0s autopkgtest [16:48:17]: starting date and time: 2024-03-24 16:48:17+0000 0s autopkgtest [16:48:17]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:48:17]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.izov_gq6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade cnvkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-13.secgroup --name adt-noble-arm64-cnvkit-20240324-164817-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 393s Creating nova instance adt-noble-arm64-cnvkit-20240324-164817-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)... 393s nova boot failed (attempt #1): 393s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader') 393s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader') 393s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken') 393s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth') 393s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password') 393s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token') 393s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password') 393s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP') 393s DEBUG (session:517) REQ: curl -g -i -X GET https://keystone.ps6.canonical.com:5000/v3 -H "Accept: application/json" -H "User-Agent: nova keystoneauth1/4.0.0 python-requests/2.22.0 CPython/3.8.10" 393s DEBUG (connectionpool:962) Starting new HTTPS connection (1): keystone.ps6.canonical.com:5000 393s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "GET /v3 HTTP/1.1" 200 267 393s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 267 Content-Type: application/json Date: Sun, 24 Mar 2024 16:49:13 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) Vary: X-Auth-Token x-openstack-request-id: req-71549d5f-8be2-42e8-8db6-44b7c3dbad4f 393s DEBUG (session:580) RESP BODY: {"version": {"id": "v3.14", "status": "stable", "updated": "2020-04-07T00:00:00Z", "links": [{"rel": "self", "href": "https://keystone.ps6.canonical.com:5000/v3/"}], "media-types": [{"base": "application/json", "type": "application/vnd.openstack.identity-v3+json"}]}} 393s DEBUG (session:946) GET call to https://keystone.ps6.canonical.com:5000/v3 used request id req-71549d5f-8be2-42e8-8db6-44b7c3dbad4f 393s DEBUG (base:182) Making authentication request to https://keystone.ps6.canonical.com:5000/v3/auth/tokens 393s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "POST /v3/auth/tokens HTTP/1.1" 201 12445 393s DEBUG (base:187) {"token": {"methods": ["password"], "user": {"domain": {"id": "default", "name": "Default"}, "id": "369f50a481564a2c9433776a4ebd224d", "name": "prod-proposed-migration-arm64", "password_expires_at": null}, "audit_ids": ["WTrbI2cTQ6C3AOMgGi1MiA"], "expires_at": "2024-03-25T16:49:14.000000Z", "issued_at": "2024-03-24T16:49:14.000000Z", "project": {"domain": {"id": "default", "name": "Default"}, "id": "bd8b3df3f03d43a0a9303b7c0434fdab", "name": "prod-proposed-migration-arm64_project"}, "is_domain": false, "roles": [{"id": "15cf997650e345b7b21c02b5cdb7d84a", "name": "member"}, {"id": "86bf3043974746c2bf52c2a9f362f986", "name": "reader"}], "is_admin_project": false, "catalog": [{"endpoints": [{"id": "213cdf38198c4581bd5b7d6d0836923b", "interface": "internal", "region_id": "prodstack6", "url": "https://radosgw-internal.ps6.canonical.com:443/", "region": "prodstack6"}, {"id": "67061eee26944a1a8009f9d07be19738", "interface": "public", "region_id": "prodstack6", "url": "https://radosgw.ps6.canonical.com:443/", "region": "prodstack6"}, {"id": "fc88c52c749a47d08a24a2c7efbde01b", "interface": "admin", "region_id": "prodstack6", "url": "https://radosgw-admin.ps6.canonical.com:443/", "region": "prodstack6"}], "id": "06e4714942634054bf9aa11715312b4e", "type": "s3", "name": "s3"}, {"endpoints": [{"id": "8aa44c94b63746bd9b37f1008ad55fa8", "interface": "admin", "region_id": "prodstack6", "url": "https://aodh-admin.ps6.canonical.com:8042", "region": "prodstack6"}, {"id": "92cf08a80a0242ebbca8ec893cf332b1", "interface": "public", "region_id": "prodstack6", "url": "https://aodh.ps6.canonical.com:8042", "region": "prodstack6"}, {"id": "d8139c6e11ae4edcb78981c12bd53212", "interface": "internal", "region_id": "prodstack6", "url": "https://aodh-internal.ps6.canonical.com:8042", "region": "prodstack6"}], "id": "2fb939b0b969435c8f0c5fa4edb4de94", "type": "alarming", "name": "aodh"}, {"endpoints": [{"id": "a49fcc80e658411885f88cdd8432a571", "interface": "internal", "region_id": "prodstack6", "url": "https://heat-internal.ps6.canonical.com:8000/v1", "region": "prodstack6"}, {"id": "b23866fddba8415885b06c064c34b94b", "interface": "public", "region_id": "prodstack6", "url": "https://heat.ps6.canonical.com:8000/v1", "region": "prodstack6"}, {"id": "f84ae55197f94b8392a678f35c82ca26", "interface": "admin", "region_id": "prodstack6", "url": "https://heat-admin.ps6.canonical.com:8000/v1", "region": "prodstack6"}], "id": "3d4b59f7dab644b2b527e8e96b697545", "type": "cloudformation", "name": "heat-cfn"}, {"endpoints": [{"id": "2e0143334c6241169f45f1c11970c6bc", "interface": "public", "region_id": "prodstack6", "url": "https://heat.ps6.canonical.com:8004/v1/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "5e19c32243c04a3faf1e5f9ab900c260", "interface": "internal", "region_id": "prodstack6", "url": "https://heat-internal.ps6.canonical.com:8004/v1/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "b3fc5c88ec8543a691fec75726b86967", "interface": "admin", "region_id": "prodstack6", "url": "https://heat-admin.ps6.canonical.com:8004/v1/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}], "id": "43b926205044476b8093b18d8ce0a9e4", "type": "orchestration", "name": "heat"}, {"endpoints": [{"id": "a47569b96e5b4146a312e4673504557c", "interface": "public", "region_id": "prodstack6", "url": "https://glance.ps6.canonical.com:9292", "region": "prodstack6"}, {"id": "bba35c4ab04f4114a2a34e65568537bd", "interface": "internal", "region_id": "prodstack6", "url": "https://glance-internal.ps6.canonical.com:9292", "region": "prodstack6"}, {"id": "ef769f1117c74a62a279131486c89628", "interface": "admin", "region_id": "prodstack6", "url": "https://glance-admin.ps6.canonical.com:9292", "region": "prodstack6"}], "id": "49de724549524bd78e9cd46a4477226f", "type": "image", "name": "glance"}, {"endpoints": [{"id": "a1a41e9a1e2d42e5b6cd5380cd1e21bf", "interface": "admin", "region_id": "prodstack6", "url": "https://cinder-admin.ps6.canonical.com:8776/v3/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "d2309a99724b4111827482c68a832c0c", "interface": "public", "region_id": "prodstack6", "url": "https://cinder.ps6.canonical.com:8776/v3/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "f8a02e3949ff42afa772eb5e74dbef9f", "interface": "internal", "region_id": "prodstack6", "url": "https://cinder-internal.ps6.canonical.com:8776/v3/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}], "id": "5bf6578a631349e3af4bf36d7adb18e1", "type": "volumev3", "name": "cinderv3"}, {"endpoints": [{"id": "01d84128f36444e9b01549b86bd69116", "interface": "admin", "region_id": "prodstack6", "url": "https://barbican-admin.ps6.canonical.com:9312", "region": "prodstack6"}, {"id": "0ce4a8777e0b40a88f7fc0f77e34a605", "interface": "public", "region_id": "prodstack6", "url": "https://barbican.ps6.canonical.com:9311", "region": "prodstack6"}, {"id": "f507ba49e4a7435cb330234217c92449", "interface": "internal", "region_id": "prodstack6", "url": "https://barbican-internal.ps6.canonical.com:9311", "region": "prodstack6"}], "id": "62cb1c3d9f6c45979c13516a6b3ff114", "type": "key-manager", "name": "barbican"}, {"endpoints": [{"id": "3cb6121bd8f14da8aa2fba7be823a2b4", "interface": "internal", "region_id": "prodstack6", "url": "https://neutron-internal.ps6.canonical.com:9696", "region": "prodstack6"}, {"id": "46ba11d133fe4e8f9e8f9097ba737682", "interface": "admin", "region_id": "prodstack6", "url": "https://neutron-admin.ps6.canonical.com:9696", "region": "prodstack6"}, {"id": "d872eb6aa23d40009165aa3dcdce3948", "interface": "public", "region_id": "prodstack6", "url": "https://neutron.ps6.canonical.com:9696", "region": "prodstack6"}], "id": "759cb6fdfbc146dd8b9d1ba444c4b9db", "type": "network", "name": "neutron"}, {"endpoints": [{"id": "4349d565f72446da9699269f85df5e8b", "interface": "internal", "region_id": "prodstack6", "url": "https://manila-internal.ps6.canonical.com:8786/v2/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "a483dcc58f5e415e9ec739c94474e609", "interface": "public", "region_id": "prodstack6", "url": "https://manila.ps6.canonical.com:8786/v2/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "c1f14236723e42878562d8dd63d5a6a0", "interface": "admin", "region_id": "prodstack6", "url": "https://manila-admin.ps6.canonical.com:8786/v2/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}], "id": "93fc4008035946deb1f433c2dd905a5d", "type": "sharev2", "name": "manilav2"}, {"endpoints": [{"id": "0fa148793c7249c8b187b6b4ff425731", "interface": "internal", "region_id": "prodstack6", "url": "https://radosgw-internal.ps6.canonical.com:443/swift/v1/AUTH_e4b04ca58d734ed0aa29e306adad4f79/simplestreams/data", "region": "prodstack6"}, {"id": "555ade266a6b4bcc81b6e5abf607aec5", "interface": "public", "region_id": "prodstack6", "url": "https://radosgw.ps6.canonical.com:443/swift/v1/AUTH_e4b04ca58d734ed0aa29e306adad4f79/simplestreams/data", "region": "prodstack6"}, {"id": "7dad1a7b1552465686424fc014463173", "interface": "admin", "region_id": "prodstack6", "url": "https://radosgw-admin.ps6.canonical.com:443/swift/simplestreams/data", "region": "prodstack6"}], "id": "977dd359af1a4fcc91a9daf4dc33b0f3", "type": "product-streams", "name": "image-stream"}, {"endpoints": [{"id": "12d30eabcdec4831bd15273d55b1cbab", "interface": "internal", "region_id": "prodstack6", "url": "https://manila-internal.ps6.canonical.com:8786/v1/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "29d35b2b483346479f1ff1a13604d50e", "interface": "admin", "region_id": "prodstack6", "url": "https://manila-admin.ps6.canonical.com:8786/v1/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "4aa1422b8f5945d8aed9ba6a8d670e5c", "interface": "public", "region_id": "prodstack6", "url": "https://manila.ps6.canonical.com:8786/v1/bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}], "id": "ac5e4f28fa794cde99f1d7ffc1b664e5", "type": "share", "name": "manila"}, {"endpoints": [{"id": "c7db93d54a684d8caeae1d9e18a59118", "interface": "admin", "region_id": "prodstack6", "url": "https://nova-admin.ps6.canonical.com:8774/v2.1", "region": "prodstack6"}, {"id": "dd7a796f401b477f9f1b5bbc05747d8d", "interface": "public", "region_id": "prodstack6", "url": "https://nova.ps6.canonical.com:8774/v2.1", "region": "prodstack6"}, {"id": "e7ecb038d830462ea67b0b463af5e013", "interface": "internal", "region_id": "prodstack6", "url": "https://nova-internal.ps6.canonical.com:8774/v2.1", "region": "prodstack6"}], "id": "b4519af08e174d4a8333a2d14ac3ba3b", "type": "compute", "name": "nova"}, {"endpoints": [{"id": "02ef5b6154934ffd97d8b5b8e4d70d2a", "interface": "internal", "region_id": "prodstack6", "url": "https://radosgw-internal.ps6.canonical.com:443/swift/v1/AUTH_bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "2741abe526e94842a4fa801423ba1ef0", "interface": "public", "region_id": "prodstack6", "url": "https://radosgw.ps6.canonical.com:443/swift/v1/AUTH_bd8b3df3f03d43a0a9303b7c0434fdab", "region": "prodstack6"}, {"id": "3742f9406c604516933d6fd8c29e0880", "interface": "admin", "region_id": "prodstack6", "url": "https://radosgw-admin.ps6.canonical.com:443/swift", "region": "prodstack6"}], "id": "c7f07a7b3b3c408c96200dfd1d1a0f6f", "type": "object-store", "name": "swift"}, {"endpoints": [{"id": "06d4ed6c160a43f2b7fa7f80ad1dc709", "interface": "internal", "region_id": "prodstack6", "url": "https://designate-internal.ps6.canonical.com:9001", "region": "prodstack6"}, {"id": "1e240624a50c4ca0aaa6ef63cbc94f1b", "interface": "admin", "region_id": "prodstack6", "url": "https://designate-admin.ps6.canonical.com:9001", "region": "prodstack6"}, {"id": "f94d7d17997a43fd9c63b34c43301c6e", "interface": "public", "region_id": "prodstack6", "url": "https://designate.ps6.canonical.com:9001", "region": "prodstack6"}], "id": "cf82013d63844fedbe96bcacb6bd1fef", "type": "dns", "name": "designate"}, {"endpoints": [{"id": "4a688340be464710bfa60bf3f88f41c4", "interface": "admin", "region_id": "prodstack6", "url": "https://gnocchi-admin.ps6.canonical.com:8041", "region": "prodstack6"}, {"id": "a5a95506c96d4716adb4efc3ac9051be", "interface": "public", "region_id": "prodstack6", "url": "https://gnocchi.ps6.canonical.com:8041", "region": "prodstack6"}, {"id": "eebc17a086834f8fa8bb6b35c8061a8c", "interface": "internal", "region_id": "prodstack6", "url": "https://gnocchi-internal.ps6.canonical.com:8041", "region": "prodstack6"}], "id": "d10589e854a446a5b852593f33f170a7", "type": "metric", "name": "gnocchi"}, {"endpoints": [{"id": "08f66df28d0f47f3bec12f29e06d85ac", "interface": "admin", "region_id": "prodstack6", "url": "https://keystone-admin.ps6.canonical.com:35357/v3", "region": "prodstack6"}, {"id": "46d270b45ceb42db902f4d241afa6a70", "interface": "public", "region_id": "prodstack6", "url": "https://keystone.ps6.canonical.com:5000/v3", "region": "prodstack6"}, {"id": "a4addee11d9349cfa46ec6660dbad947", "interface": "internal", "region_id": "prodstack6", "url": "https://keystone-internal.ps6.canonical.com:5000/v3", "region": "prodstack6"}], "id": "deb38a775a9b4e87a8de9e3eed779882", "type": "identity", "name": "keystone"}, {"endpoints": [{"id": "18b4af5f40664babb94e884c6a53ccf3", "interface": "admin", "region_id": "prodstack6", "url": "https://octavia-admin.ps6.canonical.com:9876", "region": "prodstack6"}, {"id": "2b6f7ba7f9944ee1aebd6dccc5223b2d", "interface": "internal", "region_id": "prodstack6", "url": "https://octavia-internal.ps6.canonical.com:9876", "region": "prodstack6"}, {"id": "5e3012e9c79e4890be4d964b6208f5c6", "interface": "public", "region_id": "prodstack6", "url": "https://octavia.ps6.canonical.com:9876", "region": "prodstack6"}], "id": "e00337be20d54948b66a1c3109b885c6", "type": "load-balancer", "name": "octavia"}, {"endpoints": [{"id": "2d2942b35f3041389ad810f679d02f22", "interface": "public", "region_id": "prodstack6", "url": "https://placement.ps6.canonical.com:8778", "region": "prodstack6"}, {"id": "2e3beaac7ac14284b72e2592820ad725", "interface": "admin", "region_id": "prodstack6", "url": "https://placement-admin.ps6.canonical.com:8778", "region": "prodstack6"}, {"id": "91060f6df9ae444f81808adf40540d94", "interface": "internal", "region_id": "prodstack6", "url": "https://placement-internal.ps6.canonical.com:8778", "region": "prodstack6"}], "id": "edc6e37f154f4c0ab3dd4d52b82bf873", "type": "placement", "name": "placement"}]}} 393s REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1 -H "Accept: application/json" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}77409dfc836f8e5a0e6e445d35aa2daf605d4db8f2d36f3d6871602566ca0e5e" 393s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1 -H "Accept: application/json" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}77409dfc836f8e5a0e6e445d35aa2daf605d4db8f2d36f3d6871602566ca0e5e" 393s DEBUG (connectionpool:962) Starting new HTTPS connection (1): nova.ps6.canonical.com:8774 393s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1 HTTP/1.1" 302 0 393s RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Sun, 24 Mar 2024 16:49:14 GMT Keep-Alive: timeout=75, max=1000 Location: https://nova.ps6.canonical.com:8774/v2.1/ Server: Apache/2.4.52 (Ubuntu) x-compute-request-id: req-7a1cd479-0522-4e5d-bc7a-b13af873bd12 x-openstack-request-id: req-7a1cd479-0522-4e5d-bc7a-b13af873bd12 393s DEBUG (session:548) RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Sun, 24 Mar 2024 16:49:14 GMT Keep-Alive: timeout=75, max=1000 Location: https://nova.ps6.canonical.com:8774/v2.1/ Server: Apache/2.4.52 (Ubuntu) x-compute-request-id: req-7a1cd479-0522-4e5d-bc7a-b13af873bd12 x-openstack-request-id: req-7a1cd479-0522-4e5d-bc7a-b13af873bd12 393s RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged. 393s DEBUG (session:580) RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged. 393s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/ HTTP/1.1" 200 397 393s RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Sun, 24 Mar 2024 16:49:14 GMT Keep-Alive: timeout=75, max=999 OpenStack-API-Version: compute 2.1 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.1 x-compute-request-id: req-630ccb59-8d98-4762-877a-b30fd4d24651 x-openstack-request-id: req-630ccb59-8d98-4762-877a-b30fd4d24651 393s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Sun, 24 Mar 2024 16:49:14 GMT Keep-Alive: timeout=75, max=999 OpenStack-API-Version: compute 2.1 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.1 x-compute-request-id: req-630ccb59-8d98-4762-877a-b30fd4d24651 x-openstack-request-id: req-630ccb59-8d98-4762-877a-b30fd4d24651 393s RESP BODY: {"version": {"id": "v2.1", "status": "CURRENT", "version": "2.90", "min_version": "2.1", "updated": "2013-07-23T11:33:21Z", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/"}, {"rel": "describedby", "type": "text/html", "href": "http://docs.openstack.org/"}], "media-types": [{"base": "application/json", "type": "application/vnd.openstack.compute+json;version=2.1"}]}} 393s DEBUG (session:580) RESP BODY: {"version": {"id": "v2.1", "status": "CURRENT", "version": "2.90", "min_version": "2.1", "updated": "2013-07-23T11:33:21Z", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/"}, {"rel": "describedby", "type": "text/html", "href": "http://docs.openstack.org/"}], "media-types": [{"base": "application/json", "type": "application/vnd.openstack.compute+json;version=2.1"}]}} 393s GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-630ccb59-8d98-4762-877a-b30fd4d24651 393s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-630ccb59-8d98-4762-877a-b30fd4d24651 393s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader') 393s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader') 393s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken') 393s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth') 393s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password') 393s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token') 393s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password') 393s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth') 393s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP') 393s DEBUG (session:517) REQ: curl -g -i -X GET https://glance.ps6.canonical.com:9292/v2/images/943dd583-2042-4622-b4ce-bdf10ad153ac -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}77409dfc836f8e5a0e6e445d35aa2daf605d4db8f2d36f3d6871602566ca0e5e" -H "X-OpenStack-Nova-API-Version: 2.87" 393s DEBUG (connectionpool:962) Starting new HTTPS connection (1): glance.ps6.canonical.com:9292 393s DEBUG (connectionpool:429) https://glance.ps6.canonical.com:9292 "GET /v2/images/943dd583-2042-4622-b4ce-bdf10ad153ac HTTP/1.1" 200 1935 393s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 1935 Content-Type: application/json Date: Sun, 24 Mar 2024 16:49:14 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) X-Openstack-Request-Id: req-a8af0fb1-fb55-47ca-a051-21e9acde5df0 393s DEBUG (session:580) RESP BODY: {"base_image_ref": "09c3944a-cd0d-425d-b22f-cde7ec51d155", "boot_roles": "member,reader", "hw_cdrom_bus": "scsi", "hw_disk_bus": "virtio", "hw_machine_type": "virt", "hw_video_model": "virtio", "hw_vif_model": "virtio", "image_location": "snapshot", "image_state": "available", "image_type": "snapshot", "instance_uuid": "bc4d8474-2306-4932-a029-eb05e6aa0070", "owner_id": "bd8b3df3f03d43a0a9303b7c0434fdab", "owner_project_name": "prod-proposed-migration-arm64_project", "owner_specified.openstack.md5": "087a26f2222dab8516c553374a9d1b4d", "owner_specified.openstack.object": "images/adt/ubuntu-noble-arm64-server-20240201.img", "owner_specified.openstack.sha256": "095b278df09de76f01843de514daf3f8eb0a0cc67fee4b3491161913153619db", "owner_user_name": "prod-proposed-migration-arm64", "user_id": "369f50a481564a2c9433776a4ebd224d", "name": "adt/ubuntu-noble-arm64-server-20240324.img", "disk_format": "qcow2", "container_format": "bare", "visibility": "private", "size": 2340683776, "virtual_size": 21474836480, "status": "active", "checksum": "02217aaa63f3d49965efbdca847c5c0e", "protected": false, "min_ram": 0, "min_disk": 20, "owner": "bd8b3df3f03d43a0a9303b7c0434fdab", "os_hidden": false, "os_hash_algo": "sha512", "os_hash_value": "fe5802fc52ec80a7347f29b260d672bc687386dd19d42565cf2df8da873e45471382efffbf170f29d30990636735cf90a3d2d75240f91e8b686c49ccc9dc9b83", "id": "943dd583-2042-4622-b4ce-bdf10ad153ac", "created_at": "2024-03-24T04:06:45Z", "updated_at": "2024-03-24T04:07:10Z", "locations": [{"url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/943dd583-2042-4622-b4ce-bdf10ad153ac/snap", "metadata": {"store": "ceph"}}], "direct_url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/943dd583-2042-4622-b4ce-bdf10ad153ac/snap", "tags": [], "self": "/v2/images/943dd583-2042-4622-b4ce-bdf10ad153ac", "file": "/v2/images/943dd583-2042-4622-b4ce-bdf10ad153ac/file", "schema": "/v2/schemas/image", "stores": "ceph"} 393s DEBUG (session:936) GET call to image for https://glance.ps6.canonical.com:9292/v2/images/943dd583-2042-4622-b4ce-bdf10ad153ac used request id req-a8af0fb1-fb55-47ca-a051-21e9acde5df0 393s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}77409dfc836f8e5a0e6e445d35aa2daf605d4db8f2d36f3d6871602566ca0e5e" -H "X-OpenStack-Nova-API-Version: 2.87" 393s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/autopkgtest HTTP/1.1" 404 84 393s DEBUG (session:548) RESP: [404] Connection: Keep-Alive Content-Length: 84 Content-Type: application/json; charset=UTF-8 Date: Sun, 24 Mar 2024 16:49:14 GMT Keep-Alive: timeout=75, max=998 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-8e782f6a-b03c-4b93-a798-540802a252f6 x-openstack-request-id: req-8e782f6a-b03c-4b93-a798-540802a252f6 393s DEBUG (session:580) RESP BODY: {"itemNotFound": {"code": 404, "message": "Flavor autopkgtest could not be found."}} 393s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest used request id req-8e782f6a-b03c-4b93-a798-540802a252f6 393s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors?is_public=None -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}77409dfc836f8e5a0e6e445d35aa2daf605d4db8f2d36f3d6871602566ca0e5e" -H "X-OpenStack-Nova-API-Version: 2.87" 393s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors?is_public=None HTTP/1.1" 200 1739 393s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 1739 Content-Type: application/json Date: Sun, 24 Mar 2024 16:49:14 GMT Keep-Alive: timeout=75, max=997 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-f116973d-9a1e-43ca-b22d-1e84bd047bee x-openstack-request-id: req-f116973d-9a1e-43ca-b22d-1e84bd047bee 393s DEBUG (session:580) RESP BODY: {"flavors": [{"id": "062428d9-35a1-461f-a33a-38436ed516b4", "name": "autopkgtest-cpu8-ram16-disk160-arm64", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/062428d9-35a1-461f-a33a-38436ed516b4"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/062428d9-35a1-461f-a33a-38436ed516b4"}], "description": null}, {"id": "8d27c5f0-65c7-4018-b3f7-50463875ab09", "name": "autopkgtest", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/8d27c5f0-65c7-4018-b3f7-50463875ab09"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/8d27c5f0-65c7-4018-b3f7-50463875ab09"}], "description": null}, {"id": "8ebe34fb-1390-4cc7-bbe5-0d38c80f2fb4", "name": "autopkgtest-cpu2-ram4-disk20-arm64", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/8ebe34fb-1390-4cc7-bbe5-0d38c80f2fb4"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/8ebe34fb-1390-4cc7-bbe5-0d38c80f2fb4"}], "description": null}, {"id": "a8256f9e-53ee-4584-ad7f-60e088825b83", "name": "autopkgtest-big", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83"}], "description": null}, {"id": "cfc564ac-9f6e-4477-91c4-a89ccb4b744e", "name": "autopkgtest-cpu4-ram8-disk100-arm64", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/cfc564ac-9f6e-4477-91c4-a89ccb4b744e"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/cfc564ac-9f6e-4477-91c4-a89ccb4b744e"}], "description": null}]} 393s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors?is_public=None used request id req-f116973d-9a1e-43ca-b22d-1e84bd047bee 393s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors/8d27c5f0-65c7-4018-b3f7-50463875ab09 -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}77409dfc836f8e5a0e6e445d35aa2daf605d4db8f2d36f3d6871602566ca0e5e" -H "X-OpenStack-Nova-API-Version: 2.87" 393s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/8d27c5f0-65c7-4018-b3f7-50463875ab09 HTTP/1.1" 200 613 393s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 613 Content-Type: application/json Date: Sun, 24 Mar 2024 16:49:15 GMT Keep-Alive: timeout=75, max=996 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-3d22c311-2103-4c16-9507-4265c4d4e5f5 x-openstack-request-id: req-3d22c311-2103-4c16-9507-4265c4d4e5f5 393s DEBUG (session:580) RESP BODY: {"flavor": {"id": "8d27c5f0-65c7-4018-b3f7-50463875ab09", "name": "autopkgtest", "ram": 4096, "disk": 20, "swap": 0, "OS-FLV-EXT-DATA:ephemeral": 0, "OS-FLV-DISABLED:disabled": false, "vcpus": 2, "os-flavor-access:is_public": false, "rxtx_factor": 1.0, "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/8d27c5f0-65c7-4018-b3f7-50463875ab09"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/8d27c5f0-65c7-4018-b3f7-50463875ab09"}], "description": null, "extra_specs": {"aggregate_instance_extra_specs:commit": "builder-arm64", "hw_rng:allowed": "True"}}} 393s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/8d27c5f0-65c7-4018-b3f7-50463875ab09 used request id req-3d22c311-2103-4c16-9507-4265c4d4e5f5 393s DEBUG (session:517) REQ: curl -g -i -X POST https://nova.ps6.canonical.com:8774/v2.1/servers -H "Accept: application/json" -H "Content-Type: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}77409dfc836f8e5a0e6e445d35aa2daf605d4db8f2d36f3d6871602566ca0e5e" -H "X-OpenStack-Nova-API-Version: 2.87" -d '{"server": {"name": "adt-noble-arm64-cnvkit-20240324-164817-juju-7f2275-prod-proposed-migration-environment-3", "imageRef": "943dd583-2042-4622-b4ce-bdf10ad153ac", "flavorRef": "8d27c5f0-65c7-4018-b3f7-50463875ab09", "user_data": "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", "key_name": "testbed-juju-7f2275-prod-proposed-migration-environment-3", "min_count": 1, "max_count": 1, "security_groups": [{"name": "autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-13.secgroup"}], "networks": [{"uuid": "6ea4839c-9760-4b54-ab7d-70a6312667d1"}]}}' 393s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "POST /v2.1/servers HTTP/1.1" 403 115 393s DEBUG (session:548) RESP: [403] Connection: Keep-Alive Content-Length: 115 Content-Type: application/json; charset=UTF-8 Date: Sun, 24 Mar 2024 16:49:15 GMT Keep-Alive: timeout=75, max=995 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-114fb0d5-ebf6-40bc-8f3b-7b686982a0c8 x-openstack-request-id: req-114fb0d5-ebf6-40bc-8f3b-7b686982a0c8 393s DEBUG (session:580) RESP BODY: {"forbidden": {"code": 403, "message": "Quota exceeded for cores: Requested 2, but already used 140 of 140 cores"}} 393s DEBUG (session:936) POST call to compute for https://nova.ps6.canonical.com:8774/v2.1/servers used request id req-114fb0d5-ebf6-40bc-8f3b-7b686982a0c8 393s DEBUG (shell:822) Quota exceeded for cores: Requested 2, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-114fb0d5-ebf6-40bc-8f3b-7b686982a0c8) 393s Traceback (most recent call last): 393s File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 820, in main 393s OpenStackComputeShell().main(argv) 393s File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 742, in main 393s args.func(self.cs, args) 393s File "/usr/lib/python3/dist-packages/novaclient/v2/shell.py", line 971, in do_boot 393s server = cs.servers.create(*boot_args, **boot_kwargs) 393s File "/usr/lib/python3/dist-packages/novaclient/v2/servers.py", line 1477, in create 393s return self._boot(response_key, *boot_args, **boot_kwargs) 393s File "/usr/lib/python3/dist-packages/novaclient/v2/servers.py", line 836, in _boot 393s return self._create('/servers', body, response_key, 393s File "/usr/lib/python3/dist-packages/novaclient/base.py", line 363, in _create 393s resp, body = self.api.client.post(url, body=body) 393s File "/usr/lib/python3/dist-packages/keystoneauth1/adapter.py", line 392, in post 393s return self.request(url, 'POST', **kwargs) 393s File "/usr/lib/python3/dist-packages/novaclient/client.py", line 78, in request 393s raise exceptions.from_response(resp, body, url, method) 393s novaclient.exceptions.Forbidden: Quota exceeded for cores: Requested 2, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-114fb0d5-ebf6-40bc-8f3b-7b686982a0c8) 393s ERROR (Forbidden): Quota exceeded for cores: Requested 2, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-114fb0d5-ebf6-40bc-8f3b-7b686982a0c8) 396s autopkgtest [16:54:53]: testbed dpkg architecture: arm64 396s autopkgtest [16:54:53]: testbed apt version: 2.7.12 396s autopkgtest [16:54:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 396s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 397s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 397s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 397s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 397s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 397s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 397s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 397s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 397s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 397s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 397s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 397s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 397s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 399s Fetched 9847 kB in 2s (5960 kB/s) 399s Reading package lists... 402s Reading package lists... 402s Building dependency tree... 402s Reading state information... 402s Calculating upgrade... 403s The following packages will be REMOVED: 403s libssl3 403s The following NEW packages will be installed: 403s libssl3t64 403s The following packages have been kept back: 403s curl 403s The following packages will be upgraded: 403s openssl 403s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 403s Need to get 2777 kB of archives. 403s After this operation, 139 kB of additional disk space will be used. 403s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 403s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 404s Fetched 2777 kB in 1s (4121 kB/s) 404s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74819 files and directories currently installed.) 404s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 404s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 404s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 404s wget depends on libssl3 (>= 3.0.0). 404s u-boot-tools depends on libssl3 (>= 3.0.0). 404s tnftp depends on libssl3 (>= 3.0.0). 404s tcpdump depends on libssl3 (>= 3.0.0). 404s systemd-resolved depends on libssl3 (>= 3.0.0). 404s systemd depends on libssl3 (>= 3.0.0). 404s sudo depends on libssl3 (>= 3.0.0). 404s sbsigntool depends on libssl3 (>= 3.0.0). 404s rsync depends on libssl3 (>= 3.0.0). 404s python3-cryptography depends on libssl3 (>= 3.0.0). 404s openssh-server depends on libssl3 (>= 3.0.10). 404s openssh-client depends on libssl3 (>= 3.0.10). 404s mtd-utils depends on libssl3 (>= 3.0.0). 404s mokutil depends on libssl3 (>= 3.0.0). 404s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 404s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 404s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 404s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 404s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 404s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 404s libnvme1 depends on libssl3 (>= 3.0.0). 404s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 404s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 404s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 404s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 404s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 404s kmod depends on libssl3 (>= 3.0.0). 404s dhcpcd-base depends on libssl3 (>= 3.0.0). 404s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 404s 404s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74819 files and directories currently installed.) 404s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 404s Selecting previously unselected package libssl3t64:arm64. 404s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74808 files and directories currently installed.) 404s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 404s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 404s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 404s Setting up openssl (3.0.13-0ubuntu2) ... 404s Processing triggers for man-db (2.12.0-3) ... 405s Processing triggers for libc-bin (2.39-0ubuntu6) ... 405s Reading package lists... 406s Building dependency tree... 406s Reading state information... 406s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 407s sh: Attempting to set up Debian/Ubuntu apt sources automatically 407s sh: Distribution appears to be Ubuntu 407s Reading package lists... 408s Building dependency tree... 408s Reading state information... 408s eatmydata is already the newest version (131-1). 408s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 408s Reading package lists... 408s Building dependency tree... 408s Reading state information... 409s dbus is already the newest version (1.14.10-4ubuntu1). 409s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 409s Reading package lists... 409s Building dependency tree... 409s Reading state information... 409s rng-tools-debian is already the newest version (2.4). 409s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 410s Reading package lists... 410s Building dependency tree... 410s Reading state information... 410s The following packages will be REMOVED: 410s cloud-init* python3-configobj* python3-debconf* 410s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 410s After this operation, 3256 kB disk space will be freed. 410s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74821 files and directories currently installed.) 410s Removing cloud-init (24.1.2-0ubuntu1) ... 411s Removing python3-configobj (5.0.8-3) ... 411s Removing python3-debconf (1.5.86) ... 411s Processing triggers for man-db (2.12.0-3) ... 411s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74432 files and directories currently installed.) 411s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 412s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 412s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 412s invoke-rc.d: policy-rc.d denied execution of try-restart. 412s Reading package lists... 412s Building dependency tree... 412s Reading state information... 413s linux-generic is already the newest version (6.8.0-11.11+1). 413s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 413s Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 413s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 413s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 415s Fetched 255 kB in 1s (313 kB/s) 415s Reading package lists... 415s Reading package lists... 416s Building dependency tree... 416s Reading state information... 416s Calculating upgrade... 416s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 416s Reading package lists... 417s Building dependency tree... 417s Reading state information... 417s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 418s autopkgtest [16:55:15]: rebooting testbed after setup commands that affected boot 444s autopkgtest [16:55:41]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 447s autopkgtest [16:55:44]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 450s Get:1 http://ftpmaster.internal/ubuntu noble/universe cnvkit 0.9.10-1 (dsc) [2455 B] 450s Get:2 http://ftpmaster.internal/ubuntu noble/universe cnvkit 0.9.10-1 (tar) [23.7 MB] 450s Get:3 http://ftpmaster.internal/ubuntu noble/universe cnvkit 0.9.10-1 (diff) [17.4 kB] 450s gpgv: Signature made Fri Jan 5 15:50:03 2024 UTC 450s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 450s gpgv: issuer "tille@debian.org" 450s gpgv: Can't check signature: No public key 450s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-1.dsc: no acceptable signature found 451s autopkgtest [16:55:48]: testing package cnvkit version 0.9.10-1 451s autopkgtest [16:55:48]: build not needed 454s autopkgtest [16:55:51]: test run-unit-test: preparing testbed 458s Reading package lists... 458s Building dependency tree... 458s Reading state information... 458s Starting pkgProblemResolver with broken count: 0 458s Starting 2 pkgProblemResolver with broken count: 0 458s Done 459s The following additional packages will be installed: 459s blt cnvkit fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-extra 459s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 459s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 459s libharfbuzz0b libhts3 libhtscodecs2 libice6 libimagequant0 libjbig0 459s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 459s liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 459s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpoppler134 459s libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 459s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 459s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 459s libxrender1 libxslt1.1 libxss1 libxt6 poppler-utils python-matplotlib-data 459s python3-appdirs python3-biopython python3-brotli python3-cairo 459s python3-contourpy python3-cycler python3-dateutil python3-decorator 459s python3-fonttools python3-freetype python3-fs python3-importlib-metadata 459s python3-joblib python3-kiwisolver python3-lxml python3-lz4 459s python3-matplotlib python3-more-itertools python3-mpmath python3-networkx 459s python3-numpy python3-packaging python3-pandas python3-pandas-lib 459s python3-pil python3-pil.imagetk python3-pomegranate python3-pyfaidx 459s python3-pysam python3-reportlab python3-rlpycairo python3-scipy 459s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 459s python3-tk python3-ufolib2 python3-unicodedata2 python3-zipp python3.11 459s python3.11-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 459s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 459s xfonts-encodings xfonts-utils xml-core zip 459s Suggested packages: 459s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 459s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 459s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 459s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 459s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 459s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 459s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 459s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 459s texlive-latex-extra python-mpmath-doc python3-gmpy2 python-networkx-doc 459s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python3-dev 459s python3-pytest python-pandas-doc python3-statsmodels python-pil-doc 459s python-pomegranate-doc pdf-viewer python3-egenix-mxtexttools 459s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 459s python-sklearn-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 459s python3.11-venv python3.11-doc binfmt-support elpa-ess r-doc-info 459s | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-s4vectors 459s r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings 459s r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 459s r-bioc-annotate r-cran-runit sgml-base-doc debhelper 459s Recommended packages: 459s javascript-common poppler-data python-biopython-doc ncbi-blast+ 459s python3-pytest python3-simplejson python3-psutil python3-bs4 459s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 459s python3-odf python3-openpyxl python3-tables python3-olefile g++ 459s | c++-compiler isympy-common r-recommended r-base-dev r-doc-html 459s libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils 459s x11-xserver-utils 459s The following NEW packages will be installed: 459s autopkgtest-satdep blt cnvkit fontconfig fontconfig-config fonts-dejavu-core 459s fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 459s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 459s libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 459s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 459s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 459s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 459s libpoppler134 libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 459s libraqm0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 459s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 459s libxft2 libxrender1 libxslt1.1 libxss1 libxt6 poppler-utils 459s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 459s python3-cairo python3-contourpy python3-cycler python3-dateutil 459s python3-decorator python3-fonttools python3-freetype python3-fs 459s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 459s python3-lz4 python3-matplotlib python3-more-itertools python3-mpmath 459s python3-networkx python3-numpy python3-packaging python3-pandas 459s python3-pandas-lib python3-pil python3-pil.imagetk python3-pomegranate 459s python3-pyfaidx python3-pysam python3-reportlab python3-rlpycairo 459s python3-scipy python3-sklearn python3-sklearn-lib python3-sympy 459s python3-threadpoolctl python3-tk python3-ufolib2 python3-unicodedata2 459s python3-zipp python3.11 python3.11-minimal r-base-core r-bioc-biocgenerics 459s r-bioc-dnacopy sgml-base tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib 459s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 459s 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. 459s Need to get 166 MB/166 MB of archives. 459s After this operation, 731 MB of additional disk space will be used. 459s Get:1 /tmp/autopkgtest.HFUjWE/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 459s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 459s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 460s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 460s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 460s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 460s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 460s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 460s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 460s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 460s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 460s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 460s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 460s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 460s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 460s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 460s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 460s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 460s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 460s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.14-1 [767 kB] 460s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] 460s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] 460s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 460s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 460s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 460s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 460s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB] 460s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] 460s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 460s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 460s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 460s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 460s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 460s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 460s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 460s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 460s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 460s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 460s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 460s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 460s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 460s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 460s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 460s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 460s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 460s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 460s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 460s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 460s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 460s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 460s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 460s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 460s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 460s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 460s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 460s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 460s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 460s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 460s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 460s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 460s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB] 460s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 460s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 460s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB] 460s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B] 460s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB] 460s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 461s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 461s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 461s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 461s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 461s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB] 461s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 461s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] 461s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.39-0exp1 [166 kB] 461s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] 461s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB] 461s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1 [362 kB] 461s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 461s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB] 461s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-2 [48.5 kB] 461s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 461s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] 461s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] 461s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 462s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 462s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-joblib all 1.3.2-1 [207 kB] 462s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 462s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pomegranate arm64 0.14.8-4 [3885 kB] 462s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 python3-more-itertools all 10.2.0-1 [52.9 kB] 462s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 python3-zipp all 1.0.0-6 [6090 B] 462s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 python3-importlib-metadata all 4.12.0-1 [17.8 kB] 462s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyfaidx all 0.8.1.1-1 [29.6 kB] 462s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 462s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 462s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 462s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 462s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sklearn-lib arm64 1.4.1.post1+dfsg-1 [6663 kB] 462s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sklearn all 1.4.1.post1+dfsg-1 [2261 kB] 462s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 462s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 462s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 462s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 462s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 462s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 462s Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 462s Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 462s Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 462s Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 463s Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 463s Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 463s Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 463s Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 463s Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 463s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 464s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocgenerics all 0.48.1-2 [595 kB] 464s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-dnacopy arm64 1.76.0-1 [379 kB] 464s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 cnvkit arm64 0.9.10-1 [20.5 MB] 464s Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 libpoppler134 arm64 24.02.0-1ubuntu2 [1072 kB] 464s Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 poppler-utils arm64 24.02.0-1ubuntu2 [202 kB] 465s Preconfiguring packages ... 465s Fetched 166 MB in 6s (29.8 MB/s) 466s Selecting previously unselected package libpython3.11-minimal:arm64. 466s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74377 files and directories currently installed.) 466s Preparing to unpack .../000-libpython3.11-minimal_3.11.8-1_arm64.deb ... 466s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 466s Selecting previously unselected package python3.11-minimal. 466s Preparing to unpack .../001-python3.11-minimal_3.11.8-1_arm64.deb ... 466s Unpacking python3.11-minimal (3.11.8-1) ... 466s Selecting previously unselected package sgml-base. 466s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 466s Unpacking sgml-base (1.31) ... 466s Selecting previously unselected package libpython3.11-stdlib:arm64. 466s Preparing to unpack .../003-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 466s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 466s Selecting previously unselected package python3.11. 466s Preparing to unpack .../004-python3.11_3.11.8-1_arm64.deb ... 466s Unpacking python3.11 (3.11.8-1) ... 466s Selecting previously unselected package libtcl8.6:arm64. 466s Preparing to unpack .../005-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 466s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 466s Selecting previously unselected package fonts-dejavu-mono. 466s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 466s Unpacking fonts-dejavu-mono (2.37-8) ... 466s Selecting previously unselected package fonts-dejavu-core. 466s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 466s Unpacking fonts-dejavu-core (2.37-8) ... 466s Selecting previously unselected package libfontenc1:arm64. 466s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1_arm64.deb ... 466s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 466s Selecting previously unselected package x11-common. 466s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu2_all.deb ... 466s Unpacking x11-common (1:7.7+23ubuntu2) ... 466s Selecting previously unselected package xfonts-encodings. 466s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 466s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 466s Selecting previously unselected package xfonts-utils. 466s Preparing to unpack .../011-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 466s Unpacking xfonts-utils (1:7.7+6build2) ... 466s Selecting previously unselected package fonts-urw-base35. 466s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 466s Unpacking fonts-urw-base35 (20200910-8) ... 466s Selecting previously unselected package fontconfig-config. 466s Preparing to unpack .../013-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 467s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 467s Selecting previously unselected package libfontconfig1:arm64. 467s Preparing to unpack .../014-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 467s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 467s Selecting previously unselected package libxrender1:arm64. 467s Preparing to unpack .../015-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 467s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 467s Selecting previously unselected package libxft2:arm64. 467s Preparing to unpack .../016-libxft2_2.3.6-1_arm64.deb ... 467s Unpacking libxft2:arm64 (2.3.6-1) ... 467s Selecting previously unselected package libxss1:arm64. 467s Preparing to unpack .../017-libxss1_1%3a1.2.3-1build2_arm64.deb ... 467s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 467s Selecting previously unselected package libtk8.6:arm64. 467s Preparing to unpack .../018-libtk8.6_8.6.14-1_arm64.deb ... 467s Unpacking libtk8.6:arm64 (8.6.14-1) ... 467s Selecting previously unselected package tk8.6-blt2.5. 467s Preparing to unpack .../019-tk8.6-blt2.5_2.5.3+dfsg-7_arm64.deb ... 467s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... 467s Selecting previously unselected package blt. 467s Preparing to unpack .../020-blt_2.5.3+dfsg-7_arm64.deb ... 467s Unpacking blt (2.5.3+dfsg-7) ... 467s Selecting previously unselected package libblas3:arm64. 467s Preparing to unpack .../021-libblas3_3.12.0-3_arm64.deb ... 467s Unpacking libblas3:arm64 (3.12.0-3) ... 467s Selecting previously unselected package libgfortran5:arm64. 467s Preparing to unpack .../022-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 467s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 467s Selecting previously unselected package liblapack3:arm64. 467s Preparing to unpack .../023-liblapack3_3.12.0-3_arm64.deb ... 467s Unpacking liblapack3:arm64 (3.12.0-3) ... 467s Selecting previously unselected package python3-numpy. 467s Preparing to unpack .../024-python3-numpy_1%3a1.24.2-2_arm64.deb ... 467s Unpacking python3-numpy (1:1.24.2-2) ... 468s Selecting previously unselected package python3-tk:arm64. 468s Preparing to unpack .../025-python3-tk_3.11.5-1_arm64.deb ... 468s Unpacking python3-tk:arm64 (3.11.5-1) ... 468s Selecting previously unselected package python3-pil.imagetk:arm64. 468s Preparing to unpack .../026-python3-pil.imagetk_10.2.0-1_arm64.deb ... 468s Unpacking python3-pil.imagetk:arm64 (10.2.0-1) ... 468s Selecting previously unselected package libgomp1:arm64. 468s Preparing to unpack .../027-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 468s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 468s Selecting previously unselected package libimagequant0:arm64. 468s Preparing to unpack .../028-libimagequant0_2.18.0-1_arm64.deb ... 468s Unpacking libimagequant0:arm64 (2.18.0-1) ... 468s Selecting previously unselected package libjpeg-turbo8:arm64. 468s Preparing to unpack .../029-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 468s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 468s Selecting previously unselected package libjpeg8:arm64. 468s Preparing to unpack .../030-libjpeg8_8c-2ubuntu11_arm64.deb ... 468s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 468s Selecting previously unselected package liblcms2-2:arm64. 468s Preparing to unpack .../031-liblcms2-2_2.14-2_arm64.deb ... 468s Unpacking liblcms2-2:arm64 (2.14-2) ... 468s Selecting previously unselected package libopenjp2-7:arm64. 468s Preparing to unpack .../032-libopenjp2-7_2.5.0-2_arm64.deb ... 468s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 468s Selecting previously unselected package libgraphite2-3:arm64. 468s Preparing to unpack .../033-libgraphite2-3_1.3.14-2_arm64.deb ... 468s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 468s Selecting previously unselected package libharfbuzz0b:arm64. 468s Preparing to unpack .../034-libharfbuzz0b_8.3.0-2_arm64.deb ... 468s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 468s Selecting previously unselected package libraqm0:arm64. 468s Preparing to unpack .../035-libraqm0_0.10.1-1_arm64.deb ... 468s Unpacking libraqm0:arm64 (0.10.1-1) ... 468s Selecting previously unselected package libdeflate0:arm64. 468s Preparing to unpack .../036-libdeflate0_1.19-1_arm64.deb ... 468s Unpacking libdeflate0:arm64 (1.19-1) ... 468s Selecting previously unselected package libjbig0:arm64. 468s Preparing to unpack .../037-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 468s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 468s Selecting previously unselected package liblerc4:arm64. 468s Preparing to unpack .../038-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 468s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 468s Selecting previously unselected package libsharpyuv0:arm64. 468s Preparing to unpack .../039-libsharpyuv0_1.3.2-0.4_arm64.deb ... 468s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 468s Selecting previously unselected package libwebp7:arm64. 468s Preparing to unpack .../040-libwebp7_1.3.2-0.4_arm64.deb ... 468s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 468s Selecting previously unselected package libtiff6:arm64. 468s Preparing to unpack .../041-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 468s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 468s Selecting previously unselected package libwebpdemux2:arm64. 468s Preparing to unpack .../042-libwebpdemux2_1.3.2-0.4_arm64.deb ... 468s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 468s Selecting previously unselected package libwebpmux3:arm64. 468s Preparing to unpack .../043-libwebpmux3_1.3.2-0.4_arm64.deb ... 468s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 468s Selecting previously unselected package python3-pil:arm64. 468s Preparing to unpack .../044-python3-pil_10.2.0-1_arm64.deb ... 468s Unpacking python3-pil:arm64 (10.2.0-1) ... 468s Selecting previously unselected package libpixman-1-0:arm64. 468s Preparing to unpack .../045-libpixman-1-0_0.42.2-1_arm64.deb ... 468s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 468s Selecting previously unselected package libxcb-render0:arm64. 468s Preparing to unpack .../046-libxcb-render0_1.15-1_arm64.deb ... 468s Unpacking libxcb-render0:arm64 (1.15-1) ... 468s Selecting previously unselected package libxcb-shm0:arm64. 468s Preparing to unpack .../047-libxcb-shm0_1.15-1_arm64.deb ... 468s Unpacking libxcb-shm0:arm64 (1.15-1) ... 468s Selecting previously unselected package libcairo2:arm64. 468s Preparing to unpack .../048-libcairo2_1.18.0-1_arm64.deb ... 468s Unpacking libcairo2:arm64 (1.18.0-1) ... 468s Selecting previously unselected package python3-cairo. 468s Preparing to unpack .../049-python3-cairo_1.25.1-2_arm64.deb ... 468s Unpacking python3-cairo (1.25.1-2) ... 468s Selecting previously unselected package python3-freetype. 468s Preparing to unpack .../050-python3-freetype_2.4.0-1_all.deb ... 468s Unpacking python3-freetype (2.4.0-1) ... 468s Selecting previously unselected package python3-rlpycairo. 468s 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previously unselected package libjs-jquery. 469s Preparing to unpack .../057-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 469s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 469s Selecting previously unselected package libjs-jquery-ui. 469s Preparing to unpack .../058-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 469s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 469s Selecting previously unselected package fonts-lyx. 469s Preparing to unpack .../059-fonts-lyx_2.4.0~RC3-1_all.deb ... 469s Unpacking fonts-lyx (2.4.0~RC3-1) ... 469s Selecting previously unselected package python-matplotlib-data. 469s Preparing to unpack .../060-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ... 469s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ... 469s Selecting previously unselected package python3-dateutil. 469s Preparing to unpack .../061-python3-dateutil_2.8.2-3_all.deb ... 469s Unpacking python3-dateutil (2.8.2-3) ... 469s Selecting previously unselected package python3-contourpy. 469s Preparing to unpack .../062-python3-contourpy_1.0.7-1build2_arm64.deb ... 469s Unpacking python3-contourpy (1.0.7-1build2) ... 469s Selecting previously unselected package python3-cycler. 469s Preparing to unpack .../063-python3-cycler_0.11.0-2_all.deb ... 469s Unpacking python3-cycler (0.11.0-2) ... 469s Selecting previously unselected package python3-brotli. 469s Preparing to unpack .../064-python3-brotli_1.1.0-2_arm64.deb ... 469s Unpacking python3-brotli (1.1.0-2) ... 469s Selecting previously unselected package python3-decorator. 469s Preparing to unpack .../065-python3-decorator_5.1.1-5_all.deb ... 469s Unpacking python3-decorator (5.1.1-5) ... 469s Selecting previously unselected package liblbfgsb0:arm64. 469s Preparing to unpack .../066-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 469s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 469s Selecting previously unselected package python3-scipy. 469s Preparing to unpack .../067-python3-scipy_1.11.4-6_arm64.deb ... 469s Unpacking python3-scipy 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python3-fonttools (4.46.0-1) ... 471s Selecting previously unselected package python3-kiwisolver. 471s Preparing to unpack .../079-python3-kiwisolver_1.4.4-2_arm64.deb ... 471s Unpacking python3-kiwisolver (1.4.4-2) ... 471s Selecting previously unselected package python3-packaging. 471s Preparing to unpack .../080-python3-packaging_23.2-1_all.deb ... 471s Unpacking python3-packaging (23.2-1) ... 471s Selecting previously unselected package libqhull-r8.0:arm64. 471s Preparing to unpack .../081-libqhull-r8.0_2020.2-6_arm64.deb ... 471s Unpacking libqhull-r8.0:arm64 (2020.2-6) ... 471s Selecting previously unselected package python3-matplotlib. 471s Preparing to unpack .../082-python3-matplotlib_3.6.3-1ubuntu3_arm64.deb ... 471s Unpacking python3-matplotlib (3.6.3-1ubuntu3) ... 471s Selecting previously unselected package python3-pandas-lib:arm64. 471s Preparing to unpack .../083-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 471s Unpacking python3-pandas-lib:arm64 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previously unselected package python3-zipp. 472s Preparing to unpack .../089-python3-zipp_1.0.0-6_all.deb ... 472s Unpacking python3-zipp (1.0.0-6) ... 472s Selecting previously unselected package python3-importlib-metadata. 472s Preparing to unpack .../090-python3-importlib-metadata_4.12.0-1_all.deb ... 472s Unpacking python3-importlib-metadata (4.12.0-1) ... 472s Selecting previously unselected package python3-pyfaidx. 472s Preparing to unpack .../091-python3-pyfaidx_0.8.1.1-1_all.deb ... 472s Unpacking python3-pyfaidx (0.8.1.1-1) ... 472s Selecting previously unselected package libhtscodecs2:arm64. 472s Preparing to unpack .../092-libhtscodecs2_1.6.0-1_arm64.deb ... 472s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 472s Selecting previously unselected package libhts3:arm64. 472s Preparing to unpack .../093-libhts3_1.18+ds-1_arm64.deb ... 472s Unpacking libhts3:arm64 (1.18+ds-1) ... 472s Selecting previously unselected package python3-pysam. 472s Preparing to unpack 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cnvkit. 473s Preparing to unpack .../116-cnvkit_0.9.10-1_arm64.deb ... 473s Unpacking cnvkit (0.9.10-1) ... 474s Selecting previously unselected package libpoppler134:arm64. 474s Preparing to unpack .../117-libpoppler134_24.02.0-1ubuntu2_arm64.deb ... 474s Unpacking libpoppler134:arm64 (24.02.0-1ubuntu2) ... 474s Selecting previously unselected package poppler-utils. 474s Preparing to unpack .../118-poppler-utils_24.02.0-1ubuntu2_arm64.deb ... 474s Unpacking poppler-utils (24.02.0-1ubuntu2) ... 474s Selecting previously unselected package autopkgtest-satdep. 474s Preparing to unpack .../119-1-autopkgtest-satdep.deb ... 474s Unpacking autopkgtest-satdep (0) ... 474s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 474s Setting up python3-more-itertools (10.2.0-1) ... 474s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 474s Setting up liblcms2-2:arm64 (2.14-2) ... 474s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 474s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 474s Setting up libpaper1:arm64 (1.1.29) ... 475s 475s Creating config file /etc/papersize with new version 475s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 475s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 475s Setting up libdatrie1:arm64 (0.2.13-3) ... 475s Setting up python3-joblib (1.3.2-1) ... 475s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 475s Setting up libxcb-render0:arm64 (1.15-1) ... 475s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 475s Setting up fonts-lyx (2.4.0~RC3-1) ... 475s Setting up unzip (6.0-28ubuntu3) ... 475s Setting up python3-threadpoolctl (3.1.0-1) ... 475s Setting up x11-common (1:7.7+23ubuntu2) ... 476s Setting up libdeflate0:arm64 (1.19-1) ... 476s Setting up libqhull-r8.0:arm64 (2020.2-6) ... 476s Setting up libxcb-shm0:arm64 (1.15-1) ... 476s Setting up libpaper-utils (1.1.29) ... 476s Setting up python3-zipp (1.0.0-6) ... 476s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 476s Setting up python3-freetype (2.4.0-1) ... 476s Setting up python3-networkx (2.8.8-1ubuntu1) ... 477s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 477s "graph [edge [ source u'u\4200' target u'u\4200' ] " 477s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 477s + "node [ id u'u\4200' label b ] ]" 477s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 477s Setting up unicode-data (15.1.0-1) ... 477s Setting up python3-decorator (5.1.1-5) ... 477s Setting up zip (3.0-13) ... 477s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 477s Setting up libblas3:arm64 (3.12.0-3) ... 477s 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 477s Setting up python3-packaging (23.2-1) ... 477s Setting up python3-brotli (1.1.0-2) ... 477s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 477s Setting up python3-cycler (0.11.0-2) ... 477s Setting up libimagequant0:arm64 (2.18.0-1) ... 477s Setting up fonts-dejavu-mono (2.37-8) ... 477s Setting up python3-kiwisolver (1.4.4-2) ... 478s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 478s Setting up fonts-dejavu-core (2.37-8) ... 478s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 478s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 478s Setting up libwebp7:arm64 (1.3.2-0.4) ... 478s Setting up fonts-dejavu-extra (2.37-8) ... 478s Setting up libxslt1.1:arm64 (1.1.39-0exp1) ... 478s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 478s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 478s Setting up libthai-data (0.1.29-2) ... 478s Setting up python3-dateutil (2.8.2-3) ... 478s Setting up sgml-base (1.31) ... 478s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 478s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 478s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 478s Setting up python3-mpmath (1.2.1-3) ... 478s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 478s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 478s Setting up python3-appdirs (1.4.4-4) ... 478s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 478s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 478s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 478s Setting up python3.11-minimal (3.11.8-1) ... 479s Setting up python3-sympy (1.12-7) ... 484s Setting up libice6:arm64 (2:1.0.10-1build2) ... 484s Setting up liblapack3:arm64 (3.12.0-3) ... 484s 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 484s Setting up libhts3:arm64 (1.18+ds-1) ... 484s Setting up python3-pysam (0.22.0+ds-1) ... 484s Setting up python3-importlib-metadata (4.12.0-1) ... 484s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 484s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 484s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 484s Setting up xfonts-utils (1:7.7+6build2) ... 484s Setting up python3-fs (2.4.16-3) ... 485s Setting up libthai0:arm64 (0.1.29-2) ... 485s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 485s Setting up libraqm0:arm64 (0.10.1-1) ... 485s Setting up python3-lxml:arm64 (5.1.0-1) ... 485s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 485s Setting up xml-core (0.19) ... 485s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 485s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 485s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 485s Setting up python3-pyfaidx (0.8.1.1-1) ... 485s Setting up python3.11 (3.11.8-1) ... 486s Setting up fontconfig (2.15.0-1ubuntu1) ... 488s Regenerating fonts cache... done. 488s Setting up libxft2:arm64 (2.3.6-1) ... 488s Setting up libpoppler134:arm64 (24.02.0-1ubuntu2) ... 488s Setting up libtk8.6:arm64 (8.6.14-1) ... 488s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 488s Setting up fonts-urw-base35 (20200910-8) ... 488s Setting up libcairo2:arm64 (1.18.0-1) ... 488s Setting up python3-pil:arm64 (10.2.0-1) ... 489s Setting up libxt6:arm64 (1:1.2.1-1.1) ... 489s Setting up python3-numpy (1:1.24.2-2) ... 490s Setting up python3-contourpy (1.0.7-1build2) ... 490s Setting up poppler-utils (24.02.0-1ubuntu2) ... 490s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 490s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 490s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 490s Setting up python3-scipy (1.11.4-6) ... 493s Setting up python3-cairo (1.25.1-2) ... 493s Setting up blt (2.5.3+dfsg-7) ... 493s Setting up python3-pomegranate (0.14.8-4) ... 493s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 493s Setting up python3-sklearn-lib:arm64 (1.4.1.post1+dfsg-1) ... 493s Setting up python3-tk:arm64 (3.11.5-1) ... 494s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 497s Setting up python3-pil.imagetk:arm64 (10.2.0-1) ... 497s Setting up python3-rlpycairo (0.3.0-3) ... 498s Setting up r-base-core (4.3.2-1build1) ... 498s 498s Creating config file /etc/R/Renviron with new version 498s Setting up python3-sklearn (1.4.1.post1+dfsg-1) ... 500s Setting up python3-reportlab (4.1.0-1) ... 501s Setting up r-bioc-biocgenerics (0.48.1-2) ... 501s Setting up r-bioc-dnacopy (1.76.0-1) ... 501s Setting up python3-fonttools (4.46.0-1) ... 501s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 501s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 503s Processing triggers for libc-bin (2.39-0ubuntu6) ... 503s Processing triggers for systemd (255.2-3ubuntu2) ... 503s Processing triggers for man-db (2.12.0-3) ... 504s Processing triggers for install-info (7.1-3) ... 504s Processing triggers for sgml-base (1.31) ... 504s Setting up w3c-sgml-lib (1.3-3) ... 527s Setting up python3-biopython (1.81+dfsg-3) ... 528s Setting up cnvkit (0.9.10-1) ... 528s Setting up autopkgtest-satdep (0) ... 533s (Reading database ... 89886 files and directories currently installed.) 533s Removing autopkgtest-satdep (0) ... 534s autopkgtest [16:57:11]: test run-unit-test: [----------------------- 534s cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/ 538s Created directory build/ 538s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 538s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 538s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 538s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 538s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 538s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 538s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 538s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 538s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 539s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 541s Number of target and antitarget files: 3, 3 541s No FASTA reference genome provided; skipping GC, RM calculations 541s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 541s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 541s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 541s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 541s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 541s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 541s Loading build/p2-20_5.targetcoverage.cnn 541s Correcting for GC bias... 541s Correcting for density bias... 541s Loading build/p2-5_5.targetcoverage.cnn 541s Correcting for GC bias... 541s Correcting for density bias... 541s Loading build/p2-9_5.targetcoverage.cnn 541s Correcting for GC bias... 542s Correcting for density bias... 542s Loading build/p2-20_5.antitargetcoverage.cnn 542s Correcting for GC bias... 542s Loading build/p2-5_5.antitargetcoverage.cnn 542s Correcting for GC bias... 542s Loading build/p2-9_5.antitargetcoverage.cnn 542s Correcting for GC bias... 542s Calculating average bin coverages 548s Calculating bin spreads 549s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 550s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 550s " chr1:2435319-2436685 log2=-0.709 spread=0.503 550s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 550s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 550s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 550s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 550s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 550s " chr1:120611883-120612051 log2=0.070 spread=0.050 550s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 550s " chr1:156842391-156842479 log2=-0.398 spread=0.290 550s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 550s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 550s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 550s " chr1:183481886-183481951 log2=-0.040 spread=0.119 550s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 550s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 550s " chr1:243800859-243801066 log2=0.023 spread=0.063 550s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 550s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 550s " chr2:25536716-25536891 log2=0.702 spread=0.033 550s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 550s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 550s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 550s REL chr2:61108881-61109061 log2=1.026 spread=0.559 550s " chr2:61128072-61128256 log2=0.115 spread=0.173 550s " chr2:61145275-61145462 log2=0.014 spread=0.099 550s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 550s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 550s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 550s " chr2:128095237-128095425 log2=0.215 spread=0.212 550s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 550s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 550s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 550s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 550s " chr3:97160189-97160367 log2=-0.050 spread=0.191 550s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 550s " chr3:142286854-142287031 log2=-0.076 spread=0.116 550s GAK chr4:896278-896357 log2=-1.505 spread=1.261 550s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 550s " chr4:1803044-1803507 log2=-0.073 spread=0.117 550s " chr4:1808792-1809022 log2=0.252 spread=0.108 550s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 550s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 550s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 550s " chr4:178514600-178514725 log2=-0.098 spread=0.096 550s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 550s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 550s " chr5:1295312-1295381 log2=-0.690 spread=0.462 550s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 550s " chr5:25519857-25520034 log2=-0.015 spread=0.095 550s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 550s " chr5:38962338-38962525 log2=0.005 spread=0.019 550s " chr5:38966685-38966862 log2=0.006 spread=0.165 550s " chr5:38978620-38978763 log2=0.040 spread=0.030 550s " chr5:39074133-39074327 log2=-0.158 spread=0.139 550s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 550s " chr5:51030131-51030313 log2=-0.034 spread=0.192 550s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 550s " chr5:56168412-56168590 log2=0.479 spread=0.038 550s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 550s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 550s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 550s " chr5:86637023-86637168 log2=0.054 spread=0.111 550s " chr5:86642414-86642592 log2=0.254 spread=0.162 550s " chr5:86648912-86649096 log2=0.092 spread=0.062 550s " chr5:86670598-86670778 log2=0.222 spread=0.198 550s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 550s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 550s APC chr5:112101965-112102138 log2=0.104 spread=0.217 550s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 550s " chr5:170837567-170837631 log2=0.085 spread=0.349 550s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 550s " chr5:180046203-180046404 log2=-1.531 spread=0.722 550s " chr5:180076418-180076603 log2=-2.224 spread=1.416 550s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 550s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 550s " chr6:31939599-31940313 log2=-19.582 spread=0.181 550s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 550s " chr6:31946632-31946824 log2=-20.052 spread=0.088 550s " chr6:31947142-31947366 log2=-20.114 spread=0.066 550s " chr6:31948176-31948360 log2=-19.982 spread=0.149 550s " chr6:31948382-31948612 log2=-19.757 spread=0.165 550s " chr6:31948730-31949253 log2=-20.048 spread=0.014 550s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 550s " chr6:32164046-32164227 log2=-19.755 spread=0.189 550s " chr6:32164652-32164888 log2=-19.984 spread=0.154 550s " chr6:32165021-32165403 log2=-19.625 spread=0.196 550s " chr6:32166163-32166545 log2=-20.043 spread=0.072 550s " chr6:32166648-32166962 log2=-3.514 spread=5.742 550s " chr6:32168554-32168821 log2=-19.601 spread=0.197 550s " chr6:32168844-32169306 log2=-19.683 spread=0.166 550s " chr6:32169801-32170391 log2=-19.405 spread=0.205 550s " chr6:32171492-32171691 log2=-20.095 spread=0.101 550s " chr6:32171861-32172198 log2=-3.141 spread=7.288 550s " chr6:32178478-32178749 log2=-19.927 spread=0.164 550s " chr6:32180197-32180441 log2=-10.902 spread=9.532 550s " chr6:32180544-32180722 log2=-19.675 spread=0.186 550s " chr6:32180857-32181062 log2=-19.562 spread=0.227 550s " chr6:32181411-32181646 log2=-19.966 spread=0.171 550s " chr6:32181832-32182066 log2=-19.961 spread=0.172 550s " chr6:32182948-32183194 log2=-19.935 spread=0.168 550s " chr6:32184667-32185079 log2=-19.923 spread=0.165 550s " chr6:32185720-32185919 log2=-19.707 spread=0.197 550s " chr6:32187317-32187601 log2=-19.765 spread=0.173 550s " chr6:32187871-32188094 log2=-19.660 spread=0.188 550s " chr6:32188127-32188451 log2=-19.622 spread=0.169 550s " chr6:32188481-32188693 log2=-19.902 spread=0.132 550s " chr6:32188704-32189133 log2=-19.501 spread=0.193 550s " chr6:32190258-32190616 log2=-19.570 spread=0.209 550s " chr6:32190724-32190908 log2=-19.540 spread=0.232 550s " chr6:32191570-32191668 log2=-19.773 spread=0.178 550s " chr6:32191676-32191753 log2=-19.374 spread=0.201 550s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 550s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 550s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 550s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 550s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 550s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 550s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 550s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 550s " chr6:128316545-128316699 log2=-0.070 spread=0.050 550s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 550s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 550s " chr6:157099442-157099991 log2=-0.846 spread=0.504 550s " chr6:157100042-157100634 log2=-1.570 spread=0.825 550s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 550s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 550s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 550s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 550s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 550s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 550s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 550s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 550s " chr7:98491365-98491541 log2=0.209 spread=0.153 550s " chr7:98493314-98493496 log2=0.389 spread=0.207 550s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 550s " chr7:128829048-128829358 log2=-0.474 spread=0.315 550s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 550s " chr7:140484736-140484912 log2=0.081 spread=0.150 550s " chr7:140487956-140488430 log2=-0.089 spread=0.142 550s " chr7:140493336-140493442 log2=-0.340 spread=0.283 550s " chr7:140624315-140624540 log2=-0.497 spread=0.342 550s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 550s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 550s " chr8:30941153-30941335 log2=0.079 spread=0.294 550s " chr8:30942625-30942802 log2=0.044 spread=0.247 550s " chr8:30947918-30948092 log2=0.151 spread=0.124 550s " chr8:31000128-31000252 log2=-0.099 spread=0.098 550s " chr8:31001006-31001182 log2=-0.002 spread=0.062 550s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 550s " chr8:37698557-37699898 log2=-0.612 spread=0.029 550s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 550s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 550s " chr8:48845528-48845758 log2=0.056 spread=0.196 550s " chr8:48866846-48867043 log2=-0.067 spread=0.097 550s " chr8:48868369-48868526 log2=-0.239 spread=0.174 550s " chr8:48872485-48872722 log2=-0.636 spread=0.464 550s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 550s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 550s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 550s " chr9:2101491-2101640 log2=0.244 spread=0.104 550s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 550s " chr9:5067014-5067883 log2=0.146 spread=0.089 550s " chr9:5068184-5070306 log2=0.133 spread=0.092 550s " chr9:5076944-5077152 log2=0.046 spread=0.137 550s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 550s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 550s " chr9:21986759-21986899 log2=0.058 spread=0.175 550s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 550s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 550s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 550s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 550s " chr9:87425375-87425452 log2=0.494 spread=0.066 550s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 550s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 550s " chr9:139250747-139251032 log2=-0.223 spread=0.273 550s " chr9:139252418-139252703 log2=-0.512 spread=0.264 550s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 550s " chr9:139417262-139417677 log2=-0.173 spread=0.191 550s " chr9:139440110-139440287 log2=-1.257 spread=0.500 550s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 550s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 550s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 550s " chr10:43600360-43600677 log2=-0.341 spread=0.222 550s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 550s " chr10:89685254-89685374 log2=0.244 spread=0.259 550s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 550s " chr10:93579008-93579121 log2=0.166 spread=0.220 550s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 550s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 550s " chr10:112679716-112679934 log2=-0.008 spread=0.028 550s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 550s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 550s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 550s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 550s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 550s " chr11:94170270-94170454 log2=0.095 spread=0.285 550s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 550s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 550s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 550s " chr11:108164020-108164234 log2=-0.056 spread=0.040 550s " chr11:108217986-108218135 log2=0.359 spread=0.277 550s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 550s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 550s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 550s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 550s " chr12:25391004-25391186 log2=0.368 spread=0.128 550s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 550s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 550s " chr12:51206782-51207287 log2=-0.012 spread=0.101 550s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 550s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 550s " chr13:26970356-26970536 log2=0.137 spread=0.121 550s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 550s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 550s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 550s " chr13:32903506-32903689 log2=0.019 spread=0.232 550s " chr13:32918645-32918823 log2=0.158 spread=0.114 550s " chr13:32920899-32921077 log2=0.014 spread=0.247 550s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 550s " chr13:48919164-48919369 log2=0.025 spread=0.094 550s " chr13:48921877-48922044 log2=0.106 spread=0.147 550s " chr13:48923026-48923204 log2=0.360 spread=0.016 550s " chr13:48938965-48939147 log2=0.084 spread=0.356 550s " chr13:48941578-48941767 log2=0.238 spread=0.212 550s " chr13:48947486-48947665 log2=0.025 spread=0.126 550s " chr13:48954166-48954251 log2=0.061 spread=0.273 550s " chr13:49037815-49038005 log2=0.063 spread=0.062 550s " chr13:49047410-49047589 log2=0.053 spread=0.170 550s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 550s " chr13:85527771-85527948 log2=0.007 spread=0.222 550s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 550s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 550s " chr13:110438332-110438432 log2=-3.643 spread=2.325 550s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 550s " chr14:20291466-20291612 log2=0.697 spread=0.248 550s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 550s " chr14:36989195-36989373 log2=0.023 spread=0.162 550s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 550s " chr14:50619741-50619923 log2=0.003 spread=0.272 550s " chr14:50697856-50698044 log2=0.277 spread=0.334 550s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 550s " chr14:71275790-71275923 log2=-2.815 spread=1.938 550s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 550s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 550s " chr15:38544477-38545455 log2=-0.348 spread=0.179 550s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 550s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 550s " chr15:41803968-41804185 log2=-2.202 spread=0.188 550s " chr15:41804261-41804494 log2=-0.402 spread=0.392 550s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 550s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 550s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 550s " chr16:2611404-2611585 log2=-5.171 spread=1.963 550s " chr16:2611721-2611943 log2=-11.810 spread=9.172 550s " chr16:2615504-2615725 log2=-20.113 spread=0.007 550s " chr16:2616307-2616486 log2=-20.054 spread=0.072 550s " chr16:2631267-2631414 log2=-20.009 spread=0.061 550s " chr16:2631583-2631734 log2=-20.089 spread=0.090 550s " chr16:2633363-2633616 log2=-20.101 spread=0.089 550s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 550s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 550s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 550s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 550s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 550s " chr16:50826460-50826650 log2=0.239 spread=0.204 550s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 550s " chr16:60005694-60005857 log2=-0.366 spread=0.298 550s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 550s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 550s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 550s " chr17:12011053-12011253 log2=0.028 spread=0.232 550s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 550s " chr17:29496854-29497046 log2=0.226 spread=0.193 550s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 550s " chr17:30519172-30519355 log2=0.163 spread=0.289 550s " chr17:30525911-30526093 log2=-0.157 spread=0.046 550s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 550s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 550s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 550s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 550s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 550s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 550s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 550s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 550s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 550s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 550s " chr19:2210351-2210545 log2=-0.860 spread=0.261 550s " chr19:2226130-2227152 log2=-0.113 spread=0.120 550s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 550s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 550s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 550s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 550s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 550s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 550s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 550s " chr19:15311544-15311749 log2=-1.887 spread=1.202 550s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 550s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 550s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 550s " chr19:33792774-33793010 log2=-1.781 spread=0.127 550s " chr19:33793014-33793356 log2=-0.541 spread=0.385 550s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 550s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 550s " chr19:45873698-45873881 log2=-0.522 spread=0.327 550s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 550s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 550s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 550s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 550s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 550s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 550s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 550s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 550s " chr21:36265140-36265318 log2=0.042 spread=0.039 550s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 550s " chr22:29115325-29115465 log2=0.055 spread=0.390 550s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 550s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 550s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 550s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 550s " chrX:1317372-1317594 log2=-21.121 spread=0.049 550s " chrX:1321225-1321435 log2=-20.851 spread=0.196 550s " chrX:1325274-1325530 log2=-21.121 spread=0.011 550s " chrX:1327651-1327830 log2=-21.000 spread=0.029 550s " chrX:1331391-1331576 log2=-21.018 spread=0.052 550s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 550s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 550s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 550s " chrX:123185143-123185290 log2=-1.018 spread=0.062 550s " chrX:123202378-123202544 log2=-0.959 spread=0.103 550s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 550s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 550s " chrY:9008607-9008759 log2=-1.012 spread=0.097 550s " chrY:13131970-13132039 log2=-1.004 spread=0.074 550s " chrY:19506485-19506650 log2=-1.018 spread=0.034 550s " chrY:21033918-21034071 log2=-1.013 spread=0.057 550s " chrY:28463435-28463622 log2=-0.952 spread=0.039 550s " chrY:28514033-28514208 log2=-0.992 spread=0.026 550s Antitargets: 108 (0.8597%) bins failed filters 550s Wrote build/reference-picard.cnn with 19209 regions 551s cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr 553s Processing target: p2-5_5 553s Keeping 6308 of 6646 bins 553s Correcting for GC bias... 553s Correcting for density bias... 553s Processing antitarget: p2-5_5 553s Keeping 12455 of 12563 bins 553s Correcting for GC bias... 553s WARNING: Skipping correction for RepeatMasker bias 553s Targets are 1.18 x more variable than antitargets 553s Wrote build/p2-5_5.cnr with 18763 regions 554s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 555s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 555s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 556s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 557s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 558s cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr 559s Processing target: p2-9_2 559s Keeping 6308 of 6646 bins 559s Correcting for GC bias... 559s Correcting for density bias... 559s Processing antitarget: p2-9_2 559s Keeping 12455 of 12563 bins 559s Correcting for GC bias... 559s WARNING: Skipping correction for RepeatMasker bias 560s Targets are 1.72 x more variable than antitargets 560s Wrote build/p2-9_2.cnr with 18763 regions 560s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 562s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 562s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 562s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 564s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 564s cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr 565s Processing target: p2-20_1 566s Keeping 6308 of 6646 bins 566s Correcting for GC bias... 566s Correcting for density bias... 566s Processing antitarget: p2-20_1 566s Keeping 12455 of 12563 bins 566s Correcting for GC bias... 566s WARNING: Skipping correction for RepeatMasker bias 566s Targets are 1.12 x more variable than antitargets 566s Wrote build/p2-20_1.cnr with 18763 regions 567s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 568s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 568s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 568s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 570s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 570s cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr 572s Processing target: p2-20_2 572s Keeping 6308 of 6646 bins 572s Correcting for GC bias... 572s Correcting for density bias... 572s Processing antitarget: p2-20_2 572s Keeping 12455 of 12563 bins 572s Correcting for GC bias... 572s WARNING: Skipping correction for RepeatMasker bias 572s Targets are 1.10 x more variable than antitargets 572s Wrote build/p2-20_2.cnr with 18763 regions 573s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 574s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 574s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 574s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 576s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 576s cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr 577s Processing target: p2-20_3 577s Keeping 6308 of 6646 bins 577s Correcting for GC bias... 577s Correcting for density bias... 578s Processing antitarget: p2-20_3 578s Keeping 12455 of 12563 bins 578s Correcting for GC bias... 578s WARNING: Skipping correction for RepeatMasker bias 578s Antitargets are 1.09 x more variable than targets 578s Wrote build/p2-20_3.cnr with 18763 regions 578s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 580s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 580s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 580s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 582s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 582s cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr 583s Processing target: p2-20_4 583s Keeping 6308 of 6646 bins 583s Correcting for GC bias... 583s Correcting for density bias... 583s Processing antitarget: p2-20_4 584s Keeping 12455 of 12563 bins 584s Correcting for GC bias... 584s WARNING: Skipping correction for RepeatMasker bias 584s Targets are 1.43 x more variable than antitargets 584s Wrote build/p2-20_4.cnr with 18763 regions 584s cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr 586s Processing target: p2-20_5 586s Keeping 6308 of 6646 bins 586s Correcting for GC bias... 586s Correcting for density bias... 586s Processing antitarget: p2-20_5 586s Keeping 12455 of 12563 bins 586s Correcting for GC bias... 586s WARNING: Skipping correction for RepeatMasker bias 587s Targets are 2.50 x more variable than antitargets 587s Wrote build/p2-20_5.cnr with 18763 regions 587s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 589s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 595s Dropped 8 / 49 bins on chromosome chrY 595s Wrote build/p2-5_5.cns with 71 regions 596s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 597s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 599s Dropped 1 / 949 bins on chromosome chr6 604s Dropped 27 / 49 bins on chromosome chrY 604s Wrote build/p2-9_2.cns with 103 regions 605s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 607s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 613s Dropped 6 / 49 bins on chromosome chrY 613s Wrote build/p2-20_1.cns with 121 regions 614s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 615s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 622s Dropped 7 / 49 bins on chromosome chrY 622s Wrote build/p2-20_2.cns with 117 regions 622s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 624s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 630s Dropped 11 / 49 bins on chromosome chrY 630s Wrote build/p2-20_3.cns with 64 regions 631s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 633s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 640s Dropped 8 / 49 bins on chromosome chrY 640s Wrote build/p2-20_4.cns with 143 regions 641s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 642s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 649s Smoothing overshot at 1 / 123 indices: (-0.30060035404086677, 0.32508880185194816) vs. original (-0.363302, 0.311218) 649s Dropped 6 / 49 bins on chromosome chrY 650s Wrote build/p2-20_5.cns with 120 regions 650s cnvkit.py scatter -s build/p2-5_5.cns build/p2-5_5.cnr -t --y-min=-2.5 -o p2-5_5-scatter.pdf 653s Wrote p2-5_5-scatter.pdf 653s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf 655s Smoothing overshot at 3 / 97 indices: (-19.90010586862171, -3.309906922372055) vs. original (-19.294, -0.16431) 656s Wrote p2-9_2-scatter.pdf 656s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 657s Showing 1480 probes and 0 selected genes in region chr1 658s Wrote p2-9_2-chr1-scatter.pdf 658s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 660s Showing 201 probes and 0 selected genes in region chr21 660s Wrote p2-9_2-chr21-scatter.pdf 660s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf 662s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 662s Wrote p2-9_2-chr9p-scatter.pdf 662s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf 664s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 664s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 664s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf 666s Detected file format: bed 666s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 666s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 666s which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr21-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf 666s /usr/bin/pdfunite 666s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 668s Treating sample p2-5_5 as female 676s Wrote p2-5_5-diagram.pdf 676s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 678s Treating sample p2-9_2 as female 685s Wrote p2-9_2-diagram.pdf 686s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 687s Treating sample p2-20_1 as female 695s Wrote p2-20_1-diagram.pdf 695s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 696s Treating sample p2-20_2 as female 705s Wrote p2-20_2-diagram.pdf 706s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 708s Treating sample p2-5_5 as female 708s Wrote p2-5_5-cbs-diagram.pdf 709s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 711s Treating sample p2-9_2 as female 711s Wrote p2-9_2-cbs-diagram.pdf 712s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 714s Treating sample p2-20_1 as female 714s Wrote p2-20_1-cbs-diagram.pdf 715s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 717s Treating sample p2-20_2 as female 717s Wrote p2-20_2-cbs-diagram.pdf 717s cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf 719s Treating sample p2-5_5 as female 724s Wrote p2-5_5-both-diagram.pdf 725s cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf 727s Treating sample p2-9_2 as female 732s Wrote p2-9_2-both-diagram.pdf 732s cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf 734s Treating sample p2-20_1 as female 738s Wrote p2-20_1-both-diagram.pdf 739s cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf 740s Treating sample p2-20_2 as female 745s Wrote p2-20_2-both-diagram.pdf 745s which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf 745s /usr/bin/pdfunite 746s cnvkit.py heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf 747s Treating sample p2-5_5 as female 747s Treating sample p2-9_2 as female 747s Treating sample p2-20_1 as female 747s Treating sample p2-20_2 as female 747s Treating sample p2-20_3 as female 747s Treating sample p2-20_4 as female 747s Treating sample p2-20_5 as female 748s Wrote heatmap-picard.pdf 749s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 750s Found 14 gene breakpoints 750s Wrote p2-9_2-breaks.txt 750s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 752s Treating sample p2-9_2 as female 753s Found 323 gene-level gains and losses 753s Wrote p2-9_2-genemetrics.txt 754s cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt 756s Wrote gender-picard.txt 756s cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt 760s Wrote p2-all.cdt 761s cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt 766s Wrote p2-all-jtv.txt 766s cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg 768s Wrote p2-all.seg 769s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 770s Wrote p2-9_2.nexus 771s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 772s Selected test sample NA12882 and control sample NA12878 772s Loaded 3654 records; skipped: 514 somatic, 394 depth 772s Kept 2631 heterozygous of 3654 VCF records 775s Placed 705 variants into 18763 bins 775s Wrote p2-9_2.nexus-ogt 776s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 777s Treating sample p2-5_5 as female 777s Rescaling sample with purity 0.65, ploidy 2 777s Wrote build/p2-5_5.call.cns with 71 regions 778s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 779s Treating sample p2-9_2 as female 779s Rescaling sample with purity 0.65, ploidy 2 779s Wrote build/p2-9_2.call.cns with 103 regions 779s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 781s Treating sample p2-20_1 as female 781s Rescaling sample with purity 0.65, ploidy 2 781s Wrote build/p2-20_1.call.cns with 121 regions 781s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 783s Treating sample p2-20_2 as female 783s Rescaling sample with purity 0.65, ploidy 2 783s Wrote build/p2-20_2.call.cns with 117 regions 783s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 784s Treating sample p2-20_3 as female 784s Rescaling sample with purity 0.65, ploidy 2 784s Wrote build/p2-20_3.call.cns with 64 regions 785s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 786s Treating sample p2-20_4 as female 786s Rescaling sample with purity 0.65, ploidy 2 786s Wrote build/p2-20_4.call.cns with 143 regions 787s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 788s Treating sample p2-20_5 as female 788s Rescaling sample with purity 0.65, ploidy 2 788s Wrote build/p2-20_5.call.cns with 120 regions 788s cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed 789s Treating sample p2-5_5.call as female 789s Treating sample p2-9_2.call as female 789s Treating sample p2-20_1.call as female 790s Treating sample p2-20_2.call as female 790s Treating sample p2-20_3.call as female 790s Treating sample p2-20_4.call as female 790s Treating sample p2-20_5.call as female 790s Wrote p2-all.bed 790s cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf 791s Treating sample p2-9_2.call as female 792s Wrote p2-9_2.vcf 792s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 793s Wrote p2-9_2.theta2.input 794s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 794s --mean --median --mode --t-test \ 794s --stdev --mad --mse --iqr --bivar \ 794s --ci --pi --sem --smooth-bootstrap 796s Wrote p2-9_2-segmetrics.cns with 103 regions 796s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 796s --ci -b 50 -a 0.5 798s Wrote p2-5_5-segmetrics.cns with 71 regions 798s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 800s Wrote p2-5_5-metrics.tsv 800s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 802s Wrote p2-9_2-metrics.tsv 802s cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv 804s Wrote p2-20-metrics.tsv 804s PASS 805s autopkgtest [17:01:42]: test run-unit-test: -----------------------] 805s autopkgtest [17:01:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 805s run-unit-test PASS 806s autopkgtest [17:01:43]: @@@@@@@@@@@@@@@@@@@@ summary 806s run-unit-test PASS