kB]
176s Get:267 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg-dev all 1.22.6ubuntu5 [1074 kB]
176s Get:268 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdpkg-perl all 1.22.6ubuntu5 [269 kB]
176s Get:269 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB]
176s Get:270 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB]
176s Get:271 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu1 [37.4 kB]
176s Get:272 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libprotobuf-c1 ppc64el 1.4.1-1ubuntu3 [25.9 kB]
176s Get:273 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gnupg-l10n all 2.4.4-2ubuntu15 [65.8 kB]
176s Get:274 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libibverbs1 ppc64el 50.0-2build1 [74.4 kB]
176s Get:275 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el ibverbs-providers ppc64el 50.0-2build1 [420 kB]
176s Get:276 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el jq ppc64el 1.7.1-3 [66.1 kB]
177s Get:277 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjq1 ppc64el 1.7.1-3 [173 kB]
177s Get:278 http://ftpmaster.internal/ubuntu noble/main ppc64el libaio1t64 ppc64el 0.3.113-6 [8188 B]
177s Get:279 http://ftpmaster.internal/ubuntu noble/main ppc64el libatm1t64 ppc64el 1:2.5.1-5.1 [26.9 kB]
177s Get:280 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu6 [21.3 kB]
177s Get:281 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu1 [190 kB]
177s Get:282 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB]
177s Get:283 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
178s Get:284 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB]
178s Get:285 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB]
178s Get:286 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB]
178s Get:287 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4build2 [28.8 kB]
178s Get:288 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libwebp7 ppc64el 1.3.2-0.4build2 [312 kB]
178s Get:289 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu1 [274 kB]
178s Get:290 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxpm4 ppc64el 1:3.5.17-1build1 [50.2 kB]
178s Get:291 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgd3 ppc64el 2.3.3-9ubuntu3 [162 kB]
178s Get:292 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-devtools ppc64el 2.39-0ubuntu6 [29.6 kB]
178s Get:293 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-libc-dev ppc64el 6.8.0-20.20 [1586 kB]
179s Get:294 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB]
179s Get:295 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB]
179s Get:296 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu6 [2102 kB]
179s Get:297 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libevent-core-2.1-7 ppc64el 2.1.12-stable-9build1 [110 kB]
179s Get:298 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libftdi1-2 ppc64el 1.5-6build4 [32.5 kB]
179s Get:299 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libldap-common all 2.6.7+dfsg-1~exp1ubuntu6 [31.3 kB]
179s Get:300 http://ftpmaster.internal/ubuntu noble/main ppc64el libunwind8 ppc64el 1.6.2-3 [59.9 kB]
179s Get:301 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-modules-6.8.0-20-generic ppc64el 6.8.0-20.20 [31.3 MB]
182s Get:302 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-image-6.8.0-20-generic ppc64el 6.8.0-20.20 [63.9 MB]
184s Get:303 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-modules-extra-6.8.0-20-generic ppc64el 6.8.0-20.20 [103 MB]
190s Get:304 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-generic ppc64el 6.8.0-20.20+1 [1734 B]
191s Get:305 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-image-generic ppc64el 6.8.0-20.20+1 [9698 B]
191s Get:306 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-virtual ppc64el 6.8.0-20.20+1 [1686 B]
191s Get:307 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-image-virtual ppc64el 6.8.0-20.20+1 [9702 B]
191s Get:308 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-headers-virtual ppc64el 6.8.0-20.20+1 [1648 B]
191s Get:309 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-headers-6.8.0-20 all 6.8.0-20.20 [13.6 MB]
193s Get:310 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-headers-6.8.0-20-generic ppc64el 6.8.0-20.20 [3728 kB]
194s Get:311 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-headers-generic ppc64el 6.8.0-20.20+1 [9612 B]
194s Get:312 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-tools-common all 6.8.0-20.20 [437 kB]
194s Get:313 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-tools-6.8.0-20 ppc64el 6.8.0-20.20 [2924 kB]
194s Get:314 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el linux-tools-6.8.0-20-generic ppc64el 6.8.0-20.20 [1730 B]
194s Get:315 http://ftpmaster.internal/ubuntu noble/main ppc64el manpages-dev all 6.05.01-1 [2018 kB]
194s Get:316 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-distutils all 3.12.2-3ubuntu1.1 [133 kB]
195s Get:317 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-lib2to3 all 3.12.2-3ubuntu1.1 [79.1 kB]
195s Get:318 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-pyrsistent ppc64el 0.20.0-1build1 [60.4 kB]
195s Get:319 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-typing-extensions all 4.10.0-1 [60.7 kB]
195s Get:320 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-kernel-accessories ppc64el 1.536build1 [10.5 kB]
195s Get:321 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el kpartx ppc64el 0.9.4-5ubuntu6 [34.4 kB]
196s Preconfiguring packages ...
196s Fetched 390 MB in 1min 3s (6211 kB/s)
196s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70153 files and directories currently installed.)
196s Preparing to unpack .../motd-news-config_13ubuntu8_all.deb ...
196s Unpacking motd-news-config (13ubuntu8) over (13ubuntu7) ...
196s Preparing to unpack .../base-files_13ubuntu8_ppc64el.deb ...
196s Unpacking base-files (13ubuntu8) over (13ubuntu7) ...
196s Setting up base-files (13ubuntu8) ...
197s motd-news.service is a disabled or a static unit not running, not starting it.
197s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 70153 files and directories currently installed.)
197s Preparing to unpack .../bash_5.2.21-2ubuntu3_ppc64el.deb ...
197s Unpacking bash (5.2.21-2ubuntu3) over (5.2.21-2ubuntu2) ...
197s Setting up bash (5.2.21-2ubuntu3) ...
197s 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
197s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70153 files and directories currently installed.)
197s Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu2_ppc64el.deb ...
197s Unpacking bsdutils (1:2.39.3-9ubuntu2) over (1:2.39.3-6ubuntu2) ...
197s Setting up bsdutils (1:2.39.3-9ubuntu2) ...
197s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70153 files and directories currently installed.)
197s Preparing to unpack .../coreutils_9.4-3ubuntu3_ppc64el.deb ...
197s Unpacking coreutils (9.4-3ubuntu3) over (9.4-2ubuntu4) ...
197s Setting up coreutils (9.4-3ubuntu3) ...
197s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70153 files and directories currently installed.)
197s Preparing to unpack .../00-libudisks2-0_2.10.1-6_ppc64el.deb ...
197s Unpacking libudisks2-0:ppc64el (2.10.1-6) over (2.10.1-1ubuntu2) ...
197s Preparing to unpack .../01-udisks2_2.10.1-6_ppc64el.deb ...
197s Unpacking udisks2 (2.10.1-6) over (2.10.1-1ubuntu2) ...
198s Preparing to unpack .../02-shared-mime-info_2.4-1build1_ppc64el.deb ...
198s Unpacking shared-mime-info (2.4-1build1) over (2.4-1) ...
198s Preparing to unpack .../03-gir1.2-girepository-2.0_1.79.1-1ubuntu6_ppc64el.deb ...
198s Unpacking gir1.2-girepository-2.0:ppc64el (1.79.1-1ubuntu6) over (1.79.1-1) ...
198s Preparing to unpack .../04-gir1.2-glib-2.0_2.79.3-3ubuntu5_ppc64el.deb ...
198s Unpacking gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
198s Preparing to unpack .../05-libgirepository-1.0-1_1.79.1-1ubuntu6_ppc64el.deb ...
198s Unpacking libgirepository-1.0-1:ppc64el (1.79.1-1ubuntu6) over (1.79.1-1) ...
198s Preparing to unpack .../06-python3-gi_3.47.0-3build1_ppc64el.deb ...
198s Unpacking python3-gi (3.47.0-3build1) over (3.47.0-3) ...
198s Preparing to unpack .../07-python3-dbus_1.3.2-5build2_ppc64el.deb ...
198s Unpacking python3-dbus (1.3.2-5build2) over (1.3.2-5build1) ...
198s Selecting previously unselected package libnetplan1:ppc64el.
198s Preparing to unpack .../08-libnetplan1_1.0-1_ppc64el.deb ...
198s Unpacking libnetplan1:ppc64el (1.0-1) ...
198s Preparing to unpack .../09-python3-netplan_1.0-1_ppc64el.deb ...
198s Unpacking python3-netplan (1.0-1) over (0.107.1-3) ...
198s Preparing to unpack .../10-netplan-generator_1.0-1_ppc64el.deb ...
198s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
198s Unpacking netplan-generator (1.0-1) over (0.107.1-3) ...
198s Preparing to unpack .../11-initramfs-tools-bin_0.142ubuntu23_ppc64el.deb ...
198s Unpacking initramfs-tools-bin (0.142ubuntu23) over (0.142ubuntu20) ...
198s Preparing to unpack .../12-initramfs-tools-core_0.142ubuntu23_all.deb ...
198s Unpacking initramfs-tools-core (0.142ubuntu23) over (0.142ubuntu20) ...
198s Preparing to unpack .../13-initramfs-tools_0.142ubuntu23_all.deb ...
198s Unpacking initramfs-tools (0.142ubuntu23) over (0.142ubuntu20) ...
198s Preparing to unpack .../14-netplan.io_1.0-1_ppc64el.deb ...
198s Unpacking netplan.io (1.0-1) over (0.107.1-3) ...
198s Preparing to unpack .../15-libxmlb2_0.3.15-1build1_ppc64el.deb ...
198s Unpacking libxmlb2:ppc64el (0.3.15-1build1) over (0.3.15-1) ...
198s dpkg: libgpgme11:ppc64el: dependency problems, but removing anyway as you requested:
198s  libvolume-key1:ppc64el depends on libgpgme11 (>= 1.4.1).
198s  libjcat1:ppc64el depends on libgpgme11 (>= 1.2.0).
198s 
198s (Reading database ... 
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(Reading database ... 80%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70157 files and directories currently installed.)
198s Removing libgpgme11:ppc64el (1.18.0-4ubuntu1) ...
198s Selecting previously unselected package libgpgme11t64:ppc64el.
198s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70151 files and directories currently installed.)
198s Preparing to unpack .../00-libgpgme11t64_1.18.0-4.1ubuntu3_ppc64el.deb ...
198s Unpacking libgpgme11t64:ppc64el (1.18.0-4.1ubuntu3) ...
198s Preparing to unpack .../01-libvolume-key1_0.3.12-7build1_ppc64el.deb ...
198s Unpacking libvolume-key1:ppc64el (0.3.12-7build1) over (0.3.12-5build2) ...
198s Preparing to unpack .../02-libqrtr-glib0_1.2.2-1ubuntu3_ppc64el.deb ...
198s Unpacking libqrtr-glib0:ppc64el (1.2.2-1ubuntu3) over (1.2.2-1ubuntu2) ...
198s Preparing to unpack .../03-libqmi-glib5_1.35.2-0ubuntu1_ppc64el.deb ...
198s Unpacking libqmi-glib5:ppc64el (1.35.2-0ubuntu1) over (1.34.0-2) ...
198s Preparing to unpack .../04-libqmi-proxy_1.35.2-0ubuntu1_ppc64el.deb ...
198s Unpacking libqmi-proxy (1.35.2-0ubuntu1) over (1.34.0-2) ...
198s Preparing to unpack .../05-libpolkit-agent-1-0_124-1ubuntu1_ppc64el.deb ...
198s Unpacking libpolkit-agent-1-0:ppc64el (124-1ubuntu1) over (124-1) ...
198s Preparing to unpack .../06-libpolkit-gobject-1-0_124-1ubuntu1_ppc64el.deb ...
198s Unpacking libpolkit-gobject-1-0:ppc64el (124-1ubuntu1) over (124-1) ...
198s Preparing to unpack .../07-libmm-glib0_1.23.4-0ubuntu1_ppc64el.deb ...
198s Unpacking libmm-glib0:ppc64el (1.23.4-0ubuntu1) over (1.22.0-3) ...
198s Preparing to unpack .../08-libmbim-glib4_1.31.2-0ubuntu2_ppc64el.deb ...
198s Unpacking libmbim-glib4:ppc64el (1.31.2-0ubuntu2) over (1.30.0-1) ...
198s Preparing to unpack .../09-libmbim-proxy_1.31.2-0ubuntu2_ppc64el.deb ...
198s Unpacking libmbim-proxy (1.31.2-0ubuntu2) over (1.30.0-1) ...
198s Preparing to unpack .../10-libjson-glib-1.0-common_1.8.0-2build1_all.deb ...
198s Unpacking libjson-glib-1.0-common (1.8.0-2build1) over (1.8.0-2) ...
198s Preparing to unpack .../11-libjson-glib-1.0-0_1.8.0-2build1_ppc64el.deb ...
198s Unpacking libjson-glib-1.0-0:ppc64el (1.8.0-2build1) over (1.8.0-2) ...
198s Preparing to unpack .../12-libgusb2_0.4.8-1build1_ppc64el.deb ...
198s Unpacking libgusb2:ppc64el (0.4.8-1build1) over (0.4.8-1) ...
198s Preparing to unpack .../13-libgudev-1.0-0_1%3a238-3ubuntu2_ppc64el.deb ...
198s Unpacking libgudev-1.0-0:ppc64el (1:238-3ubuntu2) over (1:238-3) ...
198s Preparing to unpack .../14-tnftp_20230507-2build1_ppc64el.deb ...
198s Unpacking tnftp (20230507-2build1) over (20230507-2) ...
198s Preparing to unpack .../15-tcpdump_4.99.4-3ubuntu2_ppc64el.deb ...
198s Unpacking tcpdump (4.99.4-3ubuntu2) over (4.99.4-3ubuntu1) ...
199s Preparing to unpack .../16-libsystemd0_255.4-1ubuntu5_ppc64el.deb ...
199s Unpacking libsystemd0:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
199s Setting up libsystemd0:ppc64el (255.4-1ubuntu5) ...
199s (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 ... 70158 files and directories currently installed.)
199s Preparing to unpack .../systemd-dev_255.4-1ubuntu5_all.deb ...
199s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
199s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_ppc64el.deb ...
199s Unpacking libnss-systemd:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
199s Preparing to unpack .../libudev1_255.4-1ubuntu5_ppc64el.deb ...
199s Unpacking libudev1:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
199s Setting up libudev1:ppc64el (255.4-1ubuntu5) ...
199s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested:
199s  wget depends on libssl3 (>= 3.0.0).
199s  systemd-resolved depends on libssl3 (>= 3.0.0).
199s  systemd depends on libssl3 (>= 3.0.0).
199s  sudo depends on libssl3 (>= 3.0.0).
199s  rsync depends on libssl3 (>= 3.0.0).
199s  python3-cryptography depends on libssl3 (>= 3.0.0).
199s  openssl depends on libssl3 (>= 3.0.9).
199s  openssh-server depends on libssl3 (>= 3.0.10).
199s  openssh-client depends on libssl3 (>= 3.0.10).
199s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
199s  libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0).
199s  libssh-4:ppc64el depends on libssl3 (>= 3.0.0).
199s  libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0).
199s  libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0).
199s  libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0).
199s  libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0).
199s  libnvme1 depends on libssl3 (>= 3.0.0).
199s  libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0).
199s  libkmod2:ppc64el depends on libssl3 (>= 3.0.0).
199s  libfido2-1:ppc64el depends on libssl3 (>= 3.0.0).
199s  libcurl4:ppc64el depends on libssl3 (>= 3.0.0).
199s  libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0).
199s  kmod depends on libssl3 (>= 3.0.0).
199s  dhcpcd-base depends on libssl3 (>= 3.0.0).
199s  coreutils depends on libssl3 (>= 3.0.0).
199s  bind9-libs:ppc64el depends on libssl3 (>= 3.0.0).
199s 
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199s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ...
199s Selecting previously unselected package libssl3t64:ppc64el.
199s (Reading database ... 
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199s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ...
199s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
199s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
199s (Reading database ... 
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199s Preparing to unpack .../systemd_255.4-1ubuntu5_ppc64el.deb ...
199s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
199s Preparing to unpack .../udev_255.4-1ubuntu5_ppc64el.deb ...
199s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
199s Preparing to unpack .../libsystemd-shared_255.4-1ubuntu5_ppc64el.deb ...
199s Unpacking libsystemd-shared:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
199s Setting up libsystemd-shared:ppc64el (255.4-1ubuntu5) ...
199s Setting up systemd-dev (255.4-1ubuntu5) ...
199s Setting up systemd (255.4-1ubuntu5) ...
200s (Reading database ... 
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200s Preparing to unpack .../00-systemd-sysv_255.4-1ubuntu5_ppc64el.deb ...
200s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
200s Preparing to unpack .../01-libpam-systemd_255.4-1ubuntu5_ppc64el.deb ...
200s Unpacking libpam-systemd:ppc64el (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
200s Preparing to unpack .../02-systemd-timesyncd_255.4-1ubuntu5_ppc64el.deb ...
200s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
201s Preparing to unpack .../03-systemd-resolved_255.4-1ubuntu5_ppc64el.deb ...
201s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
201s Preparing to unpack .../04-sudo_1.9.15p5-3ubuntu3_ppc64el.deb ...
201s Unpacking sudo (1.9.15p5-3ubuntu3) over (1.9.15p5-3ubuntu1) ...
201s Preparing to unpack .../05-rsync_3.2.7-1build1_ppc64el.deb ...
201s Unpacking rsync (3.2.7-1build1) over (3.2.7-1) ...
201s Preparing to unpack .../06-python3-cryptography_41.0.7-4build2_ppc64el.deb ...
201s Unpacking python3-cryptography (41.0.7-4build2) over (41.0.7-3) ...
201s Preparing to unpack .../07-openssl_3.0.13-0ubuntu2_ppc64el.deb ...
201s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
201s Preparing to unpack .../08-openssh-sftp-server_1%3a9.6p1-3ubuntu11_ppc64el.deb ...
201s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
201s Preparing to unpack .../09-openssh-client_1%3a9.6p1-3ubuntu11_ppc64el.deb ...
201s Unpacking openssh-client (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
201s Preparing to unpack .../10-openssh-server_1%3a9.6p1-3ubuntu11_ppc64el.deb ...
201s Unpacking openssh-server (1:9.6p1-3ubuntu11) over (1:9.6p1-3ubuntu2) ...
201s Preparing to unpack .../11-libssh-4_0.10.6-2build1_ppc64el.deb ...
201s Unpacking libssh-4:ppc64el (0.10.6-2build1) over (0.10.6-2) ...
201s Preparing to unpack .../12-libsasl2-modules_2.1.28+dfsg1-5ubuntu1_ppc64el.deb ...
201s Unpacking libsasl2-modules:ppc64el (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
201s Preparing to unpack .../13-python3.12_3.12.2-4build3_ppc64el.deb ...
201s Unpacking python3.12 (3.12.2-4build3) over (3.12.2-1) ...
201s Preparing to unpack .../14-python3.12-minimal_3.12.2-4build3_ppc64el.deb ...
201s Unpacking python3.12-minimal (3.12.2-4build3) over (3.12.2-1) ...
201s Preparing to unpack .../15-libpython3.12-minimal_3.12.2-4build3_ppc64el.deb ...
202s Unpacking libpython3.12-minimal:ppc64el (3.12.2-4build3) over (3.12.2-1) ...
202s Preparing to unpack .../16-grub-ieee1275_2.12-1ubuntu5_ppc64el.deb ...
202s Unpacking grub-ieee1275 (2.12-1ubuntu5) over (2.12-1ubuntu4) ...
202s Preparing to unpack .../17-grub2-common_2.12-1ubuntu5_ppc64el.deb ...
202s Unpacking grub2-common (2.12-1ubuntu5) over (2.12-1ubuntu4) ...
202s Preparing to unpack .../18-grub-common_2.12-1ubuntu5_ppc64el.deb ...
202s Unpacking grub-common (2.12-1ubuntu5) over (2.12-1ubuntu4) ...
202s Preparing to unpack .../19-grub-ieee1275-bin_2.12-1ubuntu5_ppc64el.deb ...
202s Unpacking grub-ieee1275-bin (2.12-1ubuntu5) over (2.12-1ubuntu4) ...
202s dpkg: libparted2:ppc64el: dependency problems, but removing anyway as you requested:
202s  parted depends on libparted2 (= 3.6-3).
202s 
202s (Reading database ... 
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202s Removing libparted2:ppc64el (3.6-3) ...
202s Selecting previously unselected package libparted2t64:ppc64el.
202s (Reading database ... 
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202s Preparing to unpack .../0-libparted2t64_3.6-3.1build2_ppc64el.deb ...
202s Unpacking libparted2t64:ppc64el (3.6-3.1build2) ...
202s Preparing to unpack .../1-parted_3.6-3.1build2_ppc64el.deb ...
202s Unpacking parted (3.6-3.1build2) over (3.6-3) ...
202s Preparing to unpack .../2-python3.11_3.11.8-1build4_ppc64el.deb ...
202s Unpacking python3.11 (3.11.8-1build4) over (3.11.8-1) ...
202s Preparing to unpack .../3-python3.11-minimal_3.11.8-1build4_ppc64el.deb ...
202s Unpacking python3.11-minimal (3.11.8-1build4) over (3.11.8-1) ...
202s Preparing to unpack .../4-libpython3.11-minimal_3.11.8-1build4_ppc64el.deb ...
202s Unpacking libpython3.11-minimal:ppc64el (3.11.8-1build4) over (3.11.8-1) ...
202s Preparing to unpack .../5-libpython3.11-stdlib_3.11.8-1build4_ppc64el.deb ...
203s Unpacking libpython3.11-stdlib:ppc64el (3.11.8-1build4) over (3.11.8-1) ...
203s Preparing to unpack .../6-gnupg-utils_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking gnupg-utils (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s Preparing to unpack .../7-gpg-agent_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking gpg-agent (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s Preparing to unpack .../8-gpg-wks-client_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking gpg-wks-client (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s Preparing to unpack .../9-gpg_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking gpg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s dpkg: libnpth0:ppc64el: dependency problems, but removing anyway as you requested:
203s  keyboxd depends on libnpth0 (>= 0.90).
203s  gpgv depends on libnpth0 (>= 0.90).
203s  gpgsm depends on libnpth0 (>= 0.90).
203s  dirmngr depends on libnpth0 (>= 0.90).
203s 
203s (Reading database ... 
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203s Removing libnpth0:ppc64el (1.6-3build2) ...
203s Selecting previously unselected package libnpth0t64:ppc64el.
203s (Reading database ... 
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203s Preparing to unpack .../libnpth0t64_1.6-3.1_ppc64el.deb ...
203s Unpacking libnpth0t64:ppc64el (1.6-3.1) ...
203s Setting up libnpth0t64:ppc64el (1.6-3.1) ...
203s (Reading database ... 
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203s Preparing to unpack .../gpgv_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking gpgv (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s Setting up gpgv (2.4.4-2ubuntu15) ...
203s (Reading database ... 
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203s Preparing to unpack .../dirmngr_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking dirmngr (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s Preparing to unpack .../gnupg_2.4.4-2ubuntu15_all.deb ...
203s Unpacking gnupg (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s Preparing to unpack .../keyboxd_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking keyboxd (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s Preparing to unpack .../gpgconf_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking gpgconf (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s Preparing to unpack .../gpgsm_2.4.4-2ubuntu15_ppc64el.deb ...
203s Unpacking gpgsm (2.4.4-2ubuntu15) over (2.4.4-2ubuntu7) ...
203s dpkg: libreadline8:ppc64el: dependency problems, but removing anyway as you requested:
203s  libpython3.12-stdlib:ppc64el depends on libreadline8 (>= 7.0~beta).
203s  gawk depends on libreadline8 (>= 6.0).
203s  fdisk depends on libreadline8 (>= 6.0).
203s  bc depends on libreadline8 (>= 6.0).
203s 
203s (Reading database ... 
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203s Removing libreadline8:ppc64el (8.2-3) ...
203s Selecting previously unselected package libreadline8t64:ppc64el.
203s (Reading database ... 
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203s Preparing to unpack .../libreadline8t64_8.2-4_ppc64el.deb ...
203s Adding 'diversion of /lib/powerpc64le-linux-gnu/libhistory.so.8 to /lib/powerpc64le-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
203s Adding 'diversion of /lib/powerpc64le-linux-gnu/libhistory.so.8.2 to /lib/powerpc64le-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
203s Adding 'diversion of /lib/powerpc64le-linux-gnu/libreadline.so.8 to /lib/powerpc64le-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
203s Adding 'diversion of /lib/powerpc64le-linux-gnu/libreadline.so.8.2 to /lib/powerpc64le-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
203s Unpacking libreadline8t64:ppc64el (8.2-4) ...
203s Setting up libreadline8t64:ppc64el (8.2-4) ...
203s (Reading database ... 
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203s Preparing to unpack .../gawk_1%3a5.2.1-2build2_ppc64el.deb ...
203s Unpacking gawk (1:5.2.1-2build2) over (1:5.2.1-2) ...
203s Preparing to unpack .../fdisk_2.39.3-9ubuntu2_ppc64el.deb ...
203s Unpacking fdisk (2.39.3-9ubuntu2) over (2.39.3-6ubuntu2) ...
203s Preparing to unpack .../bc_1.07.1-3ubuntu2_ppc64el.deb ...
203s Unpacking bc (1.07.1-3ubuntu2) over (1.07.1-3build1) ...
203s Preparing to unpack .../libpython3.12-stdlib_3.12.2-4build3_ppc64el.deb ...
204s Unpacking libpython3.12-stdlib:ppc64el (3.12.2-4build3) over (3.12.2-1) ...
204s Preparing to unpack .../perl-base_5.38.2-3.2_ppc64el.deb ...
204s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
204s Setting up perl-base (5.38.2-3.2) ...
204s (Reading database ... 
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204s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
204s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
204s Preparing to unpack .../python3-gdbm_3.12.2-3ubuntu1.1_ppc64el.deb ...
204s Unpacking python3-gdbm:ppc64el (3.12.2-3ubuntu1.1) over (3.11.5-1) ...
204s Preparing to unpack .../man-db_2.12.0-3build4_ppc64el.deb ...
204s Unpacking man-db (2.12.0-3build4) over (2.12.0-3) ...
205s dpkg: libgdbm-compat4:ppc64el: dependency problems, but removing anyway as you requested:
205s  libperl5.38:ppc64el depends on libgdbm-compat4 (>= 1.18-3).
205s 
205s (Reading database ... 
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205s Removing libgdbm-compat4:ppc64el (1.23-5) ...
205s dpkg: libgdbm6:ppc64el: dependency problems, but removing anyway as you requested:
205s  libperl5.38:ppc64el depends on libgdbm6 (>= 1.21).
205s 
205s Removing libgdbm6:ppc64el (1.23-5) ...
205s Selecting previously unselected package libgdbm6t64:ppc64el.
205s (Reading database ... 
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205s Preparing to unpack .../libgdbm6t64_1.23-5.1_ppc64el.deb ...
205s Unpacking libgdbm6t64:ppc64el (1.23-5.1) ...
205s Selecting previously unselected package libgdbm-compat4t64:ppc64el.
205s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_ppc64el.deb ...
205s Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1) ...
205s dpkg: libperl5.38:ppc64el: dependency problems, but removing anyway as you requested:
205s  perl depends on libperl5.38 (= 5.38.2-3).
205s 
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205s Removing libperl5.38:ppc64el (5.38.2-3) ...
205s Selecting previously unselected package libperl5.38t64:ppc64el.
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205s Preparing to unpack .../libperl5.38t64_5.38.2-3.2_ppc64el.deb ...
205s Unpacking libperl5.38t64:ppc64el (5.38.2-3.2) ...
205s Preparing to unpack .../perl_5.38.2-3.2_ppc64el.deb ...
205s Unpacking perl (5.38.2-3.2) over (5.38.2-3) ...
205s dpkg: libdb5.3:ppc64el: dependency problems, but removing anyway as you requested:
205s  libsasl2-modules-db:ppc64el depends on libdb5.3.
205s  libpam-modules:ppc64el depends on libdb5.3.
205s  iproute2 depends on libdb5.3.
205s  apt-utils depends on libdb5.3.
205s 
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205s Removing libdb5.3:ppc64el (5.3.28+dfsg2-4) ...
205s Selecting previously unselected package libdb5.3t64:ppc64el.
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205s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6_ppc64el.deb ...
205s Unpacking libdb5.3t64:ppc64el (5.3.28+dfsg2-6) ...
205s Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-5ubuntu1_ppc64el.deb ...
205s Unpacking libsasl2-modules-db:ppc64el (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
205s Preparing to unpack .../libsasl2-2_2.1.28+dfsg1-5ubuntu1_ppc64el.deb ...
205s Unpacking libsasl2-2:ppc64el (2.1.28+dfsg1-5ubuntu1) over (2.1.28+dfsg1-4) ...
205s dpkg: libnvme1: dependency problems, but removing anyway as you requested:
205s  libblockdev-nvme3:ppc64el depends on libnvme1 (>= 1.7.1).
205s 
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205s Removing libnvme1 (1.8-2) ...
205s Selecting previously unselected package libnvme1t64.
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205s Preparing to unpack .../libnvme1t64_1.8-3_ppc64el.deb ...
205s Unpacking libnvme1t64 (1.8-3) ...
205s Preparing to unpack .../wget_1.21.4-1ubuntu2_ppc64el.deb ...
205s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ...
206s dpkg: libcurl4:ppc64el: dependency problems, but removing anyway as you requested:
206s  curl depends on libcurl4 (= 8.5.0-2ubuntu2).
206s 
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206s Removing libcurl4:ppc64el (8.5.0-2ubuntu2) ...
206s Selecting previously unselected package libcurl4t64:ppc64el.
206s (Reading database ... 
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206s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu8_ppc64el.deb ...
206s Unpacking libcurl4t64:ppc64el (8.5.0-2ubuntu8) ...
206s Preparing to unpack .../curl_8.5.0-2ubuntu8_ppc64el.deb ...
206s Unpacking curl (8.5.0-2ubuntu8) over (8.5.0-2ubuntu2) ...
206s dpkg: libpsl5:ppc64el: dependency problems, but removing anyway as you requested:
206s  libcurl3-gnutls:ppc64el depends on libpsl5 (>= 0.16.0).
206s 
206s (Reading database ... 
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206s Removing libpsl5:ppc64el (0.21.2-1build1) ...
206s Selecting previously unselected package libpsl5t64:ppc64el.
206s (Reading database ... 
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206s Preparing to unpack .../libpsl5t64_0.21.2-1.1_ppc64el.deb ...
206s Unpacking libpsl5t64:ppc64el (0.21.2-1.1) ...
206s dpkg: libarchive13:ppc64el: dependency problems, but removing anyway as you requested:
206s  fwupd depends on libarchive13 (>= 3.2.1).
206s 
206s (Reading database ... 
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206s Removing libarchive13:ppc64el (3.7.2-1ubuntu2) ...
206s Selecting previously unselected package libarchive13t64:ppc64el.
206s (Reading database ... 
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206s Preparing to unpack .../libarchive13t64_3.7.2-1.1ubuntu2_ppc64el.deb ...
206s Unpacking libarchive13t64:ppc64el (3.7.2-1.1ubuntu2) ...
206s Preparing to unpack .../fwupd_1.9.15-2_ppc64el.deb ...
206s Unpacking fwupd (1.9.15-2) over (1.9.14-1) ...
206s dpkg: libcurl3-gnutls:ppc64el: dependency problems, but removing anyway as you requested:
206s  libfwupd2:ppc64el depends on libcurl3-gnutls (>= 7.63.0).
206s 
206s (Reading database ... 
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206s Removing libcurl3-gnutls:ppc64el (8.5.0-2ubuntu2) ...
206s Selecting previously unselected package libcurl3t64-gnutls:ppc64el.
206s (Reading database ... 
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206s Preparing to unpack .../00-libcurl3t64-gnutls_8.5.0-2ubuntu8_ppc64el.deb ...
206s Unpacking libcurl3t64-gnutls:ppc64el (8.5.0-2ubuntu8) ...
206s Preparing to unpack .../01-libfwupd2_1.9.15-2_ppc64el.deb ...
206s Unpacking libfwupd2:ppc64el (1.9.15-2) over (1.9.14-1) ...
206s Preparing to unpack .../02-libblockdev3_3.1.0-1build1_ppc64el.deb ...
206s Unpacking libblockdev3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
206s Preparing to unpack .../03-libblockdev-utils3_3.1.0-1build1_ppc64el.deb ...
206s Unpacking libblockdev-utils3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
206s Preparing to unpack .../04-libblockdev-swap3_3.1.0-1build1_ppc64el.deb ...
206s Unpacking libblockdev-swap3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
206s Preparing to unpack .../05-libblockdev-part3_3.1.0-1build1_ppc64el.deb ...
206s Unpacking libblockdev-part3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
206s Preparing to unpack .../06-libblockdev-nvme3_3.1.0-1build1_ppc64el.deb ...
206s Unpacking libblockdev-nvme3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
206s Preparing to unpack .../07-libblockdev-mdraid3_3.1.0-1build1_ppc64el.deb ...
206s Unpacking libblockdev-mdraid3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
206s Preparing to unpack .../08-libblockdev-loop3_3.1.0-1build1_ppc64el.deb ...
206s Unpacking libblockdev-loop3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
206s Preparing to unpack .../09-e2fsprogs-l10n_1.47.0-2.4~exp1ubuntu2_all.deb ...
206s Unpacking e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
206s Preparing to unpack .../10-logsave_1.47.0-2.4~exp1ubuntu2_ppc64el.deb ...
206s Unpacking logsave (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
207s dpkg: libext2fs2:ppc64el: dependency problems, but removing anyway as you requested:
207s  libblockdev-fs3:ppc64el depends on libext2fs2 (>= 1.42.11).
207s  e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1).
207s  btrfs-progs depends on libext2fs2 (>= 1.42).
207s 
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207s Removing libext2fs2:ppc64el (1.47.0-2ubuntu1) ...
207s Selecting previously unselected package libext2fs2t64:ppc64el.
207s (Reading database ... 
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207s Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu2_ppc64el.deb ...
207s Adding 'diversion of /lib/powerpc64le-linux-gnu/libe2p.so.2 to /lib/powerpc64le-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64'
207s Adding 'diversion of /lib/powerpc64le-linux-gnu/libe2p.so.2.3 to /lib/powerpc64le-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64'
207s Adding 'diversion of /lib/powerpc64le-linux-gnu/libext2fs.so.2 to /lib/powerpc64le-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64'
207s Adding 'diversion of /lib/powerpc64le-linux-gnu/libext2fs.so.2.4 to /lib/powerpc64le-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64'
207s Unpacking libext2fs2t64:ppc64el (1.47.0-2.4~exp1ubuntu2) ...
207s Setting up libext2fs2t64:ppc64el (1.47.0-2.4~exp1ubuntu2) ...
207s (Reading database ... 
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207s Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu2_ppc64el.deb ...
207s Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu2) over (1.47.0-2ubuntu1) ...
207s dpkg: libreiserfscore0: dependency problems, but removing anyway as you requested:
207s  btrfs-progs depends on libreiserfscore0 (>= 1:3.6.27).
207s 
207s (Reading database ... 
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207s Removing libreiserfscore0 (1:3.6.27-7) ...
207s Selecting previously unselected package libreiserfscore0t64.
207s (Reading database ... 
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207s Preparing to unpack .../libreiserfscore0t64_1%3a3.6.27-7.1_ppc64el.deb ...
207s Unpacking libreiserfscore0t64 (1:3.6.27-7.1) ...
207s Preparing to unpack .../btrfs-progs_6.6.3-1.1build1_ppc64el.deb ...
207s Unpacking btrfs-progs (6.6.3-1.1build1) over (6.6.3-1.1) ...
207s Preparing to unpack .../libblockdev-fs3_3.1.0-1build1_ppc64el.deb ...
207s Unpacking libblockdev-fs3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
207s Preparing to unpack .../libblockdev-crypto3_3.1.0-1build1_ppc64el.deb ...
207s Unpacking libblockdev-crypto3:ppc64el (3.1.0-1build1) over (3.1.0-1) ...
207s Preparing to unpack .../bolt_0.9.6-2build1_ppc64el.deb ...
207s Unpacking bolt (0.9.6-2build1) over (0.9.6-2) ...
207s dpkg: libglib2.0-0:ppc64el: dependency problems, but removing anyway as you requested:
207s  libnetplan0:ppc64el depends on libglib2.0-0 (>= 2.75.3).
207s  libjcat1:ppc64el depends on libglib2.0-0 (>= 2.75.3).
207s 
207s (Reading database ... 
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207s Removing libglib2.0-0:ppc64el (2.79.2-1~ubuntu1) ...
207s Selecting previously unselected package libglib2.0-0t64:ppc64el.
207s (Reading database ... 
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207s Preparing to unpack .../0-libglib2.0-0t64_2.79.3-3ubuntu5_ppc64el.deb ...
207s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
207s removed '/var/lib/dpkg/info/libglib2.0-0:ppc64el.postrm'
207s Unpacking libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ...
207s Preparing to unpack .../1-libjcat1_0.2.0-2build2_ppc64el.deb ...
207s Unpacking libjcat1:ppc64el (0.2.0-2build2) over (0.2.0-2) ...
207s Preparing to unpack .../2-libldap2_2.6.7+dfsg-1~exp1ubuntu6_ppc64el.deb ...
207s Unpacking libldap2:ppc64el (2.6.7+dfsg-1~exp1ubuntu6) over (2.6.7+dfsg-1~exp1ubuntu1) ...
207s Preparing to unpack .../3-ubuntu-pro-client-l10n_31.2.2_ppc64el.deb ...
207s Unpacking ubuntu-pro-client-l10n (31.2.2) over (31.1) ...
207s Preparing to unpack .../4-ubuntu-pro-client_31.2.2_ppc64el.deb ...
208s Unpacking ubuntu-pro-client (31.2.2) over (31.1) ...
208s Preparing to unpack .../5-python3-apt_2.7.7_ppc64el.deb ...
208s Unpacking python3-apt (2.7.7) over (2.7.6) ...
208s Preparing to unpack .../6-apt-utils_2.7.14_ppc64el.deb ...
208s Unpacking apt-utils (2.7.14) over (2.7.12) ...
208s dpkg: libapt-pkg6.0:ppc64el: dependency problems, but removing anyway as you requested:
208s  apt depends on libapt-pkg6.0 (>= 2.7.12).
208s 
208s (Reading database ... 
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208s Removing libapt-pkg6.0:ppc64el (2.7.12) ...
208s dpkg: libnettle8:ppc64el: dependency problems, but removing anyway as you requested:
208s  librtmp1:ppc64el depends on libnettle8.
208s  libhogweed6:ppc64el depends on libnettle8.
208s  libgnutls30:ppc64el depends on libnettle8 (>= 3.9~).
208s 
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208s dpkg: libhogweed6:ppc64el: dependency problems, but removing anyway as you requested:
208s  librtmp1:ppc64el depends on libhogweed6.
208s  libgnutls30:ppc64el depends on libhogweed6 (>= 3.6).
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208s dpkg: libgnutls30:ppc64el: dependency problems, but removing anyway as you requested:
208s  librtmp1:ppc64el depends on libgnutls30 (>= 3.7.2).
208s  apt depends on libgnutls30 (>= 3.8.1).
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210s Preparing to unpack .../libblkid1_2.39.3-9ubuntu2_ppc64el.deb ...
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210s Setting up libblkid1:ppc64el (2.39.3-9ubuntu2) ...
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210s Preparing to unpack .../kmod_31+20240202-2ubuntu4_ppc64el.deb ...
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210s Setting up libcap-ng0:ppc64el (0.8.4-2build1) ...
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210s Preparing to unpack .../libpam0g_1.5.3-5ubuntu3_ppc64el.deb ...
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210s Setting up libpam0g:ppc64el (1.5.3-5ubuntu3) ...
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210s Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu3_ppc64el.deb ...
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210s Setting up libpam-modules-bin (1.5.3-5ubuntu3) ...
211s pam_namespace.service is a disabled or a static unit not running, not starting it.
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211s Installing new version of config file /etc/security/namespace.init ...
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211s Setting up libuuid1:ppc64el (2.39.3-9ubuntu2) ...
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211s Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu2_ppc64el.deb ...
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212s Setting up libseccomp2:ppc64el (2.5.5-1ubuntu2) ...
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212s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_ppc64el.deb ...
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212s Setting up zlib1g:ppc64el (1:1.3.dfsg-3.1ubuntu1) ...
212s Setting up libpython3.12-minimal:ppc64el (3.12.2-4build3) ...
212s Setting up libexpat1:ppc64el (2.6.1-2) ...
212s Setting up python3.12-minimal (3.12.2-4build3) ...
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213s dpkg: libpng16-16:ppc64el: dependency problems, but removing anyway as you requested:
213s  libfreetype6:ppc64el depends on libpng16-16 (>= 1.6.2-1).
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214s Preparing to unpack .../13-dpkg_1.22.6ubuntu5_ppc64el.deb ...
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216s Preparing to unpack .../libbpf1_1%3a1.3.0-2build1_ppc64el.deb ...
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216s dpkg: libelf1:ppc64el: dependency problems, but removing anyway as you requested:
216s  linux-headers-6.8.0-11-generic depends on libelf1 (>= 0.144).
216s 
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216s Preparing to unpack .../file_1%3a5.45-3_ppc64el.deb ...
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217s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ...
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217s Preparing to unpack .../libtirpc3t64_1.3.4+ds-1.1_ppc64el.deb ...
217s Adding 'diversion of /lib/powerpc64le-linux-gnu/libtirpc.so.3 to /lib/powerpc64le-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
217s Adding 'diversion of /lib/powerpc64le-linux-gnu/libtirpc.so.3.0.0 to /lib/powerpc64le-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
217s Unpacking libtirpc3t64:ppc64el (1.3.4+ds-1.1) ...
217s Preparing to unpack .../multipath-tools_0.9.4-5ubuntu6_ppc64el.deb ...
217s Unpacking multipath-tools (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ...
217s dpkg: liburcu8:ppc64el: dependency problems, but removing anyway as you requested:
217s  xfsprogs depends on liburcu8 (>= 0.13.0).
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217s Preparing to unpack .../bind9-libs_1%3a9.18.24-0ubuntu3_ppc64el.deb ...
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217s Removing libuv1:ppc64el (1.48.0-1) ...
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217s Preparing to unpack .../libdebconfclient0_0.271ubuntu2_ppc64el.deb ...
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217s Setting up libdebconfclient0:ppc64el (0.271ubuntu2) ...
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217s Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ...
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218s Selecting previously unselected package xdg-user-dirs.
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219s Selecting previously unselected package manpages.
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220s Selecting previously unselected package libllvm18:ppc64el.
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221s Selecting previously unselected package libclang1-18.
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222s Selecting previously unselected package fonts-dejavu-mono.
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222s Selecting previously unselected package libfontconfig1:ppc64el.
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223s Selecting previously unselected package linux-modules-6.8.0-20-generic.
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224s Selecting previously unselected package linux-modules-extra-6.8.0-20-generic.
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225s Preparing to unpack .../088-linux-virtual_6.8.0-20.20+1_ppc64el.deb ...
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225s Preparing to unpack .../090-linux-headers-virtual_6.8.0-20.20+1_ppc64el.deb ...
225s Unpacking linux-headers-virtual (6.8.0-20.20+1) over (6.8.0-11.11+1) ...
225s Selecting previously unselected package linux-headers-6.8.0-20.
225s Preparing to unpack .../091-linux-headers-6.8.0-20_6.8.0-20.20_all.deb ...
225s Unpacking linux-headers-6.8.0-20 (6.8.0-20.20) ...
228s Selecting previously unselected package linux-headers-6.8.0-20-generic.
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230s Unpacking linux-headers-generic (6.8.0-20.20+1) over (6.8.0-11.11+1) ...
230s Selecting previously unselected package linux-tools-common.
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230s Selecting previously unselected package linux-tools-6.8.0-20.
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230s Selecting previously unselected package linux-tools-6.8.0-20-generic.
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230s Selecting previously unselected package manpages-dev.
230s Preparing to unpack .../097-manpages-dev_6.05.01-1_all.deb ...
230s Unpacking manpages-dev (6.05.01-1) ...
230s Preparing to unpack .../098-python3-distutils_3.12.2-3ubuntu1.1_all.deb ...
230s Unpacking python3-distutils (3.12.2-3ubuntu1.1) over (3.11.5-1) ...
230s Preparing to unpack .../099-python3-lib2to3_3.12.2-3ubuntu1.1_all.deb ...
230s Unpacking python3-lib2to3 (3.12.2-3ubuntu1.1) over (3.11.5-1) ...
230s Preparing to unpack .../100-python3-pyrsistent_0.20.0-1build1_ppc64el.deb ...
230s Unpacking python3-pyrsistent:ppc64el (0.20.0-1build1) over (0.20.0-1) ...
230s Preparing to unpack .../101-python3-typing-extensions_4.10.0-1_all.deb ...
230s Unpacking python3-typing-extensions (4.10.0-1) over (4.9.0-1) ...
230s Selecting previously unselected package ubuntu-kernel-accessories.
230s Preparing to unpack .../102-ubuntu-kernel-accessories_1.536build1_ppc64el.deb ...
230s Unpacking ubuntu-kernel-accessories (1.536build1) ...
230s Preparing to unpack .../103-kpartx_0.9.4-5ubuntu6_ppc64el.deb ...
230s Unpacking kpartx (0.9.4-5ubuntu6) over (0.9.4-5ubuntu3) ...
231s Setting up pinentry-curses (1.2.1-3ubuntu4) ...
231s Setting up motd-news-config (13ubuntu8) ...
231s Setting up libtext-iconv-perl:ppc64el (1.7-8build2) ...
231s Setting up libtext-charwidth-perl:ppc64el (0.04-11build2) ...
231s Setting up libsharpyuv0:ppc64el (1.3.2-0.4build2) ...
231s Setting up liburcu8t64:ppc64el (0.14.0-3.1) ...
231s Setting up tcpdump (4.99.4-3ubuntu2) ...
231s Setting up libibverbs1:ppc64el (50.0-2build1) ...
231s Setting up systemd-sysv (255.4-1ubuntu5) ...
231s Setting up ubuntu-kernel-accessories (1.536build1) ...
231s Setting up libapparmor1:ppc64el (4.0.0-beta3-0ubuntu2) ...
231s Setting up libatm1t64:ppc64el (1:2.5.1-5.1) ...
231s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ...
231s Setting up libgdbm6t64:ppc64el (1.23-5.1) ...
231s Setting up bsdextrautils (2.39.3-9ubuntu2) ...
231s Setting up libxpm4:ppc64el (1:3.5.17-1build1) ...
231s Setting up libgdbm-compat4t64:ppc64el (1.23-5.1) ...
231s Setting up xdg-user-dirs (0.18-1) ...
231s Setting up ibverbs-providers:ppc64el (50.0-2build1) ...
231s Setting up linux-headers-6.8.0-20 (6.8.0-20.20) ...
231s Setting up libmagic-mgc (1:5.45-3) ...
231s Setting up gawk (1:5.2.1-2build2) ...
231s Setting up libjq1:ppc64el (1.7.1-3) ...
231s Setting up manpages (6.05.01-1) ...
231s Setting up libtirpc-common (1.3.4+ds-1.1) ...
231s Setting up libbrotli1:ppc64el (1.1.0-2build1) ...
231s Setting up libsqlite3-0:ppc64el (3.45.1-1ubuntu1) ...
231s Setting up libsasl2-modules:ppc64el (2.1.28+dfsg1-5ubuntu1) ...
231s Setting up libuv1t64:ppc64el (1.48.0-1.1) ...
231s Setting up libmagic1t64:ppc64el (1:5.45-3) ...
231s Setting up rsyslog (8.2312.0-3ubuntu7) ...
231s info: The user `syslog' is already a member of `adm'.
232s Setting up binutils-common:ppc64el (2.42-4ubuntu1) ...
232s Setting up libpsl5t64:ppc64el (0.21.2-1.1) ...
232s Setting up libnghttp2-14:ppc64el (1.59.0-1build1) ...
232s Setting up libdeflate0:ppc64el (1.19-1) ...
232s Setting up linux-libc-dev:ppc64el (6.8.0-20.20) ...
232s Setting up bc (1.07.1-3ubuntu2) ...
232s Setting up libctf-nobfd0:ppc64el (2.42-4ubuntu1) ...
232s Setting up libnss-systemd:ppc64el (255.4-1ubuntu5) ...
232s Setting up krb5-locales (1.20.1-6ubuntu1) ...
232s Setting up libcom-err2:ppc64el (1.47.0-2.4~exp1ubuntu2) ...
232s Setting up file (1:5.45-3) ...
232s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2build2) ...
232s Setting up libldap-common (2.6.7+dfsg-1~exp1ubuntu6) ...
232s Setting up libunwind8:ppc64el (1.6.2-3) ...
232s Setting up libprotobuf-c1:ppc64el (1.4.1-1ubuntu3) ...
232s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ...
232s Setting up xxd (2:9.1.0016-1ubuntu6) ...
232s Setting up libsframe1:ppc64el (2.42-4ubuntu1) ...
232s Setting up libelf1t64:ppc64el (0.190-1.1build2) ...
232s Setting up libkrb5support0:ppc64el (1.20.1-6ubuntu1) ...
232s Setting up libdw1t64:ppc64el (0.190-1.1build2) ...
232s Setting up linux-headers-6.8.0-20-generic (6.8.0-20.20) ...
232s Setting up eject (2.39.3-9ubuntu2) ...
232s Setting up apparmor (4.0.0-beta3-0ubuntu2) ...
232s Installing new version of config file /etc/apparmor.d/abstractions/authentication ...
232s Installing new version of config file /etc/apparmor.d/abstractions/crypto ...
232s Installing new version of config file /etc/apparmor.d/abstractions/kde-open5 ...
232s Installing new version of config file /etc/apparmor.d/abstractions/openssl ...
232s Installing new version of config file /etc/apparmor.d/code ...
232s Installing new version of config file /etc/apparmor.d/firefox ...
233s Reloading AppArmor profiles 
234s Setting up libglib2.0-0t64:ppc64el (2.79.3-3ubuntu5) ...
234s No schema files found: doing nothing.
234s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
234s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
234s Setting up vim-common (2:9.1.0016-1ubuntu6) ...
234s Setting up gcc-13-base:ppc64el (13.2.0-21ubuntu1) ...
234s Setting up libqrtr-glib0:ppc64el (1.2.2-1ubuntu3) ...
234s Setting up libslang2:ppc64el (2.3.3-3build1) ...
234s Setting up libnvme1t64 (1.8-3) ...
234s Setting up mtr-tiny (0.95-1.1build1) ...
234s Setting up gnupg-l10n (2.4.4-2ubuntu15) ...
234s Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build6) ...
234s Setting up libdbus-1-3:ppc64el (1.14.10-4ubuntu2) ...
234s Setting up xz-utils (5.6.0-0.2) ...
234s Setting up perl-modules-5.38 (5.38.2-3.2) ...
234s Setting up libproc2-0:ppc64el (2:4.0.4-4ubuntu2) ...
234s Setting up fonts-dejavu-mono (2.37-8) ...
234s Setting up libpng16-16t64:ppc64el (1.6.43-3) ...
234s Setting up systemd-timesyncd (255.4-1ubuntu5) ...
234s Setting up libevent-core-2.1-7:ppc64el (2.1.12-stable-9build1) ...
234s Setting up libss2:ppc64el (1.47.0-2.4~exp1ubuntu2) ...
234s Setting up usb.ids (2024.03.18-1) ...
234s Setting up sudo (1.9.15p5-3ubuntu3) ...
234s Setting up fonts-dejavu-core (2.37-8) ...
234s Setting up dhcpcd-base (1:10.0.6-1ubuntu2) ...
234s Setting up gir1.2-glib-2.0:ppc64el (2.79.3-3ubuntu5) ...
234s Setting up libk5crypto3:ppc64el (1.20.1-6ubuntu1) ...
234s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ...
234s Setting up logsave (1.47.0-2.4~exp1ubuntu2) ...
234s Setting up libwebp7:ppc64el (1.3.2-0.4build2) ...
234s Setting up libfdisk1:ppc64el (2.39.3-9ubuntu2) ...
234s Setting up libdb5.3t64:ppc64el (5.3.28+dfsg2-6) ...
234s Setting up libdevmapper1.02.1:ppc64el (2:1.02.185-3ubuntu2) ...
234s Setting up libaio1t64:ppc64el (0.3.113-6) ...
234s Setting up python-apt-common (2.7.7) ...
234s Setting up mount (2.39.3-9ubuntu2) ...
234s Setting up dmsetup (2:1.02.185-3ubuntu2) ...
234s Setting up uuid-runtime (2.39.3-9ubuntu2) ...
235s uuidd.service is a disabled or a static unit not running, not starting it.
235s Setting up libmm-glib0:ppc64el (1.23.4-0ubuntu1) ...
235s Setting up groff-base (1.23.0-3build1) ...
235s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ...
235s Setting up libplymouth5:ppc64el (24.004.60-1ubuntu6) ...
235s Setting up dbus-session-bus-common (1.14.10-4ubuntu2) ...
235s Setting up jq (1.7.1-3) ...
235s Setting up procps (2:4.0.4-4ubuntu2) ...
236s Setting up gpgconf (2.4.4-2ubuntu15) ...
236s Setting up libcryptsetup12:ppc64el (2:2.7.0-1ubuntu2) ...
236s Setting up libgirepository-1.0-1:ppc64el (1.79.1-1ubuntu6) ...
236s Setting up libjson-glib-1.0-common (1.8.0-2build1) ...
236s Setting up libkrb5-3:ppc64el (1.20.1-6ubuntu1) ...
236s Setting up libpython3.11-minimal:ppc64el (3.11.8-1build4) ...
236s Setting up libusb-1.0-0:ppc64el (2:1.0.27-1) ...
236s Setting up libperl5.38t64:ppc64el (5.38.2-3.2) ...
236s Setting up tnftp (20230507-2build1) ...
236s Setting up libbinutils:ppc64el (2.42-4ubuntu1) ...
236s Setting up dbus-system-bus-common (1.14.10-4ubuntu2) ...
236s Setting up libfido2-1:ppc64el (1.14.0-1build1) ...
236s Setting up libc-dev-bin (2.39-0ubuntu6) ...
236s Setting up openssl (3.0.13-0ubuntu2) ...
236s Setting up linux-modules-6.8.0-20-generic (6.8.0-20.20) ...
239s Setting up linux-tools-common (6.8.0-20.20) ...
239s Setting up readline-common (8.2-4) ...
239s Setting up libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu2) ...
239s Setting up libxmuu1:ppc64el (2:1.1.3-3build1) ...
239s Setting up dbus-bin (1.14.10-4ubuntu2) ...
239s Setting up info (7.1-3build1) ...
239s Setting up liblocale-gettext-perl (1.07-6ubuntu4) ...
239s Setting up gpg (2.4.4-2ubuntu15) ...
239s Setting up libgudev-1.0-0:ppc64el (1:238-3ubuntu2) ...
239s Setting up libpolkit-gobject-1-0:ppc64el (124-1ubuntu1) ...
239s Setting up libbpf1:ppc64el (1:1.3.0-2build1) ...
239s Setting up libmbim-glib4:ppc64el (1.31.2-0ubuntu2) ...
239s Setting up rsync (3.2.7-1build1) ...
239s rsync.service is a disabled or a static unit not running, not starting it.
239s Setting up libudisks2-0:ppc64el (2.10.1-6) ...
239s Setting up libkmod2:ppc64el (31+20240202-2ubuntu4) ...
239s Setting up bolt (0.9.6-2build1) ...
240s bolt.service is a disabled or a static unit not running, not starting it.
240s Setting up libllvm18:ppc64el (1:18.1.2-1ubuntu2) ...
240s Setting up gnupg-utils (2.4.4-2ubuntu15) ...
240s Setting up initramfs-tools-bin (0.142ubuntu23) ...
240s Setting up libctf0:ppc64el (2.42-4ubuntu1) ...
240s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ...
240s Setting up cryptsetup-bin (2:2.7.0-1ubuntu2) ...
240s Setting up python3.11-minimal (3.11.8-1build4) ...
241s Setting up libclang1-18 (1:18.1.2-1ubuntu2) ...
241s Setting up manpages-dev (6.05.01-1) ...
241s Setting up linux-modules-extra-6.8.0-20-generic (6.8.0-20.20) ...
243s Setting up apt-utils (2.7.14) ...
243s Setting up gpg-agent (2.4.4-2ubuntu15) ...
243s Setting up libpython3.12-stdlib:ppc64el (3.12.2-4build3) ...
243s Setting up wget (1.21.4-1ubuntu2) ...
243s Setting up fontconfig-config (2.15.0-1.1ubuntu1) ...
243s Setting up libxmlb2:ppc64el (0.3.15-1build1) ...
243s Setting up libpython3.11-stdlib:ppc64el (3.11.8-1build4) ...
243s Setting up python3.12 (3.12.2-4build3) ...
245s Setting up gpgsm (2.4.4-2ubuntu15) ...
245s Setting up inetutils-telnet (2:2.5-3ubuntu3) ...
245s Setting up libreiserfscore0t64 (1:3.6.27-7.1) ...
245s Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu2) ...
245s update-initramfs: deferring update (trigger activated)
246s e2scrub_all.service is a disabled or a static unit not running, not starting it.
246s Setting up linux-tools-6.8.0-20 (6.8.0-20.20) ...
246s Setting up libparted2t64:ppc64el (3.6-3.1build2) ...
246s Setting up linux-headers-generic (6.8.0-20.20+1) ...
246s Setting up dbus-daemon (1.14.10-4ubuntu2) ...
246s Setting up libmbim-proxy (1.31.2-0ubuntu2) ...
246s Setting up vim-tiny (2:9.1.0016-1ubuntu6) ...
246s Setting up kmod (31+20240202-2ubuntu4) ...
246s Setting up libnetplan1:ppc64el (1.0-1) ...
246s Setting up man-db (2.12.0-3build4) ...
246s Updating database of manual pages ...
249s man-db.service is a disabled or a static unit not running, not starting it.
249s Setting up fdisk (2.39.3-9ubuntu2) ...
249s Setting up libjson-glib-1.0-0:ppc64el (1.8.0-2build1) ...
249s Setting up libsasl2-modules-db:ppc64el (2.1.28+dfsg1-5ubuntu1) ...
249s Setting up libftdi1-2:ppc64el (1.5-6build4) ...
249s Setting up perl (5.38.2-3.2) ...
249s Setting up libfreetype6:ppc64el (2.13.2+dfsg-1build2) ...
249s Setting up linux-tools-6.8.0-20-generic (6.8.0-20.20) ...
249s Setting up gir1.2-girepository-2.0:ppc64el (1.79.1-1ubuntu6) ...
249s Setting up dbus (1.14.10-4ubuntu2) ...
249s A reboot is required to replace the running dbus-daemon.
249s Please reboot the system when convenient.
249s Setting up shared-mime-info (2.4-1build1) ...
250s Setting up libblockdev-utils3:ppc64el (3.1.0-1build1) ...
250s Setting up libgssapi-krb5-2:ppc64el (1.20.1-6ubuntu1) ...
250s Setting up udev (255.4-1ubuntu5) ...
250s Setting up ftp (20230507-2build1) ...
250s Setting up keyboxd (2.4.4-2ubuntu15) ...
251s Setting up libdpkg-perl (1.22.6ubuntu5) ...
251s Setting up libsasl2-2:ppc64el (2.1.28+dfsg1-5ubuntu1) ...
251s Setting up libssh-4:ppc64el (0.10.6-2build1) ...
251s Setting up libblockdev-nvme3:ppc64el (3.1.0-1build1) ...
251s Setting up libblockdev-fs3:ppc64el (3.1.0-1build1) ...
251s Setting up ieee-data (20220827.1) ...
251s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu1) ...
251s Setting up kpartx (0.9.4-5ubuntu6) ...
251s Setting up libpam-systemd:ppc64el (255.4-1ubuntu5) ...
251s Setting up libpolkit-agent-1-0:ppc64el (124-1ubuntu1) ...
251s Setting up libc6-dev:ppc64el (2.39-0ubuntu6) ...
251s Setting up libgpgme11t64:ppc64el (1.18.0-4.1ubuntu3) ...
251s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu1) ...
251s Setting up binutils-powerpc64le-linux-gnu (2.42-4ubuntu1) ...
251s Setting up netplan-generator (1.0-1) ...
251s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator'
251s Setting up initramfs-tools-core (0.142ubuntu23) ...
251s Setting up libclang-cpp18 (1:18.1.2-1ubuntu2) ...
251s Setting up libbpfcc:ppc64el (0.29.1+ds-1ubuntu4) ...
251s Setting up libarchive13t64:ppc64el (3.7.2-1.1ubuntu2) ...
251s Setting up libldap2:ppc64el (2.6.7+dfsg-1~exp1ubuntu6) ...
251s Setting up libpython3-stdlib:ppc64el (3.12.2-0ubuntu1) ...
251s Setting up systemd-resolved (255.4-1ubuntu5) ...
251s Setting up python3.11 (3.11.8-1build4) ...
253s Setting up telnet (0.17+2.5-3ubuntu3) ...
253s Setting up initramfs-tools (0.142ubuntu23) ...
253s update-initramfs: deferring update (trigger activated)
253s Setting up libblockdev-mdraid3:ppc64el (3.1.0-1build1) ...
253s Setting up linux-headers-virtual (6.8.0-20.20+1) ...
253s Setting up libcurl4t64:ppc64el (8.5.0-2ubuntu8) ...
253s Setting up bpftrace (0.20.2-1ubuntu1) ...
253s Setting up bind9-libs:ppc64el (1:9.18.24-0ubuntu3) ...
253s Setting up linux-image-6.8.0-20-generic (6.8.0-20.20) ...
255s I: /boot/vmlinux is now a symlink to vmlinux-6.8.0-20-generic
255s I: /boot/initrd.img is now a symlink to initrd.img-6.8.0-20-generic
255s Setting up libtirpc3t64:ppc64el (1.3.4+ds-1.1) ...
255s Setting up e2fsprogs-l10n (1.47.0-2.4~exp1ubuntu2) ...
255s Setting up libblockdev-swap3:ppc64el (3.1.0-1build1) ...
255s Setting up plymouth (24.004.60-1ubuntu6) ...
255s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic
255s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
261s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
262s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
262s Setting up iproute2 (6.1.0-1ubuntu5) ...
262s Setting up openssh-client (1:9.6p1-3ubuntu11) ...
262s Setting up libgusb2:ppc64el (0.4.8-1build1) ...
262s Setting up btrfs-progs (6.6.3-1.1build1) ...
262s Setting up libblockdev-loop3:ppc64el (3.1.0-1build1) ...
262s Setting up libcurl3t64-gnutls:ppc64el (8.5.0-2ubuntu8) ...
262s Setting up parted (3.6-3.1build2) ...
262s Setting up libqmi-glib5:ppc64el (1.35.2-0ubuntu1) ...
262s Setting up python3 (3.12.2-0ubuntu1) ...
262s Setting up binutils (2.42-4ubuntu1) ...
262s Setting up libblockdev3:ppc64el (3.1.0-1build1) ...
262s Setting up libjcat1:ppc64el (0.2.0-2build2) ...
262s Setting up multipath-tools (0.9.4-5ubuntu6) ...
263s Setting up dpkg-dev (1.22.6ubuntu5) ...
263s Setting up libblockdev-part3:ppc64el (3.1.0-1build1) ...
263s Setting up dirmngr (2.4.4-2ubuntu15) ...
263s Setting up dbus-user-session (1.14.10-4ubuntu2) ...
263s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu6) ...
263s update-initramfs: deferring update (trigger activated)
263s Setting up python3-cryptography (41.0.7-4build2) ...
264s Setting up python3-gi (3.47.0-3build1) ...
264s Setting up libgd3:ppc64el (2.3.3-9ubuntu3) ...
264s Setting up python3-typing-extensions (4.10.0-1) ...
264s Setting up lsof (4.95.0-1build2) ...
264s Setting up python3-pyrsistent:ppc64el (0.20.0-1build1) ...
264s Setting up python3-netaddr (0.8.0-2ubuntu1) ...
264s Setting up libnsl2:ppc64el (1.3.0-3build2) ...
264s Setting up gnupg (2.4.4-2ubuntu15) ...
264s Setting up python3-netplan (1.0-1) ...
264s Setting up curl (8.5.0-2ubuntu8) ...
264s Setting up libvolume-key1:ppc64el (0.3.12-7build1) ...
265s Setting up linux-image-virtual (6.8.0-20.20+1) ...
265s Setting up bind9-host (1:9.18.24-0ubuntu3) ...
265s Setting up python3-lib2to3 (3.12.2-3ubuntu1.1) ...
265s Setting up python3-bpfcc (0.29.1+ds-1ubuntu4) ...
265s Setting up libc-devtools (2.39-0ubuntu6) ...
265s Setting up python3-pkg-resources (68.1.2-2ubuntu1) ...
265s Setting up python3-distutils (3.12.2-3ubuntu1.1) ...
266s python3.12: can't get files for byte-compilation
266s Setting up openssh-sftp-server (1:9.6p1-3ubuntu11) ...
266s Setting up linux-image-generic (6.8.0-20.20+1) ...
266s Setting up python3-dbus (1.3.2-5build2) ...
266s Setting up python3-setuptools (68.1.2-2ubuntu1) ...
266s Setting up gpg-wks-client (2.4.4-2ubuntu15) ...
266s Setting up openssh-server (1:9.6p1-3ubuntu11) ...
267s Replacing config file /etc/ssh/sshd_config with new version
268s Created symlink /etc/systemd/system/ssh.service.requires/ssh.socket → /usr/lib/systemd/system/ssh.socket.

270s Setting up linux-generic (6.8.0-20.20+1) ...
270s Setting up libblockdev-crypto3:ppc64el (3.1.0-1build1) ...
270s Setting up python3-gdbm:ppc64el (3.12.2-3ubuntu1.1) ...
270s Setting up python3-apt (2.7.7) ...
270s Setting up libfwupd2:ppc64el (1.9.15-2) ...
270s Setting up python3-yaml (6.0.1-2build1) ...
270s Setting up libqmi-proxy (1.35.2-0ubuntu1) ...
270s Setting up netplan.io (1.0-1) ...
270s Setting up linux-virtual (6.8.0-20.20+1) ...
270s Setting up grub-common (2.12-1ubuntu5) ...
271s Setting up bpfcc-tools (0.29.1+ds-1ubuntu4) ...
271s Setting up bind9-dnsutils (1:9.18.24-0ubuntu3) ...
271s Setting up ubuntu-pro-client (31.2.2) ...
273s Setting up fwupd (1.9.15-2) ...
273s fwupd-offline-update.service is a disabled or a static unit not running, not starting it.
273s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
274s Setting up ubuntu-pro-client-l10n (31.2.2) ...
274s Setting up udisks2 (2.10.1-6) ...
274s Setting up grub2-common (2.12-1ubuntu5) ...
274s Setting up grub-ieee1275-bin (2.12-1ubuntu5) ...
274s Setting up grub-ieee1275 (2.12-1ubuntu5) ...
275s Installing for powerpc-ieee1275 platform.
275s Installation finished. No error reported.
275s Sourcing file `/etc/default/grub'
275s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
275s Generating grub configuration file ...
275s Found linux image: /boot/vmlinux-6.8.0-20-generic
275s Found linux image: /boot/vmlinux-6.8.0-11-generic
275s Found initrd image: /boot/initrd.img-6.8.0-11-generic
275s Warning: os-prober will not be executed to detect other bootable partitions.
275s Systems on them will not be added to the GRUB boot configuration.
275s Check GRUB_DISABLE_OS_PROBER documentation entry.
275s Adding boot menu entry for UEFI Firmware Settings ...
275s done
275s Processing triggers for ufw (0.36.2-5) ...
275s Processing triggers for systemd (255.4-1ubuntu5) ...
275s Processing triggers for debianutils (5.17) ...
275s Processing triggers for install-info (7.1-3build1) ...
275s Processing triggers for libc-bin (2.39-0ubuntu6) ...
276s Processing triggers for initramfs-tools (0.142ubuntu23) ...
276s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic
276s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
282s Processing triggers for linux-image-6.8.0-20-generic (6.8.0-20.20) ...
282s /etc/kernel/postinst.d/initramfs-tools:
282s update-initramfs: Generating /boot/initrd.img-6.8.0-20-generic
282s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
288s /etc/kernel/postinst.d/zz-update-grub:
288s Sourcing file `/etc/default/grub'
288s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
288s Generating grub configuration file ...
288s Found linux image: /boot/vmlinux-6.8.0-20-generic
288s Found initrd image: /boot/initrd.img-6.8.0-20-generic
288s Found linux image: /boot/vmlinux-6.8.0-11-generic
288s Found initrd image: /boot/initrd.img-6.8.0-11-generic
288s Warning: os-prober will not be executed to detect other bootable partitions.
288s Systems on them will not be added to the GRUB boot configuration.
288s Check GRUB_DISABLE_OS_PROBER documentation entry.
288s Adding boot menu entry for UEFI Firmware Settings ...
288s done
290s Reading package lists...
290s Building dependency tree...
290s Reading state information...
290s The following packages will be REMOVED:
290s   libaio1* libnetplan0* python3-distutils* python3-lib2to3*
291s 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded.
291s After this operation, 1613 kB disk space will be freed.
291s (Reading database ... 
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(Reading database ... 112169 files and directories currently installed.)
291s Removing libaio1:ppc64el (0.3.113-5) ...
291s Removing libnetplan0:ppc64el (0.107.1-3) ...
291s Removing python3-distutils (3.12.2-3ubuntu1.1) ...
291s Removing python3-lib2to3 (3.12.2-3ubuntu1.1) ...
291s Processing triggers for libc-bin (2.39-0ubuntu6) ...
291s autopkgtest [02:13:40]: rebooting testbed after setup commands that affected boot
330s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
340s autopkgtest [02:14:29]: testbed running kernel: Linux 6.8.0-20-generic #20-Ubuntu SMP Mon Mar 18 11:46:05 UTC 2024
343s autopkgtest [02:14:32]: @@@@@@@@@@@@@@@@@@@@ apt-source tombo
350s Get:1 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (dsc) [2292 B]
350s Get:2 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (tar) [22.3 MB]
350s Get:3 http://ftpmaster.internal/ubuntu noble/universe tombo 1.5.1-6 (diff) [7024 B]
350s gpgv: Signature made Sun Dec 17 19:23:46 2023 UTC
350s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
350s gpgv:                issuer "tille@debian.org"
350s gpgv: Can't check signature: No public key
350s dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-6.dsc: no acceptable signature found
351s autopkgtest [02:14:40]: testing package tombo version 1.5.1-6
351s autopkgtest [02:14:40]: build not needed
356s autopkgtest [02:14:45]: test run-unit-test: preparing testbed
357s Reading package lists...
357s Building dependency tree...
357s Reading state information...
358s Starting pkgProblemResolver with broken count: 0
358s Starting 2 pkgProblemResolver with broken count: 0
358s Done
358s The following additional packages will be installed:
358s   fonts-font-awesome fonts-lato fonts-mathjax libaec0 libblas3 libgfortran5
358s   libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery libjs-mathjax
358s   libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2
358s   python3-decorator python3-h5py python3-h5py-serial python3-mappy
358s   python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo
358s   tombo-doc
358s Suggested packages:
358s   fonts-mathjax-extras fonts-stix libjs-mathjax-doc python-h5py-doc gcc
358s   gfortran python3-dev python3-pytest python-scipy-doc
358s Recommended packages:
358s   javascript-common g++ | c++-compiler python3-pil python3-pyfaidx
358s   python3-rpy2
358s The following NEW packages will be installed:
358s   autopkgtest-satdep fonts-font-awesome fonts-lato fonts-mathjax libaec0
358s   libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 libjs-jquery
358s   libjs-mathjax libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1
358s   libsz2 python3-decorator python3-h5py python3-h5py-serial python3-mappy
358s   python3-numpy python3-scipy python3-tqdm sphinx-rtd-theme-common tombo
358s   tombo-doc
358s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded.
358s Need to get 67.3 MB/67.3 MB of archives.
358s After this operation, 256 MB of additional disk space will be used.
358s Get:1 /tmp/autopkgtest.U79dwE/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B]
358s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-lato all 2.015-1 [2781 kB]
359s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
359s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
360s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB]
360s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB]
360s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgfortran5 ppc64el 14-20240315-1ubuntu1 [574 kB]
360s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B]
360s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-3.1ubuntu3 [1395 kB]
361s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-3.1ubuntu3 [70.9 kB]
361s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
361s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
361s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjs-sphinxdoc all 7.2.6-6 [149 kB]
361s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB]
362s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB]
362s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B]
362s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB]
362s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el python3-numpy ppc64el 1:1.24.2-3ubuntu1 [4457 kB]
365s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu2 [955 kB]
366s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-h5py all 3.10.0-1ubuntu2 [7980 B]
366s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-mappy ppc64el 2.26+dfsg-1 [193 kB]
367s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-tqdm all 4.66.2-2 [91.1 kB]
367s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB]
368s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB]
382s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el tombo ppc64el 1.5.1-6 [514 kB]
383s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
388s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el tombo-doc all 1.5.1-6 [21.7 MB]
403s Fetched 67.3 MB in 45s (1490 kB/s)
403s Selecting previously unselected package fonts-lato.
403s (Reading database ... 
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(Reading database ... 111945 files and directories currently installed.)
403s Preparing to unpack .../00-fonts-lato_2.015-1_all.deb ...
403s Unpacking fonts-lato (2.015-1) ...
404s Selecting previously unselected package fonts-font-awesome.
404s Preparing to unpack .../01-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
404s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
404s Selecting previously unselected package fonts-mathjax.
404s Preparing to unpack .../02-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
404s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
404s Selecting previously unselected package libaec0:ppc64el.
404s Preparing to unpack .../03-libaec0_1.1.2-1_ppc64el.deb ...
404s Unpacking libaec0:ppc64el (1.1.2-1) ...
404s Selecting previously unselected package libblas3:ppc64el.
404s Preparing to unpack .../04-libblas3_3.12.0-3_ppc64el.deb ...
404s Unpacking libblas3:ppc64el (3.12.0-3) ...
404s Selecting previously unselected package libgfortran5:ppc64el.
404s Preparing to unpack .../05-libgfortran5_14-20240315-1ubuntu1_ppc64el.deb ...
404s Unpacking libgfortran5:ppc64el (14-20240315-1ubuntu1) ...
404s Selecting previously unselected package libsz2:ppc64el.
404s Preparing to unpack .../06-libsz2_1.1.2-1_ppc64el.deb ...
404s Unpacking libsz2:ppc64el (1.1.2-1) ...
404s Selecting previously unselected package libhdf5-103-1t64:ppc64el.
404s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu3_ppc64el.deb ...
404s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu3) ...
404s Selecting previously unselected package libhdf5-hl-100t64:ppc64el.
404s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu3_ppc64el.deb ...
404s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu3) ...
404s Selecting previously unselected package libjs-jquery.
404s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
404s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
404s Selecting previously unselected package libjs-underscore.
404s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
404s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
404s Selecting previously unselected package libjs-sphinxdoc.
404s Preparing to unpack .../11-libjs-sphinxdoc_7.2.6-6_all.deb ...
404s Unpacking libjs-sphinxdoc (7.2.6-6) ...
404s Selecting previously unselected package liblapack3:ppc64el.
404s Preparing to unpack .../12-liblapack3_3.12.0-3_ppc64el.deb ...
404s Unpacking liblapack3:ppc64el (3.12.0-3) ...
404s Selecting previously unselected package liblbfgsb0:ppc64el.
404s Preparing to unpack .../13-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ...
404s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ...
404s Selecting previously unselected package liblzf1:ppc64el.
404s Preparing to unpack .../14-liblzf1_3.6-4_ppc64el.deb ...
404s Unpacking liblzf1:ppc64el (3.6-4) ...
404s Selecting previously unselected package python3-decorator.
404s Preparing to unpack .../15-python3-decorator_5.1.1-5_all.deb ...
404s Unpacking python3-decorator (5.1.1-5) ...
404s Selecting previously unselected package python3-numpy.
404s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-3ubuntu1_ppc64el.deb ...
404s Unpacking python3-numpy (1:1.24.2-3ubuntu1) ...
405s Selecting previously unselected package python3-h5py-serial.
405s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu2_ppc64el.deb ...
405s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ...
405s Selecting previously unselected package python3-h5py.
405s Preparing to unpack .../18-python3-h5py_3.10.0-1ubuntu2_all.deb ...
405s Unpacking python3-h5py (3.10.0-1ubuntu2) ...
405s Selecting previously unselected package python3-mappy.
405s Preparing to unpack .../19-python3-mappy_2.26+dfsg-1_ppc64el.deb ...
405s Unpacking python3-mappy (2.26+dfsg-1) ...
405s Selecting previously unselected package python3-tqdm.
405s Preparing to unpack .../20-python3-tqdm_4.66.2-2_all.deb ...
405s Unpacking python3-tqdm (4.66.2-2) ...
405s Selecting previously unselected package sphinx-rtd-theme-common.
405s Preparing to unpack .../21-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ...
405s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ...
405s Selecting previously unselected package python3-scipy.
405s Preparing to unpack .../22-python3-scipy_1.11.4-6_ppc64el.deb ...
405s Unpacking python3-scipy (1.11.4-6) ...
406s Selecting previously unselected package tombo.
406s Preparing to unpack .../23-tombo_1.5.1-6_ppc64el.deb ...
406s Unpacking tombo (1.5.1-6) ...
406s Selecting previously unselected package libjs-mathjax.
406s Preparing to unpack .../24-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
406s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
407s Selecting previously unselected package tombo-doc.
407s Preparing to unpack .../25-tombo-doc_1.5.1-6_all.deb ...
407s Unpacking tombo-doc (1.5.1-6) ...
407s Selecting previously unselected package autopkgtest-satdep.
407s Preparing to unpack .../26-1-autopkgtest-satdep.deb ...
407s Unpacking autopkgtest-satdep (0) ...
407s Setting up fonts-lato (2.015-1) ...
407s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
407s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
407s Setting up python3-tqdm (4.66.2-2) ...
407s Setting up python3-mappy (2.26+dfsg-1) ...
407s Setting up libaec0:ppc64el (1.1.2-1) ...
407s Setting up python3-decorator (5.1.1-5) ...
407s Setting up libblas3:ppc64el (3.12.0-3) ...
407s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
407s Setting up liblzf1:ppc64el (3.6-4) ...
407s Setting up libgfortran5:ppc64el (14-20240315-1ubuntu1) ...
407s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
407s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
407s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ...
407s Setting up libsz2:ppc64el (1.1.2-1) ...
407s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
407s Setting up liblapack3:ppc64el (3.12.0-3) ...
407s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
407s Setting up python3-numpy (1:1.24.2-3ubuntu1) ...
410s Setting up libjs-sphinxdoc (7.2.6-6) ...
410s Setting up tombo-doc (1.5.1-6) ...
410s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu3) ...
410s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ...
410s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu3) ...
410s Setting up python3-scipy (1.11.4-6) ...
414s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ...
415s Setting up python3-h5py (3.10.0-1ubuntu2) ...
415s Setting up tombo (1.5.1-6) ...
415s /usr/lib/python3/dist-packages/tombo/_event_resquiggle.py:68: SyntaxWarning: invalid escape sequence '\d'
415s   CIGAR_PAT = re.compile('(\d+)([MIDNSHP=X])')
415s /usr/lib/python3/dist-packages/tombo/_plot_commands.py:2253: SyntaxWarning: invalid escape sequence '\|'
415s   '`conda list | grep "r-base\|rpy2"` (last columns should match).')
415s /usr/lib/python3/dist-packages/tombo/_preprocess.py:156: SyntaxWarning: invalid escape sequence '\+'
415s   re.match('\+', fastq_rec[2]) is None):
415s Setting up autopkgtest-satdep (0) ...
415s Processing triggers for man-db (2.12.0-3build4) ...
416s Processing triggers for libc-bin (2.39-0ubuntu6) ...
419s (Reading database ... 119287 files and directories currently installed.)
419s Removing autopkgtest-satdep (0) ...
420s autopkgtest [02:15:48]: test run-unit-test: [-----------------------
420s ********* Testing help commands **********
420s usage: tombo [-h] [-v]
420s              {resquiggle,preprocess,filter,detect_modifications,text_output,build_model,plot}
420s              ...
420s 
420s ********** Tombo *********
420s 
420s Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.
420s 
420s Tombo also provides tools for the analysis and visualization of raw nanopore signal.
420s 
420s Tombo command groups (additional help available within each command group):
420s 	resquiggle               Re-annotate raw signal with genomic alignment from existing basecalls.
420s 	preprocess               Pre-process nanopore reads for Tombo processing.
420s 	filter                   Apply filter to Tombo index file for specified criterion.
420s 	detect_modifications     Perform statistical testing to detect non-standard nucleotides.
420s 	text_output              Output Tombo results in text files.
420s 	build_model              Create canonical and alternative base Tombo models.
420s 	plot                     Save plots to visualize raw nanopore signal or testing results.
420s 
420s options:
420s   -h, --help            show this help message and exit
420s   -v, --version         show Tombo version and exit.
420s usage: tombo resquiggle [--dna] [--rna]
420s                         [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]]
420s                         [--q-score Q_SCORE]
420s                         [--signal-matching-score SIGNAL_MATCHING_SCORE]
420s                         [--processes PROCESSES]
420s                         [--corrected-group CORRECTED_GROUP]
420s                         [--basecall-group BASECALL_GROUP]
420s                         [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
420s                         [--overwrite]
420s                         [--failed-reads-filename FAILED_READS_FILENAME]
420s                         [--num-most-common-errors NUM_MOST_COMMON_ERRORS]
420s                         [--print-advanced-arguments] [--quiet] [--help]
420s                         fast5s_basedir reference
420s 
420s Required Arguments:
420s   fast5s_basedir        Directory containing fast5 files. All files ending in
420s                         "fast5" found recursively within this base directory
420s                         will be processed.
420s   reference             Reference genome/transcriptome FASTA file or minimap2
420s                         index (with "map-ont" preset) for mapping.
420s 
420s Model Parameters:
420s   --dna                 Explicitly select canonical DNA model. Default:
420s                         Automatically determine from FAST5s
420s   --rna                 Explicitly select canonical RNA model. Default:
420s                         Automatically determine from FAST5s
420s 
420s Read Filtering Argument:
420s   --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]
420s                         Filter reads based on observations per base percentile
420s                         thresholds. Format thresholds as "percentile:thresh
420s                         [pctl2:thresh2 ...]". For example to filter reads with
420s                         99th pctl > 200 obs/base or max > 5k obs/base use
420s                         "99:200 100:5000".
420s   --q-score Q_SCORE     Q-score threshold for filtering low quality reads.
420s                         Default: 0.000000
420s   --signal-matching-score SIGNAL_MATCHING_SCORE
420s                         Observed to expected signal matching score (higher
420s                         score indicates poor matching). Sample type defaults:
420s                         RNA : 2 || DNA : 1.1
420s 
420s Multiprocessing Arguments:
420s   --processes PROCESSES
420s                         Number of processes. Default: 1
420s 
420s FAST5 Data Arguments:
420s   --corrected-group CORRECTED_GROUP
420s                         FAST5 group created by resquiggle command. Default:
420s                         RawGenomeCorrected_000
420s   --basecall-group BASECALL_GROUP
420s                         FAST5 group obtain original basecalls (under Analyses
420s                         group). Default: Basecall_1D_000
420s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
420s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
420s                         group]/) containing basecalls and created within
420s                         [--corrected-group] containing re-squiggle results.
420s                         Default: ['BaseCalled_template']
420s   --overwrite           Overwrite previous corrected group in FAST5 files.
420s                         Note: only effects --corrected-group or --new-
420s                         corrected-group.
420s 
420s Input/Output Arguments:
420s   --failed-reads-filename FAILED_READS_FILENAME
420s                         Output failed read filenames with assoicated error.
420s                         Default: Do not store failed reads.
420s   --num-most-common-errors NUM_MOST_COMMON_ERRORS
420s                         Dynamically show this many most common errors so far
420s                         through run. Default: 0; Just show progress
420s 
420s Advanced Arguments:
420s   --print-advanced-arguments
420s                         Print advanced re-squiggle arguments and exit.
420s 
420s Miscellaneous Arguments:
420s   --quiet, -q           Don't print status information.
420s   --help, -h            Print this help message and exit
420s usage: tombo preprocess annotate_raw_with_fastqs --fast5-basedir FAST5_BASEDIR
420s                                                  --fastq-filenames
420s                                                  FASTQ_FILENAMES
420s                                                  [FASTQ_FILENAMES ...]
420s                                                  [--basecall-group BASECALL_GROUP]
420s                                                  [--basecall-subgroup BASECALL_SUBGROUP]
420s                                                  [--overwrite]
420s                                                  [--sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]]
420s                                                  [--processes PROCESSES]
420s                                                  [--quiet] [--help]
420s 
420s Required Arguments:
420s   --fast5-basedir FAST5_BASEDIR
420s                         Directory containing fast5 files.
420s   --fastq-filenames FASTQ_FILENAMES [FASTQ_FILENAMES ...]
420s                         FASTQ filenames containing basecalls to be added to
420s                         raw FAST5 files.
420s 
420s FAST5 Data Arguments:
420s   --basecall-group BASECALL_GROUP
420s                         FAST5 group obtain original basecalls (under Analyses
420s                         group). Default: Basecall_1D_000
420s   --basecall-subgroup BASECALL_SUBGROUP
420s                         FAST5 subgroup (under /Analyses/[--basecall-group]/)
420s                         under which to store basecalls from FASTQs. Default:
420s                         BaseCalled_template
420s   --overwrite           Overwrite previous corrected group in FAST5 files.
420s                         Note: only effects --corrected-group or --new-
420s                         corrected-group.
420s 
420s Sequencing Summary Argument:
420s   --sequencing-summary-filenames SEQUENCING_SUMMARY_FILENAMES [SEQUENCING_SUMMARY_FILENAMES ...]
420s                         Sequencing summary filenames produced by albacore.
420s                         These can make annotation of raw FAST5 files with
420s                         FASTQ sequence much faster.
420s 
420s Multiprocessing Argument:
420s   --processes PROCESSES
420s                         Number of processes. Default: 1
420s 
420s Miscellaneous Arguments:
420s   --quiet, -q           Don't print status information.
420s   --help, -h            Print this help message and exit
420s usage: tombo filter clear_filters --fast5-basedirs FAST5_BASEDIRS
420s                                   [FAST5_BASEDIRS ...]
420s                                   [--corrected-group CORRECTED_GROUP]
420s                                   [--quiet] [--help]
420s 
420s Required Argument:
420s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
420s                         Directories containing fast5 files.
420s 
420s FAST5 Data Argument:
420s   --corrected-group CORRECTED_GROUP
420s                         FAST5 group created by resquiggle command. Default:
420s                         RawGenomeCorrected_000
420s 
420s Miscellaneous Arguments:
420s   --quiet, -q           Don't print status information.
420s   --help, -h            Print this help message and exit
420s usage: tombo filter stuck --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
420s                           [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]]
420s                           [--corrected-group CORRECTED_GROUP] [--quiet]
420s                           [--help]
420s 
420s Required Argument:
420s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
420s                         Directories containing fast5 files.
420s 
420s Read Filtering Argument:
420s   --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]
420s                         Filter reads based on observations per base percentile
420s                         thresholds. Format thresholds as "percentile:thresh
420s                         [pctl2:thresh2 ...]". For example to filter reads with
420s                         99th pctl > 200 obs/base or max > 5k obs/base use
420s                         "99:200 100:5000".
420s 
420s FAST5 Data Argument:
420s   --corrected-group CORRECTED_GROUP
420s                         FAST5 group created by resquiggle command. Default:
420s                         RawGenomeCorrected_000
420s 
420s Miscellaneous Arguments:
420s   --quiet, -q           Don't print status information.
420s   --help, -h            Print this help message and exit
420s usage: tombo filter level_coverage --fast5-basedirs FAST5_BASEDIRS
420s                                    [FAST5_BASEDIRS ...]
420s                                    [--percent-to-filter PERCENT_TO_FILTER]
420s                                    [--corrected-group CORRECTED_GROUP]
420s                                    [--quiet] [--help]
420s 
420s Required Arguments:
420s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
420s                         Directories containing fast5 files.
420s 
420s Read Filtering Argument:
420s   --percent-to-filter PERCENT_TO_FILTER
420s                         Percentage of all reads to filter. Reads are randomly
420s                         selected weighted according to the approximate
420s                         coverage at the mapped genomic location. This can be
420s                         useful in modeling and testing. Default: 10.000000
420s 
420s FAST5 Data Arguments:
420s   --corrected-group CORRECTED_GROUP
420s                         FAST5 group created by resquiggle command. Default:
420s                         RawGenomeCorrected_000
420s 
420s Miscellaneous Arguments:
420s   --quiet, -q           Don't print status information.
420s   --help, -h            Print this help message and exit
420s usage: tombo filter q_score --fast5-basedirs FAST5_BASEDIRS
420s                             [FAST5_BASEDIRS ...] [--q-score Q_SCORE]
420s                             [--corrected-group CORRECTED_GROUP]
420s                             [--basecall-group BASECALL_GROUP] [--quiet]
420s                             [--help]
420s 
420s Required Arguments:
420s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
420s                         Directories containing fast5 files.
420s 
420s Read Filtering Argument:
420s   --q-score Q_SCORE     Q-score threshold for filtering low quality reads.
420s                         Default: 7.000000
420s 
420s FAST5 Data Arguments:
420s   --corrected-group CORRECTED_GROUP
420s                         FAST5 group created by resquiggle command. Default:
420s                         RawGenomeCorrected_000
420s   --basecall-group BASECALL_GROUP
420s                         FAST5 group obtain original basecalls (under Analyses
420s                         group). Default: Basecall_1D_000
420s 
420s Miscellaneous Arguments:
420s   --quiet, -q           Don't print status information.
420s   --help, -h            Print this help message and exit
421s usage: tombo filter raw_signal_matching --fast5-basedirs FAST5_BASEDIRS
421s                                         [FAST5_BASEDIRS ...]
421s                                         --signal-matching-score
421s                                         SIGNAL_MATCHING_SCORE
421s                                         [--corrected-group CORRECTED_GROUP]
421s                                         [--quiet] [--help]
421s 
421s Required Arguments:
421s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
421s                         Directories containing fast5 files.
421s   --signal-matching-score SIGNAL_MATCHING_SCORE
421s                         Observed to expected signal matching score (higher
421s                         score indicates poor matching). Sample type defaults:
421s                         RNA : 2 || DNA : 1.1
421s 
421s FAST5 Data Arguments:
421s   --corrected-group CORRECTED_GROUP
421s                         FAST5 group created by resquiggle command. Default:
421s                         RawGenomeCorrected_000
421s 
421s Miscellaneous Arguments:
421s   --quiet, -q           Don't print status information.
421s   --help, -h            Print this help message and exit
421s usage: tombo filter genome_locations --fast5-basedirs FAST5_BASEDIRS
421s                                      [FAST5_BASEDIRS ...]
421s                                      [--include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]]
421s                                      [--include-partial-overlap]
421s                                      [--corrected-group CORRECTED_GROUP]
421s                                      [--quiet] [--help]
421s 
421s Required Arguments:
421s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
421s                         Directories containing fast5 files.
421s   --include-regions INCLUDE_REGIONS [INCLUDE_REGIONS ...]
421s                         Filter out reads not falling completely within include
421s                         regions. Omit start and end coordinates to include an
421s                         entire chromosome/sequence record. Format regions as
421s                         "chrm[:start-end] [chrm2[:start2-end2] ...]".
421s 
421s Filter Argument:
421s   --include-partial-overlap
421s                         Include reads that partially overlap the specified
421s                         region. Default: Only include reads completely
421s                         contained in a specified region
421s 
421s FAST5 Data Argument:
421s   --corrected-group CORRECTED_GROUP
421s                         FAST5 group created by resquiggle command. Default:
421s                         RawGenomeCorrected_000
421s 
421s Miscellaneous Arguments:
421s   --quiet, -q           Don't print status information.
421s   --help, -h            Print this help message and exit
421s usage: tombo detect_modifications de_novo --fast5-basedirs FAST5_BASEDIRS
421s                                           [FAST5_BASEDIRS ...]
421s                                           --statistics-file-basename
421s                                           STATISTICS_FILE_BASENAME [--dna]
421s                                           [--rna]
421s                                           [--fishers-method-context FISHERS_METHOD_CONTEXT]
421s                                           [--minimum-test-reads MINIMUM_TEST_READS]
421s                                           [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]]
421s                                           [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
421s                                           [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME]
421s                                           [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
421s                                           [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
421s                                           [--processes PROCESSES]
421s                                           [--corrected-group CORRECTED_GROUP]
421s                                           [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
421s                                           [--quiet] [--help]
421s 
421s Required Argument:
421s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
421s                         Directories containing fast5 files.
421s   --statistics-file-basename STATISTICS_FILE_BASENAME
421s                         File base name to save base by base statistics from
421s                         testing. Filenames will be [--statistics-file-
421s                         basename].[--alternate-bases]?.tombo.stats
421s 
421s Comparison Model Arguments:
421s   --dna                 Explicitly select canonical DNA model. Default:
421s                         Automatically determine from FAST5s
421s   --rna                 Explicitly select canonical RNA model. Default:
421s                         Automatically determine from FAST5s
421s 
421s Significance Test Arguments:
421s   --fishers-method-context FISHERS_METHOD_CONTEXT
421s                         Number of context bases up and downstream over which
421s                         to compute Fisher's method combined p-values. Note:
421s                         Not applicable for alternative model likelihood ratio
421s                         tests. Default: 1.
421s   --minimum-test-reads MINIMUM_TEST_READS
421s                         Number of reads required at a position to perform
421s                         significance testing or contribute to model
421s                         estimation. Default: 1
421s   --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]
421s                         P-value threshold when computing fraction of
421s                         significant reads at each genomic position. If two
421s                         values are provided, statistics between these values
421s                         are not considered. Default thresholds: DNA:0.15-0.5 ,
421s                         RNA:0.05-0.4
421s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
421s                         Dampen fraction modified estimates for low coverage
421s                         sites. Two parameters are unmodified and modified
421s                         pseudo read counts. This is equivalent to a beta prior
421s                         on the fraction estimate. Set to "0 0" to disable
421s                         dampened fraction estimation. Default: [2, 0]
421s 
421s Output Argument:
421s   --per-read-statistics-basename PER_READ_STATISTICS_BASENAME
421s                         Base for binary files containing per-read statistics
421s                         from statistical testing. Filenames will be [--per-
421s                         read-statistics-basename].[--alternate-
421s                         bases]?.tombo.per_read_stats
421s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
421s                         Number of the most significant sites to store for
421s                         faster access. If a longer list of most significant
421s                         sites is required the list must be re-computed from
421s                         all batches. Very large values can increase RAM usage.
421s                         Default: 100000
421s 
421s Multiprocessing Arguments:
421s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
421s                         Size of regions over which to multiprocesses statistic
421s                         computation. For very deep samples a smaller value is
421s                         recommmended in order to control memory consumption.
421s                         Default: 10000
421s   --processes PROCESSES
421s                         Number of processes. Default: 1
421s 
421s FAST5 Data Arguments:
421s   --corrected-group CORRECTED_GROUP
421s                         FAST5 group created by resquiggle command. Default:
421s                         RawGenomeCorrected_000
421s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
421s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
421s                         group]/) containing basecalls and created within
421s                         [--corrected-group] containing re-squiggle results.
421s                         Default: ['BaseCalled_template']
421s 
421s Miscellaneous Arguments:
421s   --quiet, -q           Don't print status information.
421s   --help, -h            Print this help message and exit
421s usage: tombo detect_modifications alternative_model
421s                                                     [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
421s                                                     [--statistics-file-basename STATISTICS_FILE_BASENAME]
421s                                                     [--alternate-bases {dcm,dam,5mC,6mA,CpG} [{dcm,dam,5mC,6mA,CpG} ...]]
421s                                                     [--print-available-models]
421s                                                     [--dna] [--rna]
421s                                                     [--minimum-test-reads MINIMUM_TEST_READS]
421s                                                     [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]]
421s                                                     [--standard-log-likelihood-ratio]
421s                                                     [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
421s                                                     [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME]
421s                                                     [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
421s                                                     [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
421s                                                     [--processes PROCESSES]
421s                                                     [--corrected-group CORRECTED_GROUP]
421s                                                     [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
421s                                                     [--quiet] [--help]
421s 
421s Required Argument:
421s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
421s                         Directories containing fast5 files.
421s   --statistics-file-basename STATISTICS_FILE_BASENAME
421s                         File base name to save base by base statistics from
421s                         testing. Filenames will be [--statistics-file-
421s                         basename].[--alternate-bases]?.tombo.stats
421s   --alternate-bases {dcm,dam,5mC,6mA,CpG} [{dcm,dam,5mC,6mA,CpG} ...]
421s                         Default non-standard base model for testing (not
421s                         required if user created --alternate-model-filenames
421s                         is provided).
421s 
421s Comparison Arguments:
421s   --print-available-models
421s                         Print available alternative models and exit.
421s   --dna                 Explicitly select canonical DNA model. Default:
421s                         Automatically determine from FAST5s
421s   --rna                 Explicitly select canonical RNA model. Default:
421s                         Automatically determine from FAST5s
421s 
421s Significance Test Arguments:
421s   --minimum-test-reads MINIMUM_TEST_READS
421s                         Number of reads required at a position to perform
421s                         significance testing or contribute to model
421s                         estimation. Default: 1
421s   --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]
421s                         Log likelihood ratio threshold when computing fraction
421s                         of significant reads at each genomic position. If two
421s                         values are provided, statistics between these values
421s                         are not considered. Default thresholds: DNA:-1.5-2.5 ,
421s                         RNA:-2.5-2.5
421s   --standard-log-likelihood-ratio
421s                         Use a standard log likelihood ratio (LLR) statistic.
421s                         Default is to use an outlier-robust LLR-like
421s                         statistic. Detail in full online documentation.
421s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
421s                         Dampen fraction modified estimates for low coverage
421s                         sites. Two parameters are unmodified and modified
421s                         pseudo read counts. This is equivalent to a beta prior
421s                         on the fraction estimate. Set to "0 0" to disable
421s                         dampened fraction estimation. Default: [2, 0]
421s 
421s Output Argument:
421s   --per-read-statistics-basename PER_READ_STATISTICS_BASENAME
421s                         Base for binary files containing per-read statistics
421s                         from statistical testing. Filenames will be [--per-
421s                         read-statistics-basename].[--alternate-
421s                         bases]?.tombo.per_read_stats
421s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
421s                         Number of the most significant sites to store for
421s                         faster access. If a longer list of most significant
421s                         sites is required the list must be re-computed from
421s                         all batches. Very large values can increase RAM usage.
421s                         Default: 100000
421s 
421s Multiprocessing Arguments:
421s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
421s                         Size of regions over which to multiprocesses statistic
421s                         computation. For very deep samples a smaller value is
421s                         recommmended in order to control memory consumption.
421s                         Default: 10000
421s   --processes PROCESSES
421s                         Number of processes. Default: 1
421s 
421s FAST5 Data Arguments:
421s   --corrected-group CORRECTED_GROUP
421s                         FAST5 group created by resquiggle command. Default:
421s                         RawGenomeCorrected_000
421s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
421s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
421s                         group]/) containing basecalls and created within
421s                         [--corrected-group] containing re-squiggle results.
421s                         Default: ['BaseCalled_template']
421s 
421s Miscellaneous Arguments:
421s   --quiet, -q           Don't print status information.
421s   --help, -h            Print this help message and exit
421s usage: tombo detect_modifications model_sample_compare --fast5-basedirs
421s                                                        FAST5_BASEDIRS
421s                                                        [FAST5_BASEDIRS ...]
421s                                                        --statistics-file-basename
421s                                                        STATISTICS_FILE_BASENAME
421s                                                        --control-fast5-basedirs
421s                                                        CONTROL_FAST5_BASEDIRS
421s                                                        [CONTROL_FAST5_BASEDIRS ...]
421s                                                        [--sample-only-estimates]
421s                                                        [--model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS]
421s                                                        [--dna] [--rna]
421s                                                        [--fishers-method-context FISHERS_METHOD_CONTEXT]
421s                                                        [--minimum-test-reads MINIMUM_TEST_READS]
421s                                                        [--single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]]
421s                                                        [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
421s                                                        [--per-read-statistics-basename PER_READ_STATISTICS_BASENAME]
421s                                                        [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
421s                                                        [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
421s                                                        [--processes PROCESSES]
421s                                                        [--corrected-group CORRECTED_GROUP]
421s                                                        [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
421s                                                        [--quiet] [--help]
421s 
421s Required Argument:
421s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
421s                         Directories containing fast5 files.
421s   --statistics-file-basename STATISTICS_FILE_BASENAME
421s                         File base name to save base by base statistics from
421s                         testing. Filenames will be [--statistics-file-
421s                         basename].[--alternate-bases]?.tombo.stats
421s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
421s                         Set of directories containing fast5 files for control
421s                         reads, containing only canonical nucleotides.
421s 
421s Model Prior Arguments:
421s   --sample-only-estimates
421s                         Only use canonical sample to estimate expected signal
421s                         level and spread. Default: Use canonical model to
421s                         improve estimtates (esp. for low coverage regions)
421s                         using baysian posterior estimates.
421s   --model-prior-weights MODEL_PRIOR_WEIGHTS MODEL_PRIOR_WEIGHTS
421s                         Prior weights (one each for mean and spread) applied
421s                         to canonical base model for estimating posterior model
421s                         parameters for sample comparison. Default: [5, 40]
421s   --dna                 Explicitly select canonical DNA model. Default:
421s                         Automatically determine from FAST5s
421s   --rna                 Explicitly select canonical RNA model. Default:
421s                         Automatically determine from FAST5s
421s 
421s Significance Test Arguments:
421s   --fishers-method-context FISHERS_METHOD_CONTEXT
421s                         Number of context bases up and downstream over which
421s                         to compute Fisher's method combined p-values. Note:
421s                         Not applicable for alternative model likelihood ratio
421s                         tests. Default: 1.
421s   --minimum-test-reads MINIMUM_TEST_READS
421s                         Number of reads required at a position to perform
421s                         significance testing or contribute to model
421s                         estimation. Default: 1
421s   --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]
421s                         P-value threshold when computing fraction of
421s                         significant reads at each genomic position. If two
421s                         values are provided, statistics between these values
421s                         are not considered. Default thresholds: DNA:0.15-0.5 ,
421s                         RNA:0.05-0.4
421s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
421s                         Dampen fraction modified estimates for low coverage
421s                         sites. Two parameters are unmodified and modified
421s                         pseudo read counts. This is equivalent to a beta prior
421s                         on the fraction estimate. Set to "0 0" to disable
421s                         dampened fraction estimation. Default: [2, 0]
421s 
421s Output Argument:
421s   --per-read-statistics-basename PER_READ_STATISTICS_BASENAME
421s                         Base for binary files containing per-read statistics
421s                         from statistical testing. Filenames will be [--per-
421s                         read-statistics-basename].[--alternate-
421s                         bases]?.tombo.per_read_stats
421s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
421s                         Number of the most significant sites to store for
421s                         faster access. If a longer list of most significant
421s                         sites is required the list must be re-computed from
421s                         all batches. Very large values can increase RAM usage.
421s                         Default: 100000
421s 
421s Multiprocessing Arguments:
421s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
421s                         Size of regions over which to multiprocesses statistic
421s                         computation. For very deep samples a smaller value is
421s                         recommmended in order to control memory consumption.
421s                         Default: 10000
421s   --processes PROCESSES
421s                         Number of processes. Default: 1
421s 
421s FAST5 Data Arguments:
421s   --corrected-group CORRECTED_GROUP
421s                         FAST5 group created by resquiggle command. Default:
421s                         RawGenomeCorrected_000
421s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
421s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
421s                         group]/) containing basecalls and created within
421s                         [--corrected-group] containing re-squiggle results.
421s                         Default: ['BaseCalled_template']
421s 
421s Miscellaneous Arguments:
421s   --quiet, -q           Don't print status information.
421s   --help, -h            Print this help message and exit
421s usage: tombo detect_modifications level_sample_compare --fast5-basedirs
421s                                                        FAST5_BASEDIRS
421s                                                        [FAST5_BASEDIRS ...]
421s                                                        --statistics-file-basename
421s                                                        STATISTICS_FILE_BASENAME
421s                                                        --alternate-fast5-basedirs
421s                                                        ALTERNATE_FAST5_BASEDIRS
421s                                                        [ALTERNATE_FAST5_BASEDIRS ...]
421s                                                        [--fishers-method-context FISHERS_METHOD_CONTEXT]
421s                                                        [--minimum-test-reads MINIMUM_TEST_READS]
421s                                                        [--statistic-type {ks,u,t}]
421s                                                        [--store-p-value]
421s                                                        [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
421s                                                        [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
421s                                                        [--processes PROCESSES]
421s                                                        [--corrected-group CORRECTED_GROUP]
421s                                                        [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
421s                                                        [--quiet] [--help]
421s 
421s Required Argument:
421s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
421s                         Directories containing fast5 files.
421s   --statistics-file-basename STATISTICS_FILE_BASENAME
421s                         File base name to save base by base statistics from
421s                         testing. Filenames will be [--statistics-file-
421s                         basename].[--alternate-bases]?.tombo.stats
421s   --alternate-fast5-basedirs ALTERNATE_FAST5_BASEDIRS [ALTERNATE_FAST5_BASEDIRS ...]
421s                         Set of directories containing fast5 files for
421s                         alternate set of reads.
421s 
421s Significance Test Arguments:
421s   --fishers-method-context FISHERS_METHOD_CONTEXT
421s                         Number of context bases up and downstream over which
421s                         to compute Fisher's method combined p-values. Note:
421s                         Not applicable for alternative model likelihood ratio
421s                         tests. Default: 1.
421s   --minimum-test-reads MINIMUM_TEST_READS
421s                         Number of reads required at a position to perform
421s                         significance testing or contribute to model
421s                         estimation. Default: 50
421s   --statistic-type {ks,u,t}
421s                         Type of statistical test to apply. Default: "ks"
421s   --store-p-value       Store p-value instead of effect-size statistic.
421s                         Statistics are D-statistic (KS-test), deviation from
421s                         even common language effect size (u-test), and Cohen's
421s                         D (t-test).
421s 
421s Output Argument:
421s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
421s                         Number of the most significant sites to store for
421s                         faster access. If a longer list of most significant
421s                         sites is required the list must be re-computed from
421s                         all batches. Very large values can increase RAM usage.
421s                         Default: 100000
421s 
421s Multiprocessing Arguments:
421s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
421s                         Size of regions over which to multiprocesses statistic
421s                         computation. For very deep samples a smaller value is
421s                         recommmended in order to control memory consumption.
421s                         Default: 10000
421s   --processes PROCESSES
421s                         Number of processes. Default: 1
421s 
421s FAST5 Data Arguments:
421s   --corrected-group CORRECTED_GROUP
421s                         FAST5 group created by resquiggle command. Default:
421s                         RawGenomeCorrected_000
421s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
421s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
421s                         group]/) containing basecalls and created within
421s                         [--corrected-group] containing re-squiggle results.
421s                         Default: ['BaseCalled_template']
421s 
421s Miscellaneous Arguments:
421s   --quiet, -q           Don't print status information.
421s   --help, -h            Print this help message and exit
421s usage: tombo detect_modifications aggregate_per_read_stats
421s                                                            --per-read-statistics-filename
421s                                                            PER_READ_STATISTICS_FILENAME
421s                                                            --statistics-filename
421s                                                            STATISTICS_FILENAME
421s                                                            --single-read-threshold
421s                                                            SINGLE_READ_THRESHOLD
421s                                                            [SINGLE_READ_THRESHOLD ...]
421s                                                            [--minimum-test-reads MINIMUM_TEST_READS]
421s                                                            [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
421s                                                            [--num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED]
421s                                                            [--processes PROCESSES]
421s                                                            [--corrected-group CORRECTED_GROUP]
421s                                                            [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
421s                                                            [--quiet] [--help]
421s 
421s Required Argument:
421s   --per-read-statistics-filename PER_READ_STATISTICS_FILENAME
421s                         Binary file containing per-read statistics from
421s                         statistical testing.
421s   --statistics-filename STATISTICS_FILENAME
421s                         File to save/load genomic base anchored statistics.
421s   --single-read-threshold SINGLE_READ_THRESHOLD [SINGLE_READ_THRESHOLD ...]
421s                         P-value or log likelihood ratio threshold when
421s                         computing fraction of significant reads at each
421s                         genomic position. If two values are provided,
421s                         statistics between these values are not considered.
421s 
421s Significance Test Arguments:
421s   --minimum-test-reads MINIMUM_TEST_READS
421s                         Number of reads required at a position to perform
421s                         significance testing or contribute to model
421s                         estimation. Default: 1
421s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
421s                         Dampen fraction modified estimates for low coverage
421s                         sites. Two parameters are unmodified and modified
421s                         pseudo read counts. This is equivalent to a beta prior
421s                         on the fraction estimate. Set to "0 0" to disable
421s                         dampened fraction estimation. Default: [2, 0]
421s 
421s Output Argument:
421s   --num-most-significant-stored NUM_MOST_SIGNIFICANT_STORED
421s                         Number of the most significant sites to store for
421s                         faster access. If a longer list of most significant
421s                         sites is required the list must be re-computed from
421s                         all batches. Very large values can increase RAM usage.
421s                         Default: 100000
421s 
421s Multiprocessing Arguments:
421s   --processes PROCESSES
421s                         Number of processes. Default: 1
421s 
421s FAST5 Data Arguments:
421s   --corrected-group CORRECTED_GROUP
421s                         FAST5 group created by resquiggle command. Default:
421s                         RawGenomeCorrected_000
421s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
421s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
421s                         group]/) containing basecalls and created within
421s                         [--corrected-group] containing re-squiggle results.
421s                         Default: ['BaseCalled_template']
421s 
421s Miscellaneous Arguments:
421s   --quiet, -q           Don't print status information.
421s   --help, -h            Print this help message and exit
421s usage: tombo text_output browser_files
421s                                        [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
421s                                        [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
421s                                        [--statistics-filename STATISTICS_FILENAME]
421s                                        [--genome-fasta GENOME_FASTA]
421s                                        [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]]
421s                                        [--browser-file-basename BROWSER_FILE_BASENAME]
421s                                        [--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} ...]]
421s                                        [--corrected-group CORRECTED_GROUP]
421s                                        [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
421s                                        [--quiet] [--help]
421s 
421s Data Arguments:
421s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
421s                         Directories containing fast5 files.
421s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
421s                         Set of directories containing fast5 files for control
421s                         reads, containing only canonical nucleotides.
421s   --statistics-filename STATISTICS_FILENAME
421s                         File to save/load genomic base anchored statistics.
421s 
421s Statistic Motif Filter Arguments:
421s   --genome-fasta GENOME_FASTA
421s                         FASTA file used to re-squiggle. For faster sequence
421s                         access.
421s   --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]
421s                         Ground truth, motif centered, modified base
421s                         descriptions for output filtering. Format descriptions
421s                         as: "motif:mod_pos:name". The mod_pos indicates the
421s                         modified base within the motif (1-based index).
421s                         Example: CCWGG:2:dcm_5mC GATC:2:dam_6mA would filter
421s                         output for identification of E. coli dam and dcm
421s                         methylation.
421s 
421s Output Arguments:
421s   --browser-file-basename BROWSER_FILE_BASENAME
421s                         Basename for output browser files. Two files (plus and
421s                         minus strand) will be produced for each --file-types
421s                         supplied. Filenames formatted as "[browser-file-
421s                         basename].[file-
421s                         type].[sample|control]?.[plus|minus].[wig|bedgraph]".
421s                         Default: tombo_results
421s   --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} ...]
421s                         Data types of genome browser files to produce.
421s                         Produced coverage files are in bedGraph format, while
421s                         all other file types will be in wiggle format
421s                         (https://genome.ucsc.edu/goldenpath/help/wiggle.html).
421s                         Default: "coverage"
421s 
421s FAST5 Data Arguments:
421s   --corrected-group CORRECTED_GROUP
421s                         FAST5 group created by resquiggle command. Default:
421s                         RawGenomeCorrected_000
421s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
421s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
421s                         group]/) containing basecalls and created within
421s                         [--corrected-group] containing re-squiggle results.
421s                         Default: ['BaseCalled_template']
421s 
421s Miscellaneous Arguments:
421s   --quiet, -q           Don't print status information.
421s   --help, -h            Print this help message and exit
422s usage: tombo text_output signif_sequence_context --statistics-filename
422s                                                  STATISTICS_FILENAME
422s                                                  [--genome-fasta GENOME_FASTA]
422s                                                  [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
422s                                                  [--num-regions NUM_REGIONS]
422s                                                  [--num-bases NUM_BASES]
422s                                                  [--sequences-filename SEQUENCES_FILENAME]
422s                                                  [--corrected-group CORRECTED_GROUP]
422s                                                  [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
422s                                                  [--quiet] [--help]
422s 
422s Required Argument:
422s   --statistics-filename STATISTICS_FILENAME
422s                         File to save/load genomic base anchored statistics.
422s 
422s Sequence Arguments (Provide either FAST5s dir or genome FASTA):
422s   --genome-fasta GENOME_FASTA
422s                         FASTA file used to re-squiggle. For faster sequence
422s                         access.
422s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
422s                         Directories containing fast5 files.
422s 
422s Region Selection Arguments:
422s   --num-regions NUM_REGIONS
422s                         Number of regions to plot. Default: 100
422s   --num-bases NUM_BASES
422s                         Number of bases to plot/output. Default: 15
422s 
422s Output Arguments:
422s   --sequences-filename SEQUENCES_FILENAME
422s                         File for sequences from selected regions. Sequences
422s                         will be stored in FASTA format. Default:
422s                         tombo_results.significant_regions.fasta.
422s 
422s FAST5 Data Arguments:
422s   --corrected-group CORRECTED_GROUP
422s                         FAST5 group created by resquiggle command. Default:
422s                         RawGenomeCorrected_000
422s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
422s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
422s                         group]/) containing basecalls and created within
422s                         [--corrected-group] containing re-squiggle results.
422s                         Default: ['BaseCalled_template']
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
422s usage: tombo plot max_coverage --fast5-basedirs FAST5_BASEDIRS
422s                                [FAST5_BASEDIRS ...]
422s                                [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
422s                                [--plot-standard-model]
422s                                [--plot-alternate-model {CpG,dam,5mC,6mA,dcm}]
422s                                [--overplot-threshold OVERPLOT_THRESHOLD]
422s                                [--overplot-type {Downsample,Boxplot,Quantile,Density}]
422s                                [--num-regions NUM_REGIONS]
422s                                [--num-bases NUM_BASES]
422s                                [--pdf-filename PDF_FILENAME]
422s                                [--corrected-group CORRECTED_GROUP]
422s                                [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
422s                                [--quiet] [--help]
422s 
422s Required Argument:
422s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
422s                         Directories containing fast5 files.
422s 
422s Comparison Arguments:
422s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
422s                         Set of directories containing fast5 files for control
422s                         reads, containing only canonical nucleotides.
422s   --plot-standard-model
422s                         Add default standard model distribution to the plot.
422s   --plot-alternate-model {CpG,dam,5mC,6mA,dcm}
422s                         Add alternative model distribution to the plot.
422s 
422s Overplotting Arguments:
422s   --overplot-threshold OVERPLOT_THRESHOLD
422s                         Coverage level to trigger alternative plot type
422s                         instead of raw signal. Default: 50
422s   --overplot-type {Downsample,Boxplot,Quantile,Density}
422s                         Plot type for regions with higher coverage. Default:
422s                         Downsample
422s 
422s Plotting Region Arguments:
422s   --num-regions NUM_REGIONS
422s                         Number of regions to plot. Default: 10
422s   --num-bases NUM_BASES
422s                         Number of bases to plot/output. Default: 21
422s 
422s Output Argument:
422s   --pdf-filename PDF_FILENAME
422s                         PDF filename to store plot(s). Default:
422s                         tombo_results.max_coverage.pdf
422s 
422s FAST5 Data Arguments:
422s   --corrected-group CORRECTED_GROUP
422s                         FAST5 group created by resquiggle command. Default:
422s                         RawGenomeCorrected_000
422s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
422s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
422s                         group]/) containing basecalls and created within
422s                         [--corrected-group] containing re-squiggle results.
422s                         Default: ['BaseCalled_template']
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
422s usage: tombo plot genome_locations --fast5-basedirs FAST5_BASEDIRS
422s                                    [FAST5_BASEDIRS ...] --genome-locations
422s                                    GENOME_LOCATIONS [GENOME_LOCATIONS ...]
422s                                    [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
422s                                    [--plot-standard-model]
422s                                    [--plot-alternate-model {CpG,dam,5mC,dcm,6mA}]
422s                                    [--overplot-threshold OVERPLOT_THRESHOLD]
422s                                    [--overplot-type {Downsample,Boxplot,Quantile,Density}]
422s                                    [--num-bases NUM_BASES]
422s                                    [--pdf-filename PDF_FILENAME]
422s                                    [--corrected-group CORRECTED_GROUP]
422s                                    [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
422s                                    [--quiet] [--help]
422s 
422s Required Arguments:
422s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
422s                         Directories containing fast5 files.
422s   --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...]
422s                         Genomic locations at which to plot signal. Format
422s                         locations as "chrm:position[:strand]
422s                         [chrm2:position2[:strand2] ...]" (strand not
422s                         applicable for all applications)
422s 
422s Comparison Arguments:
422s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
422s                         Set of directories containing fast5 files for control
422s                         reads, containing only canonical nucleotides.
422s   --plot-standard-model
422s                         Add default standard model distribution to the plot.
422s   --plot-alternate-model {CpG,dam,5mC,dcm,6mA}
422s                         Add alternative model distribution to the plot.
422s 
422s Overplotting Arguments:
422s   --overplot-threshold OVERPLOT_THRESHOLD
422s                         Coverage level to trigger alternative plot type
422s                         instead of raw signal. Default: 50
422s   --overplot-type {Downsample,Boxplot,Quantile,Density}
422s                         Plot type for regions with higher coverage. Default:
422s                         Downsample
422s 
422s Plotting Region Argument:
422s   --num-bases NUM_BASES
422s                         Number of bases to plot/output. Default: 21
422s 
422s Output Argument:
422s   --pdf-filename PDF_FILENAME
422s                         PDF filename to store plot(s). Default:
422s                         tombo_results.genome_locations.pdf
422s 
422s FAST5 Data Arguments:
422s   --corrected-group CORRECTED_GROUP
422s                         FAST5 group created by resquiggle command. Default:
422s                         RawGenomeCorrected_000
422s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
422s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
422s                         group]/) containing basecalls and created within
422s                         [--corrected-group] containing re-squiggle results.
422s                         Default: ['BaseCalled_template']
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
422s usage: tombo plot motif_centered --fast5-basedirs FAST5_BASEDIRS
422s                                  [FAST5_BASEDIRS ...] --motif MOTIF
422s                                  --genome-fasta GENOME_FASTA
422s                                  [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
422s                                  [--plot-standard-model]
422s                                  [--plot-alternate-model {6mA,dam,CpG,dcm,5mC}]
422s                                  [--overplot-threshold OVERPLOT_THRESHOLD]
422s                                  [--overplot-type {Downsample,Boxplot,Quantile,Density}]
422s                                  [--num-regions NUM_REGIONS]
422s                                  [--num-bases NUM_BASES] [--deepest-coverage]
422s                                  [--pdf-filename PDF_FILENAME]
422s                                  [--corrected-group CORRECTED_GROUP]
422s                                  [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
422s                                  [--quiet] [--help]
422s 
422s Required Arguments:
422s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
422s                         Directories containing fast5 files.
422s   --motif MOTIF         Motif of interest at which to plot signal and
422s                         statsitics. Supports IUPAC single letter codes (use T
422s                         for RNA).
422s   --genome-fasta GENOME_FASTA
422s                         FASTA file used to re-squiggle. For faster sequence
422s                         access.
422s 
422s Comparison Arguments:
422s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
422s                         Set of directories containing fast5 files for control
422s                         reads, containing only canonical nucleotides.
422s   --plot-standard-model
422s                         Add default standard model distribution to the plot.
422s   --plot-alternate-model {6mA,dam,CpG,dcm,5mC}
422s                         Add alternative model distribution to the plot.
422s 
422s Overplotting Arguments:
422s   --overplot-threshold OVERPLOT_THRESHOLD
422s                         Coverage level to trigger alternative plot type
422s                         instead of raw signal. Default: 50
422s   --overplot-type {Downsample,Boxplot,Quantile,Density}
422s                         Plot type for regions with higher coverage. Default:
422s                         Downsample
422s 
422s Plotting Region Arguments:
422s   --num-regions NUM_REGIONS
422s                         Number of regions to plot. Default: 10
422s   --num-bases NUM_BASES
422s                         Number of bases to plot/output. Default: 21
422s   --deepest-coverage    Plot the deepest coverage regions.
422s 
422s Output Argument:
422s   --pdf-filename PDF_FILENAME
422s                         PDF filename to store plot(s). Default:
422s                         tombo_results.motif_centered.pdf
422s 
422s FAST5 Data Arguments:
422s   --corrected-group CORRECTED_GROUP
422s                         FAST5 group created by resquiggle command. Default:
422s                         RawGenomeCorrected_000
422s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
422s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
422s                         group]/) containing basecalls and created within
422s                         [--corrected-group] containing re-squiggle results.
422s                         Default: ['BaseCalled_template']
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
422s usage: tombo plot max_difference --fast5-basedirs FAST5_BASEDIRS
422s                                  [FAST5_BASEDIRS ...] --control-fast5-basedirs
422s                                  CONTROL_FAST5_BASEDIRS
422s                                  [CONTROL_FAST5_BASEDIRS ...]
422s                                  [--overplot-threshold OVERPLOT_THRESHOLD]
422s                                  [--overplot-type {Downsample,Boxplot,Quantile,Density}]
422s                                  [--num-regions NUM_REGIONS]
422s                                  [--num-bases NUM_BASES]
422s                                  [--pdf-filename PDF_FILENAME]
422s                                  [--sequences-filename SEQUENCES_FILENAME]
422s                                  [--corrected-group CORRECTED_GROUP]
422s                                  [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
422s                                  [--quiet] [--help]
422s 
422s Required Arguments:
422s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
422s                         Directories containing fast5 files.
422s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
422s                         Set of directories containing fast5 files for control
422s                         reads, containing only canonical nucleotides.
422s 
422s Overplotting Arguments:
422s   --overplot-threshold OVERPLOT_THRESHOLD
422s                         Coverage level to trigger alternative plot type
422s                         instead of raw signal. Default: 50
422s   --overplot-type {Downsample,Boxplot,Quantile,Density}
422s                         Plot type for regions with higher coverage. Default:
422s                         Downsample
422s 
422s Plotting Region Arguments:
422s   --num-regions NUM_REGIONS
422s                         Number of regions to plot. Default: 10
422s   --num-bases NUM_BASES
422s                         Number of bases to plot/output. Default: 21
422s 
422s Output Arguments:
422s   --pdf-filename PDF_FILENAME
422s                         PDF filename to store plot(s). Default:
422s                         tombo_results.max_difference.pdf
422s   --sequences-filename SEQUENCES_FILENAME
422s                         File for sequences from selected regions. Sequences
422s                         will be stored in FASTA format. Default: None.
422s 
422s FAST5 Data Arguments:
422s   --corrected-group CORRECTED_GROUP
422s                         FAST5 group created by resquiggle command. Default:
422s                         RawGenomeCorrected_000
422s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
422s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
422s                         group]/) containing basecalls and created within
422s                         [--corrected-group] containing re-squiggle results.
422s                         Default: ['BaseCalled_template']
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
422s usage: tombo plot most_significant --fast5-basedirs FAST5_BASEDIRS
422s                                    [FAST5_BASEDIRS ...] --statistics-filename
422s                                    STATISTICS_FILENAME
422s                                    [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
422s                                    [--plot-standard-model]
422s                                    [--plot-alternate-model {6mA,dam,CpG,dcm,5mC}]
422s                                    [--overplot-threshold OVERPLOT_THRESHOLD]
422s                                    [--overplot-type {Downsample,Boxplot,Quantile,Density}]
422s                                    [--num-regions NUM_REGIONS]
422s                                    [--num-bases NUM_BASES]
422s                                    [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
422s                                    [--pdf-filename PDF_FILENAME]
422s                                    [--sequences-filename SEQUENCES_FILENAME]
422s                                    [--corrected-group CORRECTED_GROUP]
422s                                    [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
422s                                    [--quiet] [--help]
422s 
422s Required Arguments:
422s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
422s                         Directories containing fast5 files.
422s   --statistics-filename STATISTICS_FILENAME
422s                         File to save/load genomic base anchored statistics.
422s 
422s Comparison Arguments:
422s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
422s                         Set of directories containing fast5 files for control
422s                         reads, containing only canonical nucleotides.
422s   --plot-standard-model
422s                         Add default standard model distribution to the plot.
422s   --plot-alternate-model {6mA,dam,CpG,dcm,5mC}
422s                         Add alternative model distribution to the plot.
422s 
422s Overplotting Arguments:
422s   --overplot-threshold OVERPLOT_THRESHOLD
422s                         Coverage level to trigger alternative plot type
422s                         instead of raw signal. Default: 50
422s   --overplot-type {Downsample,Boxplot,Quantile,Density}
422s                         Plot type for regions with higher coverage. Default:
422s                         Downsample
422s 
422s Plotting Region Arguments:
422s   --num-regions NUM_REGIONS
422s                         Number of regions to plot. Default: 10
422s   --num-bases NUM_BASES
422s                         Number of bases to plot/output. Default: 21
422s 
422s Statistical Argument:
422s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
422s                         Dampen fraction modified estimates for low coverage
422s                         sites. Two parameters are unmodified and modified
422s                         pseudo read counts. This is equivalent to a beta prior
422s                         on the fraction estimate. Set to "0 0" to disable
422s                         dampened fraction estimation. Default: [2, 0]
422s 
422s Output Arguments:
422s   --pdf-filename PDF_FILENAME
422s                         PDF filename to store plot(s). Default:
422s                         tombo_results.significant_difference.pdf
422s   --sequences-filename SEQUENCES_FILENAME
422s                         File for sequences from selected regions. Sequences
422s                         will be stored in FASTA format. Default: None.
422s 
422s FAST5 Data Arguments:
422s   --corrected-group CORRECTED_GROUP
422s                         FAST5 group created by resquiggle command. Default:
422s                         RawGenomeCorrected_000
422s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
422s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
422s                         group]/) containing basecalls and created within
422s                         [--corrected-group] containing re-squiggle results.
422s                         Default: ['BaseCalled_template']
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
422s usage: tombo plot motif_with_stats --fast5-basedirs FAST5_BASEDIRS
422s                                    [FAST5_BASEDIRS ...] --motif MOTIF
422s                                    --statistics-filename STATISTICS_FILENAME
422s                                    --genome-fasta GENOME_FASTA
422s                                    [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
422s                                    [--plot-standard-model]
422s                                    [--plot-alternate-model {5mC,dam,dcm,CpG,6mA}]
422s                                    [--overplot-threshold OVERPLOT_THRESHOLD]
422s                                    [--num-regions NUM_REGIONS]
422s                                    [--num-context NUM_CONTEXT]
422s                                    [--num-statistics NUM_STATISTICS]
422s                                    [--coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS]
422s                                    [--pdf-filename PDF_FILENAME]
422s                                    [--corrected-group CORRECTED_GROUP]
422s                                    [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
422s                                    [--quiet] [--help]
422s 
422s Required Arguments:
422s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
422s                         Directories containing fast5 files.
422s   --motif MOTIF         Motif of interest at which to plot signal and
422s                         statsitics. Supports IUPAC single letter codes (use T
422s                         for RNA).
422s   --statistics-filename STATISTICS_FILENAME
422s                         File to save/load genomic base anchored statistics.
422s   --genome-fasta GENOME_FASTA
422s                         FASTA file used to re-squiggle. For faster sequence
422s                         access.
422s 
422s Comparison Arguments:
422s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
422s                         Set of directories containing fast5 files for control
422s                         reads, containing only canonical nucleotides.
422s   --plot-standard-model
422s                         Add default standard model distribution to the plot.
422s   --plot-alternate-model {5mC,dam,dcm,CpG,6mA}
422s                         Add alternative model distribution to the plot.
422s 
422s Overplotting Argument:
422s   --overplot-threshold OVERPLOT_THRESHOLD
422s                         Coverage level to trigger alternative plot type
422s                         instead of raw signal. Default: 50
422s 
422s Plotting Region Arguments:
422s   --num-regions NUM_REGIONS
422s                         Number of regions to plot. Default: 3
422s   --num-context NUM_CONTEXT
422s                         Number of context bases around motif. Default: 5
422s   --num-statistics NUM_STATISTICS
422s                         Number of motif centered regions to include in
422s                         statistic distributions. Default: 200
422s 
422s Statistical Argument:
422s   --coverage-dampen-counts COVERAGE_DAMPEN_COUNTS COVERAGE_DAMPEN_COUNTS
422s                         Dampen fraction modified estimates for low coverage
422s                         sites. Two parameters are unmodified and modified
422s                         pseudo read counts. This is equivalent to a beta prior
422s                         on the fraction estimate. Set to "0 0" to disable
422s                         dampened fraction estimation. Default: [2, 0]
422s 
422s Output Argument:
422s   --pdf-filename PDF_FILENAME
422s                         PDF filename to store plot(s). Default:
422s                         tombo_results.motif_statistics.pdf
422s 
422s FAST5 Data Arguments:
422s   --corrected-group CORRECTED_GROUP
422s                         FAST5 group created by resquiggle command. Default:
422s                         RawGenomeCorrected_000
422s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
422s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
422s                         group]/) containing basecalls and created within
422s                         [--corrected-group] containing re-squiggle results.
422s                         Default: ['BaseCalled_template']
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
422s usage: tombo plot per_read --genome-locations GENOME_LOCATIONS
422s                            [GENOME_LOCATIONS ...]
422s                            --per-read-statistics-filename
422s                            PER_READ_STATISTICS_FILENAME
422s                            [--genome-fasta GENOME_FASTA]
422s                            [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
422s                            [--num-reads NUM_READS] [--num-bases NUM_BASES]
422s                            [--box-center] [--pdf-filename PDF_FILENAME]
422s                            [--corrected-group CORRECTED_GROUP]
422s                            [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
422s                            [--quiet] [--help]
422s 
422s Required Arguments:
422s   --genome-locations GENOME_LOCATIONS [GENOME_LOCATIONS ...]
422s                         Genomic locations at which to plot signal. Format
422s                         locations as "chrm:position[:strand]
422s                         [chrm2:position2[:strand2] ...]" (strand not
422s                         applicable for all applications)
422s   --per-read-statistics-filename PER_READ_STATISTICS_FILENAME
422s                         Binary file containing per-read statistics from
422s                         statistical testing.
422s 
422s Sequence Arguments (Provide either FAST5s dir or genome FASTA):
422s   --genome-fasta GENOME_FASTA
422s                         FASTA file used to re-squiggle. For faster sequence
422s                         access.
422s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
422s                         Directories containing fast5 files.
422s 
422s Plotting Region Arguments:
422s   --num-reads NUM_READS
422s                         Number of reads to plot. Default: 100
422s   --num-bases NUM_BASES
422s                         Number of bases to plot/output. Default: 51
422s   --box-center          Plot a box around the central base.
422s 
422s Output Argument:
422s   --pdf-filename PDF_FILENAME
422s                         PDF filename to store plot(s). Default:
422s                         tombo_results.per_read_stats.pdf
422s 
422s FAST5 Data Arguments:
422s   --corrected-group CORRECTED_GROUP
422s                         FAST5 group created by resquiggle command. Default:
422s                         RawGenomeCorrected_000
422s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
422s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
422s                         group]/) containing basecalls and created within
422s                         [--corrected-group] containing re-squiggle results.
422s                         Default: ['BaseCalled_template']
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
422s usage: tombo plot roc --statistics-filenames STATISTICS_FILENAMES
422s                       [STATISTICS_FILENAMES ...]
422s                       [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]]
422s                       [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]]
422s                       [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]]
422s                       [--genome-fasta GENOME_FASTA]
422s                       [--pdf-filename PDF_FILENAME]
422s                       [--statistics-per-block STATISTICS_PER_BLOCK]
422s                       [--total-statistics-limit TOTAL_STATISTICS_LIMIT]
422s                       [--quiet] [--help]
422s 
422s Required Argument:
422s   --statistics-filenames STATISTICS_FILENAMES [STATISTICS_FILENAMES ...]
422s                         Files to load genomic base anchored statistics.
422s 
422s Ground Truth Arguments (provide bed files or motifs):
422s   --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]
422s                         Modification description and bed format files
422s                         containing single base locations of ground truth
422s                         modified sites. Bed files should contain 6 fields
422s                         including strand. Format descriptions as
422s                         "mod_name:locs.bed". Example: "CpG
422s                         bisulfite":bisulfite_locs.bed
422s   --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]
422s                         Bed format files containing single base locations of
422s                         ground truth unmodified sites. Bed files should
422s                         contain 6 fields including strand.
422s   --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]
422s                         Ground truth, motif centered, modified base
422s                         descriptions for computing ROC and PR curves. Each
422s                         statistics file is associated with a set of motif
422s                         descriptions. Format descriptions as:
422s                         "motif:mod_pos:name[::motif2:mod_pos2:name2...]".
422s                         mod_pos indicates the alternate-base within the motif
422s                         (1-based index). Example: CCWGG:2:"dcm
422s                         5mC"::GATC:2:"dam 6mA" would assess the performance of
422s                         a single Tombo statistics file for identification of
422s                         E. coli dam and dcm methylation.
422s   --genome-fasta GENOME_FASTA
422s                         FASTA file used to re-squiggle. For faster sequence
422s                         access.
422s 
422s Output Arguments:
422s   --pdf-filename PDF_FILENAME
422s                         PDF filename to store plot(s). Default:
422s                         tombo_results.roc.pdf
422s 
422s Down-sampling Arguments:
422s   --statistics-per-block STATISTICS_PER_BLOCK
422s                         Number of randomly selected per-read, per-base
422s                         statistics to extract from each genomic block for
422s                         plotting. Default: Include all stats
422s   --total-statistics-limit TOTAL_STATISTICS_LIMIT
422s                         Total per-read statistics to be extracted for
422s                         plotting. Avoids memory overflow for large runs.
422s                         Default: 5000000
422s 
422s Miscellaneous Arguments:
422s   --quiet, -q           Don't print status information.
422s   --help, -h            Print this help message and exit
423s usage: tombo plot per_read_roc --per-read-statistics-filenames
423s                                PER_READ_STATISTICS_FILENAMES
423s                                [PER_READ_STATISTICS_FILENAMES ...]
423s                                [--modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]]
423s                                [--unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]]
423s                                [--motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]]
423s                                [--genome-fasta GENOME_FASTA]
423s                                [--statistics-per-block STATISTICS_PER_BLOCK]
423s                                [--total-statistics-limit TOTAL_STATISTICS_LIMIT]
423s                                [--pdf-filename PDF_FILENAME] [--quiet]
423s                                [--help]
423s 
423s Required Argument:
423s   --per-read-statistics-filenames PER_READ_STATISTICS_FILENAMES [PER_READ_STATISTICS_FILENAMES ...]
423s                         Binary files containing per-read statistics from
423s                         statistical testing.
423s 
423s Ground Truth Arguments (provide bed files or motifs):
423s   --modified-locations MODIFIED_LOCATIONS [MODIFIED_LOCATIONS ...]
423s                         Modification description and bed format files
423s                         containing single base locations of ground truth
423s                         modified sites. Bed files should contain 6 fields
423s                         including strand. Format descriptions as
423s                         "mod_name:locs.bed". Example: "CpG
423s                         bisulfite":bisulfite_locs.bed
423s   --unmodified-locations UNMODIFIED_LOCATIONS [UNMODIFIED_LOCATIONS ...]
423s                         Bed format files containing single base locations of
423s                         ground truth unmodified sites. Bed files should
423s                         contain 6 fields including strand.
423s   --motif-descriptions MOTIF_DESCRIPTIONS [MOTIF_DESCRIPTIONS ...]
423s                         Ground truth, motif centered, modified base
423s                         descriptions for computing ROC and PR curves. Each
423s                         statistics file is associated with a set of motif
423s                         descriptions. Format descriptions as:
423s                         "motif:mod_pos:name[::motif2:mod_pos2:name2...]".
423s                         mod_pos indicates the alternate-base within the motif
423s                         (1-based index). Example: CCWGG:2:"dcm
423s                         5mC"::GATC:2:"dam 6mA" would assess the performance of
423s                         a single Tombo statistics file for identification of
423s                         E. coli dam and dcm methylation.
423s   --genome-fasta GENOME_FASTA
423s                         FASTA file used to re-squiggle. For faster sequence
423s                         access.
423s 
423s Down-sampling Arguments:
423s   --statistics-per-block STATISTICS_PER_BLOCK
423s                         Number of randomly selected per-read, per-base
423s                         statistics to extract from each genomic block for
423s                         plotting. Default: 100000
423s   --total-statistics-limit TOTAL_STATISTICS_LIMIT
423s                         Total per-read statistics to be extracted for
423s                         plotting. Avoids memory overflow for large runs.
423s                         Default: 5000000
423s 
423s Output Arguments:
423s   --pdf-filename PDF_FILENAME
423s                         PDF filename to store plot(s). Default:
423s                         tombo_results.per_reads_roc.pdf
423s 
423s Miscellaneous Arguments:
423s   --quiet, -q           Don't print status information.
423s   --help, -h            Print this help message and exit
423s usage: tombo plot kmer --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
423s                        [--upstream-bases {0,1,2,3,4}]
423s                        [--downstream-bases {0,1,2,3,4}] [--read-mean]
423s                        [--num-kmer-threshold NUM_KMER_THRESHOLD]
423s                        [--num-reads NUM_READS] [--pdf-filename PDF_FILENAME]
423s                        [--r-data-filename R_DATA_FILENAME] [--dont-plot]
423s                        [--corrected-group CORRECTED_GROUP]
423s                        [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
423s                        [--quiet] [--help]
423s 
423s Required Argument:
423s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
423s                         Directories containing fast5 files.
423s 
423s Data Processing Arguments:
423s   --upstream-bases {0,1,2,3,4}
423s                         Upstream bases in k-mer. Default: 1
423s   --downstream-bases {0,1,2,3,4}
423s                         Downstream bases in k-mer. Default: 2
423s   --read-mean           Plot k-mer means across whole reads as opposed to
423s                         individual k-mer event levels.
423s   --num-kmer-threshold NUM_KMER_THRESHOLD
423s                         Observations of each k-mer required to include a read
423s                         in read level averages. Default: 1
423s 
423s Plotting Region Arguments:
423s   --num-reads NUM_READS
423s                         Number of reads to plot. Default: 100
423s 
423s Output Arguments:
423s   --pdf-filename PDF_FILENAME
423s                         PDF filename to store plot(s). Default:
423s                         tombo_results.kmer_distribution.pdf
423s   --r-data-filename R_DATA_FILENAME
423s                         Filename to save R data structure. Default: Don't save
423s   --dont-plot           Don't plot result. Useful to produce only R data file.
423s 
423s FAST5 Data Arguments:
423s   --corrected-group CORRECTED_GROUP
423s                         FAST5 group created by resquiggle command. Default:
423s                         RawGenomeCorrected_000
423s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
423s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
423s                         group]/) containing basecalls and created within
423s                         [--corrected-group] containing re-squiggle results.
423s                         Default: ['BaseCalled_template']
423s 
423s Miscellaneous Arguments:
423s   --quiet, -q           Don't print status information.
423s   --help, -h            Print this help message and exit
423s usage: tombo plot cluster_most_significant --fast5-basedirs FAST5_BASEDIRS
423s                                            [FAST5_BASEDIRS ...]
423s                                            --control-fast5-basedirs
423s                                            CONTROL_FAST5_BASEDIRS
423s                                            [CONTROL_FAST5_BASEDIRS ...]
423s                                            --statistics-filename
423s                                            STATISTICS_FILENAME
423s                                            [--genome-fasta GENOME_FASTA]
423s                                            [--processes PROCESSES]
423s                                            [--num-regions NUM_REGIONS]
423s                                            [--num-bases NUM_BASES]
423s                                            [--slide-span SLIDE_SPAN]
423s                                            [--pdf-filename PDF_FILENAME]
423s                                            [--r-data-filename R_DATA_FILENAME]
423s                                            [--corrected-group CORRECTED_GROUP]
423s                                            [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
423s                                            [--quiet] [--help]
423s 
423s Required Arguments:
423s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
423s                         Directories containing fast5 files.
423s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
423s                         Set of directories containing fast5 files for control
423s                         reads, containing only canonical nucleotides.
423s   --statistics-filename STATISTICS_FILENAME
423s                         File to save/load genomic base anchored statistics.
423s 
423s FASTA Sequence Argument:
423s   --genome-fasta GENOME_FASTA
423s                         FASTA file used to re-squiggle. For faster sequence
423s                         access.
423s 
423s Multiprocessing Argument:
423s   --processes PROCESSES
423s                         Number of processes. Default: 1
423s 
423s Plotting Region Arguments:
423s   --num-regions NUM_REGIONS
423s                         Number of regions to plot. Default: 10
423s   --num-bases NUM_BASES
423s                         Number of bases to plot/output. Default: 21
423s   --slide-span SLIDE_SPAN
423s                         Number of bases offset over which to search when
423s                         computing distances for signal cluster plotting.
423s                         Default: 0 (exact position)
423s 
423s Output Arguments:
423s   --pdf-filename PDF_FILENAME
423s                         PDF filename to store plot(s). Default:
423s                         tombo_results.signal_clusters.pdf
423s   --r-data-filename R_DATA_FILENAME
423s                         Filename to save R data structure. Default: Don't save
423s 
423s FAST5 Data Arguments:
423s   --corrected-group CORRECTED_GROUP
423s                         FAST5 group created by resquiggle command. Default:
423s                         RawGenomeCorrected_000
423s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
423s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
423s                         group]/) containing basecalls and created within
423s                         [--corrected-group] containing re-squiggle results.
423s                         Default: ['BaseCalled_template']
423s 
423s Miscellaneous Arguments:
423s   --quiet, -q           Don't print status information.
423s   --help, -h            Print this help message and exit
423s usage: tombo build_model estimate_scale [--quiet] [--help] fast5s_basedir
423s 
423s Required Arguments:
423s   fast5s_basedir  Directory containing fast5 files. All files ending in
423s                   "fast5" found recursively within this base directory will be
423s                   processed.
423s 
423s Miscellaneous Arguments:
423s   --quiet, -q     Don't print status information.
423s   --help, -h      Print this help message and exit
423s usage: tombo build_model event_resquiggle
423s                                           [--minimap2-executable MINIMAP2_EXECUTABLE]
423s                                           [--minimap2-index MINIMAP2_INDEX]
423s                                           [--bwa-mem-executable BWA_MEM_EXECUTABLE]
423s                                           [--graphmap-executable GRAPHMAP_EXECUTABLE]
423s                                           [--alignment-batch-size ALIGNMENT_BATCH_SIZE]
423s                                           [--normalization-type {median,pA,pA_raw,none}]
423s                                           [--pore-model-filename PORE_MODEL_FILENAME]
423s                                           [--outlier-threshold OUTLIER_THRESHOLD]
423s                                           [--segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS]
423s                                           [--obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]]
423s                                           [--timeout TIMEOUT]
423s                                           [--cpts-limit CPTS_LIMIT]
423s                                           [--skip-index] [--overwrite]
423s                                           [--failed-reads-filename FAILED_READS_FILENAME]
423s                                           [--include-event-stdev]
423s                                           [--corrected-group CORRECTED_GROUP]
423s                                           [--basecall-group BASECALL_GROUP]
423s                                           [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
423s                                           [--processes PROCESSES]
423s                                           [--align-processes ALIGN_PROCESSES]
423s                                           [--align-threads-per-process ALIGN_THREADS_PER_PROCESS]
423s                                           [--resquiggle-processes RESQUIGGLE_PROCESSES]
423s                                           [--quiet] [--help]
423s                                           fast5s_basedir reference_fasta
423s 
423s Required Arguments:
423s   fast5s_basedir        Directory containing fast5 files. All files ending in
423s                         "fast5" found recursively within this base directory
423s                         will be processed.
423s   reference_fasta       Reference genome/transcriptome FASTA file for mapping.
423s 
423s Mapper Arguments (One mapper is required):
423s   --minimap2-executable MINIMAP2_EXECUTABLE
423s                         Path to minimap2 executable.
423s   --minimap2-index MINIMAP2_INDEX
423s                         Path to minimap2 index (with map-ont preset) file
423s                         corresponding to the [genome_fasta] provided.
423s   --bwa-mem-executable BWA_MEM_EXECUTABLE
423s                         Path to bwa-mem executable.
423s   --graphmap-executable GRAPHMAP_EXECUTABLE
423s                         Path to graphmap executable.
423s   --alignment-batch-size ALIGNMENT_BATCH_SIZE
423s                         Number of reads included in each alignment call. Note:
423s                         A new system mapping call is made for each batch
423s                         (including loading of the genome), so it is advised to
423s                         use larger values for larger genomes. Default: 1000
423s 
423s Signal Processing Arguments:
423s   --normalization-type {median,pA,pA_raw,none}
423s                         Choices: "none": raw 16-bit DAQ values, "pA_raw": pA
423s                         as in the ONT events (using offset, range and
423s                         digitization), "pA": k-mer-based correction for pA
423s                         drift as in nanopolish (requires [--pore-model-
423s                         filename]), "median": median and MAD from raw signal.
423s                         Default: median
423s   --pore-model-filename PORE_MODEL_FILENAME
423s                         File containing kmer model parameters (level_mean and
423s                         level_stdv) used in order to compute kmer-based
423s                         corrected pA values. E.g. https://github.com/jts/nanop
423s                         olish/blob/master/etc/r9-
423s                         models/template_median68pA.5mers.model
423s   --outlier-threshold OUTLIER_THRESHOLD
423s                         Windosrize the signal at this number of scale values.
423s                         Negative value disables outlier clipping. Default:
423s                         5.000000
423s   --segmentation-parameters SEGMENTATION_PARAMETERS SEGMENTATION_PARAMETERS
423s                         Specify the 2 parameters for segmentation 1) running
423s                         neighboring windows width 2) minimum raw observations
423s                         per genomic base. Sample type defaults: RNA : 12 6 ||
423s                         DNA : 5 3
423s 
423s Read Filtering Arguments:
423s   --obs-per-base-filter OBS_PER_BASE_FILTER [OBS_PER_BASE_FILTER ...]
423s                         Filter reads based on observations per base percentile
423s                         thresholds. Format thresholds as "percentile:thresh
423s                         [pctl2:thresh2 ...]". For example to filter reads with
423s                         99th pctl > 200 obs/base or max > 5k obs/base use
423s                         "99:200 100:5000".
423s   --timeout TIMEOUT     Timeout in seconds for processing a single read.
423s                         Default: No timeout.
423s   --cpts-limit CPTS_LIMIT
423s                         Maximum number of changepoints to find within a single
423s                         indel group. Default: No limit.
423s 
423s Input/Output Arguments:
423s   --skip-index          Skip creation of tombo index. This drastically slows
423s                         downstream tombo commands. Default stores tombo index
423s                         named ".[--fast5-basedir].[--corrected-
423s                         group].tombo.index" to be loaded automatically for
423s                         downstream commands.
423s   --overwrite           Overwrite previous corrected group in FAST5 files.
423s                         Note: only effects --corrected-group or --new-
423s                         corrected-group.
423s   --failed-reads-filename FAILED_READS_FILENAME
423s                         Output failed read filenames with assoicated error.
423s                         Default: Do not store failed reads.
423s   --include-event-stdev
423s                         Include corrected event standard deviation in output
423s                         FAST5 data.
423s 
423s FAST5 Data Arguments:
423s   --corrected-group CORRECTED_GROUP
423s                         FAST5 group created by resquiggle command. Default:
423s                         RawGenomeCorrected_000
423s   --basecall-group BASECALL_GROUP
423s                         FAST5 group obtain original basecalls (under Analyses
423s                         group). Default: Basecall_1D_000
423s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
423s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
423s                         group]/) containing basecalls and created within
423s                         [--corrected-group] containing re-squiggle results.
423s                         Default: ['BaseCalled_template']
423s 
423s Multiprocessing Arguments:
423s   --processes PROCESSES
423s                         Number of processes. Default: 2
423s   --align-processes ALIGN_PROCESSES
423s                         Number of processes to use for parsing and aligning
423s                         original basecalls. Each process will independently
423s                         load the genome into memory, so use caution with
423s                         larger genomes (e.g. human). Default: 1
423s   --align-threads-per-process ALIGN_THREADS_PER_PROCESS
423s                         Number of threads to use for aligner system call.
423s                         Default: [--processes] / (2 * [--align-processes)]
423s   --resquiggle-processes RESQUIGGLE_PROCESSES
423s                         Number of processes to use for resquiggle algorithm.
423s                         Default: [--processes] / 2
423s 
423s Miscellaneous Arguments:
423s   --quiet, -q           Don't print status information.
423s   --help, -h            Print this help message and exit
423s usage: tombo build_model estimate_reference --fast5-basedirs FAST5_BASEDIRS
423s                                             [FAST5_BASEDIRS ...]
423s                                             --tombo-model-filename
423s                                             TOMBO_MODEL_FILENAME
423s                                             [--estimate-mean]
423s                                             [--kmer-specific-sd]
423s                                             [--upstream-bases {0,1,2,3,4}]
423s                                             [--downstream-bases {0,1,2,3,4}]
423s                                             [--minimum-test-reads MINIMUM_TEST_READS]
423s                                             [--coverage-threshold COVERAGE_THRESHOLD]
423s                                             [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS]
423s                                             [--multiprocess-region-size MULTIPROCESS_REGION_SIZE]
423s                                             [--processes PROCESSES]
423s                                             [--corrected-group CORRECTED_GROUP]
423s                                             [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
423s                                             [--quiet] [--help]
423s 
423s Required Arguments:
423s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
423s                         Directories containing fast5 files.
423s   --tombo-model-filename TOMBO_MODEL_FILENAME
423s                         Filename to save Tombo model.
423s 
423s Modeling Arguments:
423s   --estimate-mean       Use the mean instead of median for model level
423s                         estimation. Note: This can cause poor fits due to
423s                         outliers
423s   --kmer-specific-sd    Estimate standard deviation for each k-mers
423s                         individually.
423s   --upstream-bases {0,1,2,3,4}
423s                         Upstream bases in k-mer. Default: 1
423s   --downstream-bases {0,1,2,3,4}
423s                         Downstream bases in k-mer. Default: 2
423s 
423s Filtering Arguments:
423s   --minimum-test-reads MINIMUM_TEST_READS
423s                         Number of reads required at a position to perform
423s                         significance testing or contribute to model
423s                         estimation. Default: 10
423s   --coverage-threshold COVERAGE_THRESHOLD
423s                         Maximum mean coverage per region when estimating k-mer
423s                         model (limits compute time for deep samples). Default:
423s                         100
423s   --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS
423s                         Number of each k-mer observations required in order to
423s                         produce a reference (genomic locations for standard
423s                         reference and per-read for alternative reference).
423s                         Default: 5
423s 
423s Multiprocessing Arguments:
423s   --multiprocess-region-size MULTIPROCESS_REGION_SIZE
423s                         Size of regions over which to multiprocesses statistic
423s                         computation. For very deep samples a smaller value is
423s                         recommmended in order to control memory consumption.
423s                         Default: 10000
423s   --processes PROCESSES
423s                         Number of processes. Default: 1
423s 
423s FAST5 Data Arguments:
423s   --corrected-group CORRECTED_GROUP
423s                         FAST5 group created by resquiggle command. Default:
423s                         RawGenomeCorrected_000
423s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
423s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
423s                         group]/) containing basecalls and created within
423s                         [--corrected-group] containing re-squiggle results.
423s                         Default: ['BaseCalled_template']
423s 
423s Miscellaneous Arguments:
423s   --quiet, -q           Don't print status information.
423s   --help, -h            Print this help message and exit
423s usage: tombo build_model estimate_alt_reference --alternate-model-filename
423s                                                 ALTERNATE_MODEL_FILENAME
423s                                                 --alternate-model-name
423s                                                 ALTERNATE_MODEL_NAME
423s                                                 --alternate-model-base
423s                                                 {A,C,G,T}
423s                                                 [--fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]]
423s                                                 [--control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]]
423s                                                 [--alternate-density-filename ALTERNATE_DENSITY_FILENAME]
423s                                                 [--control-density-filename CONTROL_DENSITY_FILENAME]
423s                                                 [--dna] [--rna]
423s                                                 [--tombo-model-filename TOMBO_MODEL_FILENAME]
423s                                                 [--alt-fraction-percentile ALT_FRACTION_PERCENTILE]
423s                                                 [--kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH]
423s                                                 [--minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS]
423s                                                 [--save-density-basename SAVE_DENSITY_BASENAME]
423s                                                 [--processes PROCESSES]
423s                                                 [--corrected-group CORRECTED_GROUP]
423s                                                 [--basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]]
423s                                                 [--quiet] [--help]
423s 
423s Required Arguments:
423s   --alternate-model-filename ALTERNATE_MODEL_FILENAME
423s                         Tombo model for alternative likelihood ratio
423s                         significance testing.
423s   --alternate-model-name ALTERNATE_MODEL_NAME
423s                         A short name to associate with this alternate model
423s                         (e.g. 5mC, 6mA, etc.). This text will be included in
423s                         output filenames when this model is used for testing.
423s   --alternate-model-base {A,C,G,T}
423s                         Non-standard base is an alternative to this base.
423s 
423s Signal Data Arguments (Must provide either FAST5 dirs or previous density estimates):
423s   --fast5-basedirs FAST5_BASEDIRS [FAST5_BASEDIRS ...]
423s                         Directories containing fast5 files.
423s   --control-fast5-basedirs CONTROL_FAST5_BASEDIRS [CONTROL_FAST5_BASEDIRS ...]
423s                         Set of directories containing fast5 files for control
423s                         reads, containing only canonical nucleotides.
423s   --alternate-density-filename ALTERNATE_DENSITY_FILENAME
423s                         File containing k-mer level kernel density estimates
423s                         for the alternative sample saved using --save-density-
423s                         basename.
423s   --control-density-filename CONTROL_DENSITY_FILENAME
423s                         File containing k-mer level kernel density estimates
423s                         for the control sample saved using --save-density-
423s                         basename.
423s 
423s Standard Model Arguments:
423s   --dna                 Explicitly select canonical DNA model. Default:
423s                         Automatically determine from FAST5s
423s   --rna                 Explicitly select canonical RNA model. Default:
423s                         Automatically determine from FAST5s
423s   --tombo-model-filename TOMBO_MODEL_FILENAME
423s                         Tombo model filename. If no file is provided, the
423s                         default DNA or RNA Tombo model will be used.
423s 
423s Model Fitting Arguments:
423s   --alt-fraction-percentile ALT_FRACTION_PERCENTILE
423s                         When esitmating the alternative base incorporation
423s                         rate, this percent of k-mers are assumed to have
423s                         significantly shifted signal so the alternative
423s                         distribution minimally overlaps the standard base
423s                         distribution. Default: 5.000000
423s   --kernel-density-bandwidth KERNEL_DENSITY_BANDWIDTH
423s                         Bandwidth applied when performing Gaussian kernal
423s                         density esitmation on standard and alternative base
423s                         signal distributions. Default: 0.050000
423s 
423s Filtering Argument:
423s   --minimum-kmer-observations MINIMUM_KMER_OBSERVATIONS
423s                         Number of each k-mer observations required in order to
423s                         produce a reference (genomic locations for standard
423s                         reference and per-read for alternative reference).
423s                         Default: 1000
423s 
423s Output Argument:
423s   --save-density-basename SAVE_DENSITY_BASENAME
423s                         Basename to save alternative model estimation density
423s                         estimation information. See scripts/debug_est_alt.R
423s                         for info use example. Default: Don't save.
423s 
423s Multiprocessing Arguments:
423s   --processes PROCESSES
423s                         Number of processes. Default: 1
423s 
423s FAST5 Data Arguments:
423s   --corrected-group CORRECTED_GROUP
423s                         FAST5 group created by resquiggle command. Default:
423s                         RawGenomeCorrected_000
423s   --basecall-subgroups BASECALL_SUBGROUPS [BASECALL_SUBGROUPS ...]
423s                         FAST5 subgroup(s) (under /Analyses/[--basecall-
423s                         group]/) containing basecalls and created within
423s                         [--corrected-group] containing re-squiggle results.
423s                         Default: ['BaseCalled_template']
423s 
423s Miscellaneous Arguments:
423s   --quiet, -q           Don't print status information.
423s   --help, -h            Print this help message and exit
423s This test only tests the help system
423s There is an extensive test in 
423s 
423s   tombo/tests/shell_tests.sh
423s 
423s but this requires to download larger data
423s sets which is not done for the moment.
424s autopkgtest [02:15:53]: test run-unit-test: -----------------------]
424s autopkgtest [02:15:53]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
424s run-unit-test        PASS
425s autopkgtest [02:15:54]: @@@@@@@@@@@@@@@@@@@@ summary
425s run-unit-test        PASS
437s Creating nova instance adt-noble-ppc64el-tombo-20240327-020849-juju-7f2275-prod-proposed-migration-environment-2-26efedcb-8433-4892-98ca-fba585653f5b from image adt/ubuntu-noble-ppc64el-server-20240326.img (UUID a856d654-cf86-4db9-9789-e03c818e8ed3)...