0s autopkgtest [17:13:05]: starting date and time: 2024-03-16 17:13:05+0000
  0s autopkgtest [17:13:05]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [17:13:05]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3fetfm7b/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade lumpy-sv --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-8.secgroup --name adt-noble-arm64-lumpy-sv-20240316-171305-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/
115s autopkgtest [17:15:00]: testbed dpkg architecture: arm64
115s autopkgtest [17:15:00]: testbed apt version: 2.7.12
115s autopkgtest [17:15:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup
116s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
117s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
118s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB]
118s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
118s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB]
118s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB]
118s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
118s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
118s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
118s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB]
118s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
118s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB]
118s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
120s Fetched 9063 kB in 3s (3206 kB/s)
120s Reading package lists...
125s Reading package lists...
125s Building dependency tree...
125s Reading state information...
126s Calculating upgrade...
127s The following packages will be REMOVED:
127s   libssl3
127s The following NEW packages will be installed:
127s   libssl3t64
127s The following packages have been kept back:
127s   curl
127s The following packages will be upgraded:
127s   openssl ubuntu-minimal ubuntu-standard
127s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
127s Need to get 2775 kB of archives.
127s After this operation, 72.7 kB of additional disk space will be used.
127s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
127s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
127s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB]
127s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB]
128s Fetched 2775 kB in 1s (3997 kB/s)
129s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
129s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
129s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
129s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
129s  wget depends on libssl3 (>= 3.0.0).
129s  u-boot-tools depends on libssl3 (>= 3.0.0).
129s  tnftp depends on libssl3 (>= 3.0.0).
129s  tcpdump depends on libssl3 (>= 3.0.0).
129s  systemd-resolved depends on libssl3 (>= 3.0.0).
129s  systemd depends on libssl3 (>= 3.0.0).
129s  sudo depends on libssl3 (>= 3.0.0).
129s  sbsigntool depends on libssl3 (>= 3.0.0).
129s  rsync depends on libssl3 (>= 3.0.0).
129s  python3-cryptography depends on libssl3 (>= 3.0.0).
129s  openssh-server depends on libssl3 (>= 3.0.10).
129s  openssh-client depends on libssl3 (>= 3.0.10).
129s  mtd-utils depends on libssl3 (>= 3.0.0).
129s  mokutil depends on libssl3 (>= 3.0.0).
129s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
129s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
129s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
129s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
129s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
129s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
129s  libnvme1 depends on libssl3 (>= 3.0.0).
129s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
129s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
129s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
129s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
129s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
129s  kmod depends on libssl3 (>= 3.0.0).
129s  dhcpcd-base depends on libssl3 (>= 3.0.0).
129s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
129s 
129s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74758 files and directories currently installed.)
129s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
129s Selecting previously unselected package libssl3t64:arm64.
129s (Reading database ... 
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(Reading database ... 74747 files and directories currently installed.)
129s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
129s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
130s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ...
130s Unpacking ubuntu-minimal (1.536) over (1.535) ...
130s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ...
130s Unpacking ubuntu-standard (1.536) over (1.535) ...
130s Setting up ubuntu-minimal (1.536) ...
130s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
130s Setting up ubuntu-standard (1.536) ...
130s Setting up openssl (3.0.13-0ubuntu1) ...
130s Processing triggers for man-db (2.12.0-3) ...
130s Processing triggers for libc-bin (2.39-0ubuntu2) ...
131s Reading package lists...
131s Building dependency tree...
131s Reading state information...
132s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
133s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
133s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
136s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
136s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
149s Reading package lists...
149s Reading package lists...
150s Building dependency tree...
150s Reading state information...
150s Calculating upgrade...
151s The following packages have been kept back:
151s   curl
151s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
151s Reading package lists...
152s Building dependency tree...
152s Reading state information...
153s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
155s autopkgtest [17:15:40]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
156s autopkgtest [17:15:41]: @@@@@@@@@@@@@@@@@@@@ apt-source lumpy-sv
161s Get:1 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (dsc) [2384 B]
161s Get:2 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (tar) [112 kB]
161s Get:3 http://ftpmaster.internal/ubuntu noble/universe lumpy-sv 0.3.1+dfsg-7build1 (diff) [39.2 MB]
161s gpgv: Signature made Sat Nov 19 21:49:32 2022 UTC
161s gpgv:                using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D
161s gpgv:                issuer "steve.langasek@ubuntu.com"
161s gpgv: Can't check signature: No public key
161s dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-7build1.dsc: no acceptable signature found
166s autopkgtest [17:15:51]: testing package lumpy-sv version 0.3.1+dfsg-7build1
176s autopkgtest [17:16:01]: build not needed
187s autopkgtest [17:16:12]: test run-unit-test: preparing testbed
188s Reading package lists...
189s Building dependency tree...
189s Reading state information...
189s Starting pkgProblemResolver with broken count: 0
189s Starting 2 pkgProblemResolver with broken count: 0
189s Done
190s The following additional packages will be installed:
190s   bamkit libbamtools2.5.2 libblas3 libdeflate0 libgfortran5 libgzstream0
190s   libhts3 libhtscodecs2 liblapack3 libpython3.11-minimal libpython3.11-stdlib
190s   lumpy-sv lumpy-sv-examples python3-numpy python3-pysam python3.11
190s   python3.11-minimal samblaster samtools
190s Suggested packages:
190s   gcc gfortran python3-dev python3-pytest python3.11-venv python3.11-doc
190s   binfmt-support cwltool
190s Recommended packages:
190s   sambamba
190s The following NEW packages will be installed:
190s   autopkgtest-satdep bamkit libbamtools2.5.2 libblas3 libdeflate0 libgfortran5
190s   libgzstream0 libhts3 libhtscodecs2 liblapack3 libpython3.11-minimal
190s   libpython3.11-stdlib lumpy-sv lumpy-sv-examples python3-numpy python3-pysam
190s   python3.11 python3.11-minimal samblaster samtools
190s 0 upgraded, 20 newly installed, 0 to remove and 1 not upgraded.
190s Need to get 73.3 MB/73.3 MB of archives.
190s After this operation, 158 MB of additional disk space will be used.
190s Get:1 /tmp/autopkgtest.q2dMV1/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B]
190s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
191s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
191s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
191s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
191s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
191s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
191s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts3 arm64 1.19+ds-1 [429 kB]
191s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB]
191s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 bamkit all 0.0.1+git20170413.ccd079d-3 [14.9 kB]
191s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB]
191s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
191s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
191s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libgzstream0 arm64 1.5+git20171107.9a20658-1 [7406 B]
191s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
192s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 samblaster arm64 0.1.26-4 [23.7 kB]
192s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB]
192s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
192s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 lumpy-sv arm64 0.3.1+dfsg-7build1 [133 kB]
192s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 lumpy-sv-examples all 0.3.1+dfsg-7build1 [54.6 MB]
195s Fetched 73.3 MB in 3s (21.4 MB/s)
195s Selecting previously unselected package libpython3.11-minimal:arm64.
195s (Reading database ... 
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(Reading database ... 74760 files and directories currently installed.)
195s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ...
195s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ...
196s Selecting previously unselected package python3.11-minimal.
196s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ...
196s Unpacking python3.11-minimal (3.11.8-1) ...
196s Selecting previously unselected package libpython3.11-stdlib:arm64.
196s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ...
196s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
196s Selecting previously unselected package python3.11.
196s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ...
196s Unpacking python3.11 (3.11.8-1) ...
196s Selecting previously unselected package libdeflate0:arm64.
197s Preparing to unpack .../04-libdeflate0_1.19-1_arm64.deb ...
197s Unpacking libdeflate0:arm64 (1.19-1) ...
197s Selecting previously unselected package libhtscodecs2:arm64.
197s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_arm64.deb ...
197s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
197s Selecting previously unselected package libhts3:arm64.
197s Preparing to unpack .../06-libhts3_1.19+ds-1_arm64.deb ...
197s Unpacking libhts3:arm64 (1.19+ds-1) ...
197s Selecting previously unselected package python3-pysam.
197s Preparing to unpack .../07-python3-pysam_0.22.0+ds-1_arm64.deb ...
197s Unpacking python3-pysam (0.22.0+ds-1) ...
198s Selecting previously unselected package bamkit.
198s Preparing to unpack .../08-bamkit_0.0.1+git20170413.ccd079d-3_all.deb ...
198s Unpacking bamkit (0.0.1+git20170413.ccd079d-3) ...
198s Selecting previously unselected package libbamtools2.5.2:arm64.
198s Preparing to unpack .../09-libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb ...
198s Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ...
198s Selecting previously unselected package libblas3:arm64.
199s Preparing to unpack .../10-libblas3_3.12.0-3_arm64.deb ...
199s Unpacking libblas3:arm64 (3.12.0-3) ...
200s Selecting previously unselected package libgfortran5:arm64.
201s Preparing to unpack .../11-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
201s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
201s Selecting previously unselected package libgzstream0:arm64.
201s Preparing to unpack .../12-libgzstream0_1.5+git20171107.9a20658-1_arm64.deb ...
201s Unpacking libgzstream0:arm64 (1.5+git20171107.9a20658-1) ...
201s Selecting previously unselected package liblapack3:arm64.
202s Preparing to unpack .../13-liblapack3_3.12.0-3_arm64.deb ...
202s Unpacking liblapack3:arm64 (3.12.0-3) ...
202s Selecting previously unselected package samblaster.
202s Preparing to unpack .../14-samblaster_0.1.26-4_arm64.deb ...
202s Unpacking samblaster (0.1.26-4) ...
202s Selecting previously unselected package samtools.
203s Preparing to unpack .../15-samtools_1.19.2-1_arm64.deb ...
203s Unpacking samtools (1.19.2-1) ...
203s Selecting previously unselected package python3-numpy.
203s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_arm64.deb ...
203s Unpacking python3-numpy (1:1.24.2-2) ...
203s Selecting previously unselected package lumpy-sv.
204s Preparing to unpack .../17-lumpy-sv_0.3.1+dfsg-7build1_arm64.deb ...
204s Unpacking lumpy-sv (0.3.1+dfsg-7build1) ...
204s Selecting previously unselected package lumpy-sv-examples.
204s Preparing to unpack .../18-lumpy-sv-examples_0.3.1+dfsg-7build1_all.deb ...
204s Unpacking lumpy-sv-examples (0.3.1+dfsg-7build1) ...
204s Selecting previously unselected package autopkgtest-satdep.
205s Preparing to unpack .../19-1-autopkgtest-satdep.deb ...
205s Unpacking autopkgtest-satdep (0) ...
205s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
205s Setting up samblaster (0.1.26-4) ...
205s Setting up libdeflate0:arm64 (1.19-1) ...
205s Setting up lumpy-sv-examples (0.3.1+dfsg-7build1) ...
205s Setting up libblas3:arm64 (3.12.0-3) ...
205s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
205s Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ...
205s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
205s Setting up libgzstream0:arm64 (1.5+git20171107.9a20658-1) ...
205s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ...
205s Setting up python3.11-minimal (3.11.8-1) ...
206s Setting up liblapack3:arm64 (3.12.0-3) ...
206s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
206s Setting up libhts3:arm64 (1.19+ds-1) ...
206s Setting up python3-pysam (0.22.0+ds-1) ...
206s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ...
206s Setting up bamkit (0.0.1+git20170413.ccd079d-3) ...
206s Setting up samtools (1.19.2-1) ...
206s Setting up python3.11 (3.11.8-1) ...
207s Setting up python3-numpy (1:1.24.2-2) ...
209s Setting up lumpy-sv (0.3.1+dfsg-7build1) ...
209s Setting up autopkgtest-satdep (0) ...
209s Processing triggers for systemd (255.2-3ubuntu2) ...
209s Processing triggers for man-db (2.12.0-3) ...
209s Processing triggers for libc-bin (2.39-0ubuntu2) ...
214s (Reading database ... 77081 files and directories currently installed.)
214s Removing autopkgtest-satdep (0) ...
215s autopkgtest [17:16:40]: test run-unit-test: [-----------------------
215s + cp -a /usr/share/doc/lumpy-sv/examples/data /usr/share/doc/lumpy-sv/examples/lumpy_tests /usr/share/doc/lumpy-sv/examples/test /tmp/autopkgtest.q2dMV1/autopkgtest_tmp
215s + cd /tmp/autopkgtest.q2dMV1/autopkgtest_tmp
215s + gunzip -r data lumpy_tests test
216s + cd test
216s + sed -i -e 's:\.\./scripts:/usr/share/lumpy-sv/scripts:' -e 's:\.\./bin/lumpy:/usr/bin/lumpy:' bp_pe.sh bp_pe_pl.sh bp_pesr.sh bp_pesr_pl.sh bp_sr.sh functional-test.sh test.sh test_pl.sh
216s + ./test.sh
216s Testing lumpy paired-end
216s Removed 12 outliers with isize >= 850
216s 549	0
216s chr10	1000000
219s Install bedtools to compare result to known deletions
219s Testing lumpy split-read
219s chr10	1000000
219s Install bedtools to compare result to known deletions
219s Testing lumpy paired-end and split-read
219s Removed 12 outliers with isize >= 850
219s 549	0
219s chr10	1000000
223s Install bedtools to compare result to known deletions
224s autopkgtest [17:16:49]: test run-unit-test: -----------------------]
224s run-unit-test        PASS
224s autopkgtest [17:16:49]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
225s autopkgtest [17:16:50]: @@@@@@@@@@@@@@@@@@@@ summary
225s run-unit-test        PASS
236s Creating nova instance adt-noble-arm64-lumpy-sv-20240316-171305-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...