0s autopkgtest [16:12:19]: starting date and time: 2024-03-25 16:12:19+0000 0s autopkgtest [16:12:19]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:12:19]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zm30xexm/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 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=alsa-lib/1.2.11-1build1 at-spi2-core/2.51.90-3 cups/2.4.7-1.2ubuntu1 glib2.0/2.79.3-3ubuntu5 gnutls28/3.8.3-1.1ubuntu2 gtk+3.0/3.24.41-1.1ubuntu3 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 openjdk-23/23~15ea-1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-17.secgroup --name adt-noble-arm64-bbmap-20240325-161219-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 672s Creating nova instance adt-noble-arm64-bbmap-20240325-161219-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240325.img (UUID cb04e91c-f09d-46d2-869e-b1eb502de8d7)... 672s nova boot failed (attempt #1): 672s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader') 672s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader') 672s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken') 672s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth') 672s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP') 672s 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" 672s DEBUG (connectionpool:962) Starting new HTTPS connection (1): keystone.ps6.canonical.com:5000 672s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "GET /v3 HTTP/1.1" 200 267 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 267 Content-Type: application/json Date: Mon, 25 Mar 2024 16:12:46 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) Vary: X-Auth-Token x-openstack-request-id: req-effb9b6e-b8ad-4f68-8c02-3fbe7f9c1d0c 672s 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"}]}} 672s DEBUG (session:946) GET call to https://keystone.ps6.canonical.com:5000/v3 used request id req-effb9b6e-b8ad-4f68-8c02-3fbe7f9c1d0c 672s DEBUG (base:182) Making authentication request to https://keystone.ps6.canonical.com:5000/v3/auth/tokens 672s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "POST /v3/auth/tokens HTTP/1.1" 201 12445 672s 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": ["ENXShPwQTKuFp4V_XxCYew"], "expires_at": "2024-03-26T16:12:46.000000Z", "issued_at": "2024-03-25T16:12:46.000000Z", "project": {"domain": {"id": "default", "name": "Default"}, "id": "bd8b3df3f03d43a0a9303b7c0434fdab", "name": "prod-proposed-migration-arm64_project"}, "is_domain": false, "roles": [{"id": "86bf3043974746c2bf52c2a9f362f986", "name": "reader"}, {"id": "15cf997650e345b7b21c02b5cdb7d84a", "name": "member"}], "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"}]}} 672s 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}8cd8711e61e963576047c5c4a7a12f39a11491dc4630b1cf8e7b3f82137c8019" 672s 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}8cd8711e61e963576047c5c4a7a12f39a11491dc4630b1cf8e7b3f82137c8019" 672s DEBUG (connectionpool:962) Starting new HTTPS connection (1): nova.ps6.canonical.com:8774 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1 HTTP/1.1" 302 0 672s RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Mon, 25 Mar 2024 16:12:46 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-d53acf40-500d-4ab4-99ac-f19112c7625d x-openstack-request-id: req-d53acf40-500d-4ab4-99ac-f19112c7625d 672s DEBUG (session:548) RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Mon, 25 Mar 2024 16:12:46 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-d53acf40-500d-4ab4-99ac-f19112c7625d x-openstack-request-id: req-d53acf40-500d-4ab4-99ac-f19112c7625d 672s RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged. 672s DEBUG (session:580) RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged. 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/ HTTP/1.1" 200 397 672s RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Mon, 25 Mar 2024 16:12:46 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-7e46b400-55ea-4149-81ae-5f3b65ca41f3 x-openstack-request-id: req-7e46b400-55ea-4149-81ae-5f3b65ca41f3 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Mon, 25 Mar 2024 16:12:46 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-7e46b400-55ea-4149-81ae-5f3b65ca41f3 x-openstack-request-id: req-7e46b400-55ea-4149-81ae-5f3b65ca41f3 672s 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"}]}} 672s 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"}]}} 672s GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-7e46b400-55ea-4149-81ae-5f3b65ca41f3 672s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-7e46b400-55ea-4149-81ae-5f3b65ca41f3 672s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader') 672s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader') 672s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken') 672s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth') 672s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP') 672s DEBUG (session:517) REQ: curl -g -i -X GET https://glance.ps6.canonical.com:9292/v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7 -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}8cd8711e61e963576047c5c4a7a12f39a11491dc4630b1cf8e7b3f82137c8019" -H "X-OpenStack-Nova-API-Version: 2.87" 672s DEBUG (connectionpool:962) Starting new HTTPS connection (1): glance.ps6.canonical.com:9292 672s DEBUG (connectionpool:429) https://glance.ps6.canonical.com:9292 "GET /v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7 HTTP/1.1" 200 1935 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 1935 Content-Type: application/json Date: Mon, 25 Mar 2024 16:12:47 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) X-Openstack-Request-Id: req-dd6a8c3f-b896-4d1c-afb8-82d993d248a0 672s 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": "d9140d90-fe35-46dc-95d1-aa597ba0d64f", "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-20240325.img", "disk_format": "qcow2", "container_format": "bare", "visibility": "private", "size": 2309619712, "virtual_size": 21474836480, "status": "active", "checksum": "40c61dba7924622258af9a6204f016f7", "protected": false, "min_ram": 0, "min_disk": 20, "owner": "bd8b3df3f03d43a0a9303b7c0434fdab", "os_hidden": false, "os_hash_algo": "sha512", "os_hash_value": "48df420f8dbdde4f78378203755d38b5df769615a0d0562f2a8aee8cd142e28d8243926f2a525e18990c91d1121d6be28be4eb567242d990b4c68e18f8d1c9aa", "id": "cb04e91c-f09d-46d2-869e-b1eb502de8d7", "created_at": "2024-03-25T04:29:37Z", "updated_at": "2024-03-25T04:30:04Z", "locations": [{"url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/cb04e91c-f09d-46d2-869e-b1eb502de8d7/snap", "metadata": {"store": "ceph"}}], "direct_url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/cb04e91c-f09d-46d2-869e-b1eb502de8d7/snap", "tags": [], "self": "/v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7", "file": "/v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7/file", "schema": "/v2/schemas/image", "stores": "ceph"} 672s DEBUG (session:936) GET call to image for https://glance.ps6.canonical.com:9292/v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7 used request id req-dd6a8c3f-b896-4d1c-afb8-82d993d248a0 672s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest-big -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}8cd8711e61e963576047c5c4a7a12f39a11491dc4630b1cf8e7b3f82137c8019" -H "X-OpenStack-Nova-API-Version: 2.87" 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/autopkgtest-big HTTP/1.1" 404 88 672s DEBUG (session:548) RESP: [404] Connection: Keep-Alive Content-Length: 88 Content-Type: application/json; charset=UTF-8 Date: Mon, 25 Mar 2024 16:12:47 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-40fd0cfc-713b-43fa-a283-37fff1b11ad6 x-openstack-request-id: req-40fd0cfc-713b-43fa-a283-37fff1b11ad6 672s DEBUG (session:580) RESP BODY: {"itemNotFound": {"code": 404, "message": "Flavor autopkgtest-big could not be found."}} 672s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest-big used request id req-40fd0cfc-713b-43fa-a283-37fff1b11ad6 672s 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}8cd8711e61e963576047c5c4a7a12f39a11491dc4630b1cf8e7b3f82137c8019" -H "X-OpenStack-Nova-API-Version: 2.87" 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors?is_public=None HTTP/1.1" 200 1739 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 1739 Content-Type: application/json Date: Mon, 25 Mar 2024 16:12:47 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-d939e3b3-2e20-46d6-a551-a7ae2c7b7fcd x-openstack-request-id: req-d939e3b3-2e20-46d6-a551-a7ae2c7b7fcd 672s 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}]} 672s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors?is_public=None used request id req-d939e3b3-2e20-46d6-a551-a7ae2c7b7fcd 672s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83 -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}8cd8711e61e963576047c5c4a7a12f39a11491dc4630b1cf8e7b3f82137c8019" -H "X-OpenStack-Nova-API-Version: 2.87" 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83 HTTP/1.1" 200 618 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 618 Content-Type: application/json Date: Mon, 25 Mar 2024 16:12:47 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-50108b28-6836-4a8e-bffc-669fb2337a0d x-openstack-request-id: req-50108b28-6836-4a8e-bffc-669fb2337a0d 672s DEBUG (session:580) RESP BODY: {"flavor": {"id": "a8256f9e-53ee-4584-ad7f-60e088825b83", "name": "autopkgtest-big", "ram": 8192, "disk": 100, "swap": 0, "OS-FLV-EXT-DATA:ephemeral": 0, "OS-FLV-DISABLED:disabled": false, "vcpus": 4, "os-flavor-access:is_public": false, "rxtx_factor": 1.0, "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, "extra_specs": {"aggregate_instance_extra_specs:commit": "builder-arm64", "hw_rng:allowed": "True"}}} 672s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83 used request id req-50108b28-6836-4a8e-bffc-669fb2337a0d 672s 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}8cd8711e61e963576047c5c4a7a12f39a11491dc4630b1cf8e7b3f82137c8019" -H "X-OpenStack-Nova-API-Version: 2.87" -d '{"server": {"name": "adt-noble-arm64-bbmap-20240325-161219-juju-7f2275-prod-proposed-migration-environment-2", "imageRef": "cb04e91c-f09d-46d2-869e-b1eb502de8d7", "flavorRef": "a8256f9e-53ee-4584-ad7f-60e088825b83", "user_data": "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", "key_name": "testbed-juju-7f2275-prod-proposed-migration-environment-2", "min_count": 1, "max_count": 1, "security_groups": [{"name": "autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-17.secgroup"}], "networks": [{"uuid": "6ea4839c-9760-4b54-ab7d-70a6312667d1"}]}}' 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "POST /v2.1/servers HTTP/1.1" 403 115 672s DEBUG (session:548) RESP: [403] Connection: Keep-Alive Content-Length: 115 Content-Type: application/json; charset=UTF-8 Date: Mon, 25 Mar 2024 16:12:47 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-235a1f94-4cf6-41ca-a41f-a3c02c049db6 x-openstack-request-id: req-235a1f94-4cf6-41ca-a41f-a3c02c049db6 672s DEBUG (session:580) RESP BODY: {"forbidden": {"code": 403, "message": "Quota exceeded for cores: Requested 4, but already used 140 of 140 cores"}} 672s DEBUG (session:936) POST call to compute for https://nova.ps6.canonical.com:8774/v2.1/servers used request id req-235a1f94-4cf6-41ca-a41f-a3c02c049db6 672s DEBUG (shell:822) Quota exceeded for cores: Requested 4, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-235a1f94-4cf6-41ca-a41f-a3c02c049db6) 672s Traceback (most recent call last): 672s File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 820, in main 672s OpenStackComputeShell().main(argv) 672s File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 742, in main 672s args.func(self.cs, args) 672s File "/usr/lib/python3/dist-packages/novaclient/v2/shell.py", line 971, in do_boot 672s server = cs.servers.create(*boot_args, **boot_kwargs) 672s File "/usr/lib/python3/dist-packages/novaclient/v2/servers.py", line 1477, in create 672s return self._boot(response_key, *boot_args, **boot_kwargs) 672s File "/usr/lib/python3/dist-packages/novaclient/v2/servers.py", line 836, in _boot 672s return self._create('/servers', body, response_key, 672s File "/usr/lib/python3/dist-packages/novaclient/base.py", line 363, in _create 672s resp, body = self.api.client.post(url, body=body) 672s File "/usr/lib/python3/dist-packages/keystoneauth1/adapter.py", line 392, in post 672s return self.request(url, 'POST', **kwargs) 672s File "/usr/lib/python3/dist-packages/novaclient/client.py", line 78, in request 672s raise exceptions.from_response(resp, body, url, method) 672s novaclient.exceptions.Forbidden: Quota exceeded for cores: Requested 4, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-235a1f94-4cf6-41ca-a41f-a3c02c049db6) 672s ERROR (Forbidden): Quota exceeded for cores: Requested 4, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-235a1f94-4cf6-41ca-a41f-a3c02c049db6) 672s nova boot failed (attempt #2): 672s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader') 672s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader') 672s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken') 672s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth') 672s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP') 672s 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" 672s DEBUG (connectionpool:962) Starting new HTTPS connection (1): keystone.ps6.canonical.com:5000 672s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "GET /v3 HTTP/1.1" 200 267 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 267 Content-Type: application/json Date: Mon, 25 Mar 2024 16:17:48 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) Vary: X-Auth-Token x-openstack-request-id: req-8b89e587-7a06-418c-bd16-db98307bfb9a 672s 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"}]}} 672s DEBUG (session:946) GET call to https://keystone.ps6.canonical.com:5000/v3 used request id req-8b89e587-7a06-418c-bd16-db98307bfb9a 672s DEBUG (base:182) Making authentication request to https://keystone.ps6.canonical.com:5000/v3/auth/tokens 672s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "POST /v3/auth/tokens HTTP/1.1" 201 12445 672s 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": ["bT05FY2CTi6hE4wxMnujdA"], "expires_at": "2024-03-26T16:17:49.000000Z", "issued_at": "2024-03-25T16:17:49.000000Z", "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"}]}} 672s 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}37ef84b017aee3c6d35bd099810cc1f0626e426fc0ffc5273dff4763249112ac" 672s 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}37ef84b017aee3c6d35bd099810cc1f0626e426fc0ffc5273dff4763249112ac" 672s DEBUG (connectionpool:962) Starting new HTTPS connection (1): nova.ps6.canonical.com:8774 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1 HTTP/1.1" 302 0 672s RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Mon, 25 Mar 2024 16:17:49 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-cac2f153-b032-4546-bde1-42898aca4a38 x-openstack-request-id: req-cac2f153-b032-4546-bde1-42898aca4a38 672s DEBUG (session:548) RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Mon, 25 Mar 2024 16:17:49 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-cac2f153-b032-4546-bde1-42898aca4a38 x-openstack-request-id: req-cac2f153-b032-4546-bde1-42898aca4a38 672s RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged. 672s DEBUG (session:580) RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged. 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/ HTTP/1.1" 200 397 672s RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Mon, 25 Mar 2024 16:17:49 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-fc099df1-b8db-4685-9f1b-5e09cb1308b9 x-openstack-request-id: req-fc099df1-b8db-4685-9f1b-5e09cb1308b9 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Mon, 25 Mar 2024 16:17:49 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-fc099df1-b8db-4685-9f1b-5e09cb1308b9 x-openstack-request-id: req-fc099df1-b8db-4685-9f1b-5e09cb1308b9 672s 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"}]}} 672s 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"}]}} 672s GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-fc099df1-b8db-4685-9f1b-5e09cb1308b9 672s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-fc099df1-b8db-4685-9f1b-5e09cb1308b9 672s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader') 672s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader') 672s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken') 672s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth') 672s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth') 672s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP') 672s DEBUG (session:517) REQ: curl -g -i -X GET https://glance.ps6.canonical.com:9292/v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7 -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}37ef84b017aee3c6d35bd099810cc1f0626e426fc0ffc5273dff4763249112ac" -H "X-OpenStack-Nova-API-Version: 2.87" 672s DEBUG (connectionpool:962) Starting new HTTPS connection (1): glance.ps6.canonical.com:9292 672s DEBUG (connectionpool:429) https://glance.ps6.canonical.com:9292 "GET /v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7 HTTP/1.1" 200 1935 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 1935 Content-Type: application/json Date: Mon, 25 Mar 2024 16:17:49 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) X-Openstack-Request-Id: req-937228f8-d78f-4c5a-a5f1-c0dfc7f5415f 672s 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": "d9140d90-fe35-46dc-95d1-aa597ba0d64f", "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-20240325.img", "disk_format": "qcow2", "container_format": "bare", "visibility": "private", "size": 2309619712, "virtual_size": 21474836480, "status": "active", "checksum": "40c61dba7924622258af9a6204f016f7", "protected": false, "min_ram": 0, "min_disk": 20, "owner": "bd8b3df3f03d43a0a9303b7c0434fdab", "os_hidden": false, "os_hash_algo": "sha512", "os_hash_value": "48df420f8dbdde4f78378203755d38b5df769615a0d0562f2a8aee8cd142e28d8243926f2a525e18990c91d1121d6be28be4eb567242d990b4c68e18f8d1c9aa", "id": "cb04e91c-f09d-46d2-869e-b1eb502de8d7", "created_at": "2024-03-25T04:29:37Z", "updated_at": "2024-03-25T04:30:04Z", "locations": [{"url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/cb04e91c-f09d-46d2-869e-b1eb502de8d7/snap", "metadata": {"store": "ceph"}}], "direct_url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/cb04e91c-f09d-46d2-869e-b1eb502de8d7/snap", "tags": [], "self": "/v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7", "file": "/v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7/file", "schema": "/v2/schemas/image", "stores": "ceph"} 672s DEBUG (session:936) GET call to image for https://glance.ps6.canonical.com:9292/v2/images/cb04e91c-f09d-46d2-869e-b1eb502de8d7 used request id req-937228f8-d78f-4c5a-a5f1-c0dfc7f5415f 672s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest-big -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}37ef84b017aee3c6d35bd099810cc1f0626e426fc0ffc5273dff4763249112ac" -H "X-OpenStack-Nova-API-Version: 2.87" 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/autopkgtest-big HTTP/1.1" 404 88 672s DEBUG (session:548) RESP: [404] Connection: Keep-Alive Content-Length: 88 Content-Type: application/json; charset=UTF-8 Date: Mon, 25 Mar 2024 16:17:50 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-1b7ec49a-cb74-463f-a546-1d844e003348 x-openstack-request-id: req-1b7ec49a-cb74-463f-a546-1d844e003348 672s DEBUG (session:580) RESP BODY: {"itemNotFound": {"code": 404, "message": "Flavor autopkgtest-big could not be found."}} 672s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest-big used request id req-1b7ec49a-cb74-463f-a546-1d844e003348 672s 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}37ef84b017aee3c6d35bd099810cc1f0626e426fc0ffc5273dff4763249112ac" -H "X-OpenStack-Nova-API-Version: 2.87" 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors?is_public=None HTTP/1.1" 200 1739 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 1739 Content-Type: application/json Date: Mon, 25 Mar 2024 16:17:50 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-748fceaf-ce85-4b46-9636-2e52c44ad228 x-openstack-request-id: req-748fceaf-ce85-4b46-9636-2e52c44ad228 672s 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}]} 672s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors?is_public=None used request id req-748fceaf-ce85-4b46-9636-2e52c44ad228 672s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83 -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}37ef84b017aee3c6d35bd099810cc1f0626e426fc0ffc5273dff4763249112ac" -H "X-OpenStack-Nova-API-Version: 2.87" 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83 HTTP/1.1" 200 618 672s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 618 Content-Type: application/json Date: Mon, 25 Mar 2024 16:17:50 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-f7d3575b-7922-41ff-9654-913776012dc6 x-openstack-request-id: req-f7d3575b-7922-41ff-9654-913776012dc6 672s DEBUG (session:580) RESP BODY: {"flavor": {"id": "a8256f9e-53ee-4584-ad7f-60e088825b83", "name": "autopkgtest-big", "ram": 8192, "disk": 100, "swap": 0, "OS-FLV-EXT-DATA:ephemeral": 0, "OS-FLV-DISABLED:disabled": false, "vcpus": 4, "os-flavor-access:is_public": false, "rxtx_factor": 1.0, "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, "extra_specs": {"aggregate_instance_extra_specs:commit": "builder-arm64", "hw_rng:allowed": "True"}}} 672s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83 used request id req-f7d3575b-7922-41ff-9654-913776012dc6 672s 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}37ef84b017aee3c6d35bd099810cc1f0626e426fc0ffc5273dff4763249112ac" -H "X-OpenStack-Nova-API-Version: 2.87" -d '{"server": {"name": "adt-noble-arm64-bbmap-20240325-161219-juju-7f2275-prod-proposed-migration-environment-2", "imageRef": "cb04e91c-f09d-46d2-869e-b1eb502de8d7", "flavorRef": "a8256f9e-53ee-4584-ad7f-60e088825b83", "user_data": "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", "key_name": "testbed-juju-7f2275-prod-proposed-migration-environment-2", "min_count": 1, "max_count": 1, "security_groups": [{"name": "autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-17.secgroup"}], "networks": [{"uuid": "6ea4839c-9760-4b54-ab7d-70a6312667d1"}]}}' 672s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "POST /v2.1/servers HTTP/1.1" 403 115 672s DEBUG (session:548) RESP: [403] Connection: Keep-Alive Content-Length: 115 Content-Type: application/json; charset=UTF-8 Date: Mon, 25 Mar 2024 16:17:50 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-bea41876-f882-4808-ad6f-30fd83d6fca4 x-openstack-request-id: req-bea41876-f882-4808-ad6f-30fd83d6fca4 672s DEBUG (session:580) RESP BODY: {"forbidden": {"code": 403, "message": "Quota exceeded for cores: Requested 4, but already used 140 of 140 cores"}} 672s DEBUG (session:936) POST call to compute for https://nova.ps6.canonical.com:8774/v2.1/servers used request id req-bea41876-f882-4808-ad6f-30fd83d6fca4 672s DEBUG (shell:822) Quota exceeded for cores: Requested 4, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-bea41876-f882-4808-ad6f-30fd83d6fca4) 672s Traceback (most recent call last): 672s File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 820, in main 672s OpenStackComputeShell().main(argv) 672s File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 742, in main 672s args.func(self.cs, args) 672s File "/usr/lib/python3/dist-packages/novaclient/v2/shell.py", line 971, in do_boot 672s server = cs.servers.create(*boot_args, **boot_kwargs) 672s File "/usr/lib/python3/dist-packages/novaclient/v2/servers.py", line 1477, in create 672s return self._boot(response_key, *boot_args, **boot_kwargs) 672s File "/usr/lib/python3/dist-packages/novaclient/v2/servers.py", line 836, in _boot 672s return self._create('/servers', body, response_key, 672s File "/usr/lib/python3/dist-packages/novaclient/base.py", line 363, in _create 672s resp, body = self.api.client.post(url, body=body) 672s File "/usr/lib/python3/dist-packages/keystoneauth1/adapter.py", line 392, in post 672s return self.request(url, 'POST', **kwargs) 672s File "/usr/lib/python3/dist-packages/novaclient/client.py", line 78, in request 672s raise exceptions.from_response(resp, body, url, method) 672s novaclient.exceptions.Forbidden: Quota exceeded for cores: Requested 4, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-bea41876-f882-4808-ad6f-30fd83d6fca4) 672s ERROR (Forbidden): Quota exceeded for cores: Requested 4, but already used 140 of 140 cores (HTTP 403) (Request-ID: req-bea41876-f882-4808-ad6f-30fd83d6fca4) 675s autopkgtest [16:23:34]: testbed dpkg architecture: arm64 675s autopkgtest [16:23:34]: testbed apt version: 2.7.12 675s autopkgtest [16:23:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 675s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 676s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 676s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.8 kB] 676s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3992 kB] 676s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 676s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [713 kB] 676s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 676s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [39.7 kB] 676s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 676s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4354 kB] 676s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 676s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [71.0 kB] 676s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 678s Fetched 9860 kB in 2s (5942 kB/s) 678s Reading package lists... 680s Reading package lists... 680s Building dependency tree... 680s Reading state information... 681s Calculating upgrade... 681s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 681s Reading package lists... 681s Building dependency tree... 681s Reading state information... 682s 0 upgraded, 0 newly installed, 0 to remove and 240 not upgraded. 682s sh: Attempting to set up Debian/Ubuntu apt sources automatically 682s sh: Distribution appears to be Ubuntu 683s Reading package lists... 683s Building dependency tree... 683s Reading state information... 684s eatmydata is already the newest version (131-1). 684s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 684s Reading package lists... 684s Building dependency tree... 684s Reading state information... 684s dbus is already the newest version (1.14.10-4ubuntu1). 684s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 684s Reading package lists... 684s Building dependency tree... 684s Reading state information... 685s rng-tools-debian is already the newest version (2.4). 685s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 685s Reading package lists... 685s Building dependency tree... 685s Reading state information... 685s The following packages will be REMOVED: 685s cloud-init* python3-configobj* python3-debconf* 686s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 686s After this operation, 3256 kB disk space will be freed. 686s (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.) 686s Removing cloud-init (24.1.2-0ubuntu1) ... 686s Removing python3-configobj (5.0.8-3) ... 687s Removing python3-debconf (1.5.86) ... 687s Processing triggers for man-db (2.12.0-3) ... 687s (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 ... 74430 files and directories currently installed.) 687s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 688s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 688s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 688s invoke-rc.d: policy-rc.d denied execution of try-restart. 688s Reading package lists... 688s Building dependency tree... 688s Reading state information... 689s linux-generic is already the newest version (6.8.0-11.11+1). 689s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 689s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 689s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 689s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 691s Reading package lists... 691s Reading package lists... 691s Building dependency tree... 691s Reading state information... 692s Calculating upgrade... 692s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 692s Reading package lists... 692s Building dependency tree... 692s Reading state information... 692s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 693s autopkgtest [16:23:52]: rebooting testbed after setup commands that affected boot 717s autopkgtest [16:24:16]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 720s autopkgtest [16:24:19]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 724s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 724s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 724s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 724s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 724s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 724s gpgv: issuer "emollier@debian.org" 724s gpgv: Can't check signature: No public key 724s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 725s autopkgtest [16:24:24]: testing package bbmap version 39.06+dfsg-1 725s autopkgtest [16:24:24]: build not needed 726s autopkgtest [16:24:25]: test run-unit-test: preparing testbed 728s Reading package lists... 728s Building dependency tree... 728s Reading state information... 728s Starting pkgProblemResolver with broken count: 0 729s Starting 2 pkgProblemResolver with broken count: 0 729s Done 729s The following additional packages will be installed: 729s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 729s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 729s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 729s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 729s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 729s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 729s python-biopython-doc 729s Suggested packages: 729s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 729s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 729s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 729s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 729s Recommended packages: 729s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 729s The following NEW packages will be installed: 729s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 729s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 729s libasound2 libasound2-data libavahi-client3 libavahi-common-data 729s libavahi-common3 libcommons-cli-java libcommons-codec-java 729s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 729s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 729s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 729s python-biopython-doc 729s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 729s Need to get 79.2 MB/79.2 MB of archives. 729s After this operation, 238 MB of additional disk space will be used. 729s Get:1 /tmp/autopkgtest.iDd7qY/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 729s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 730s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B] 730s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 730s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 730s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-io-java all 2.11.0-2 [297 kB] 730s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB] 730s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB] 730s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 730s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 730s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 730s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 730s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 730s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 730s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 730s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 730s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 730s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 730s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 730s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 730s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 730s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 730s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 730s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 730s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 731s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 731s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-17-jre-headless arm64 17.0.10+7-1 [47.3 MB] 733s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap all 39.06+dfsg-1 [9768 kB] 733s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap-jni arm64 39.06+dfsg-1 [26.3 kB] 733s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 734s Fetched 79.2 MB in 5s (17.5 MB/s) 734s Selecting previously unselected package libcommons-cli-java. 735s (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 ... 74375 files and directories currently installed.) 735s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 735s Unpacking libcommons-cli-java (1.6.0-1) ... 735s Selecting previously unselected package libapache-pom-java. 735s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 735s Unpacking libapache-pom-java (29-2) ... 735s Selecting previously unselected package libcommons-parent-java. 735s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 735s Unpacking libcommons-parent-java (56-1) ... 735s Selecting previously unselected package libcommons-codec-java. 735s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 735s Unpacking libcommons-codec-java (1.16.0-1) ... 735s Selecting previously unselected package libcommons-io-java. 735s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 735s Unpacking libcommons-io-java (2.11.0-2) ... 735s Selecting previously unselected package liblog4j1.2-java. 735s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 735s Unpacking liblog4j1.2-java (1.2.17-11) ... 735s Selecting previously unselected package libmpj-java. 735s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 735s Unpacking libmpj-java (0.44+dfsg-4) ... 735s Selecting previously unselected package ca-certificates-java. 735s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 735s Unpacking ca-certificates-java (20240118) ... 735s Selecting previously unselected package java-common. 735s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 735s Unpacking java-common (0.75+exp1) ... 735s Selecting previously unselected package libavahi-common-data:arm64. 735s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 735s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 735s Selecting previously unselected package libavahi-common3:arm64. 735s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 735s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 735s Selecting previously unselected package libavahi-client3:arm64. 735s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 735s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 735s Selecting previously unselected package libcups2:arm64. 735s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_arm64.deb ... 735s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 735s Selecting previously unselected package liblcms2-2:arm64. 735s Preparing to unpack .../13-liblcms2-2_2.14-2_arm64.deb ... 735s Unpacking liblcms2-2:arm64 (2.14-2) ... 735s Selecting previously unselected package libjpeg-turbo8:arm64. 735s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 735s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 735s Selecting previously unselected package libjpeg8:arm64. 735s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_arm64.deb ... 735s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 735s Selecting previously unselected package fonts-dejavu-mono. 735s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 735s Unpacking fonts-dejavu-mono (2.37-8) ... 735s Selecting previously unselected package fonts-dejavu-core. 735s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 735s Unpacking fonts-dejavu-core (2.37-8) ... 735s Selecting previously unselected package fontconfig-config. 735s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 736s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 736s Selecting previously unselected package libfontconfig1:arm64. 736s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 736s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 736s Selecting previously unselected package libasound2-data. 736s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 736s Unpacking libasound2-data (1.2.10-3build1) ... 736s Selecting previously unselected package libasound2:arm64. 736s Preparing to unpack .../21-libasound2_1.2.10-3build1_arm64.deb ... 736s Unpacking libasound2:arm64 (1.2.10-3build1) ... 736s Selecting previously unselected package libgraphite2-3:arm64. 736s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_arm64.deb ... 736s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 736s Selecting previously unselected package libharfbuzz0b:arm64. 736s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_arm64.deb ... 736s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 736s Selecting previously unselected package libpcsclite1:arm64. 736s Preparing to unpack .../24-libpcsclite1_2.0.0-1_arm64.deb ... 736s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 736s Selecting previously unselected package openjdk-17-jre-headless:arm64. 736s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_arm64.deb ... 736s Unpacking openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 738s Selecting previously unselected package bbmap. 738s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 738s Unpacking bbmap (39.06+dfsg-1) ... 738s Selecting previously unselected package bbmap-jni. 738s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_arm64.deb ... 738s Unpacking bbmap-jni (39.06+dfsg-1) ... 738s Selecting previously unselected package python-biopython-doc. 738s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 738s Unpacking python-biopython-doc (1.81+dfsg-3) ... 738s Selecting previously unselected package autopkgtest-satdep. 738s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 738s Unpacking autopkgtest-satdep (0) ... 738s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 738s Setting up liblcms2-2:arm64 (2.14-2) ... 738s Setting up java-common (0.75+exp1) ... 738s Setting up libcommons-cli-java (1.6.0-1) ... 738s Setting up liblog4j1.2-java (1.2.17-11) ... 738s Setting up libasound2-data (1.2.10-3build1) ... 738s Setting up libapache-pom-java (29-2) ... 738s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 738s Setting up fonts-dejavu-mono (2.37-8) ... 738s Setting up fonts-dejavu-core (2.37-8) ... 738s Setting up libpcsclite1:arm64 (2.0.0-1) ... 738s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 738s Setting up python-biopython-doc (1.81+dfsg-3) ... 738s Setting up libasound2:arm64 (1.2.10-3build1) ... 738s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 738s Setting up bbmap-jni (39.06+dfsg-1) ... 738s Setting up ca-certificates-java (20240118) ... 738s No JRE found. Skipping Java certificates setup. 738s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 738s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 739s Setting up libcommons-parent-java (56-1) ... 739s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 739s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 739s Setting up libcommons-codec-java (1.16.0-1) ... 739s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 739s Setting up libcommons-io-java (2.11.0-2) ... 739s Setting up libmpj-java (0.44+dfsg-4) ... 739s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 739s Setting up openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 739s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 739s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 739s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 739s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 739s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 739s Processing triggers for libc-bin (2.39-0ubuntu6) ... 739s Processing triggers for man-db (2.12.0-3) ... 740s Processing triggers for ca-certificates-java (20240118) ... 740s Adding debian:ACCVRAIZ1.pem 740s Adding debian:AC_RAIZ_FNMT-RCM.pem 740s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 740s Adding debian:ANF_Secure_Server_Root_CA.pem 740s Adding debian:Actalis_Authentication_Root_CA.pem 740s Adding debian:AffirmTrust_Commercial.pem 740s Adding debian:AffirmTrust_Networking.pem 740s Adding debian:AffirmTrust_Premium.pem 740s Adding debian:AffirmTrust_Premium_ECC.pem 740s Adding debian:Amazon_Root_CA_1.pem 740s Adding debian:Amazon_Root_CA_2.pem 740s Adding debian:Amazon_Root_CA_3.pem 740s Adding debian:Amazon_Root_CA_4.pem 740s Adding debian:Atos_TrustedRoot_2011.pem 740s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 740s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 740s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 740s Adding debian:BJCA_Global_Root_CA1.pem 740s Adding debian:BJCA_Global_Root_CA2.pem 740s Adding debian:Baltimore_CyberTrust_Root.pem 740s Adding debian:Buypass_Class_2_Root_CA.pem 740s Adding debian:Buypass_Class_3_Root_CA.pem 740s Adding debian:CA_Disig_Root_R2.pem 740s Adding debian:CFCA_EV_ROOT.pem 740s Adding debian:COMODO_Certification_Authority.pem 740s Adding debian:COMODO_ECC_Certification_Authority.pem 740s Adding debian:COMODO_RSA_Certification_Authority.pem 740s Adding debian:Certainly_Root_E1.pem 740s Adding debian:Certainly_Root_R1.pem 740s Adding debian:Certigna.pem 740s Adding debian:Certigna_Root_CA.pem 740s Adding debian:Certum_EC-384_CA.pem 740s Adding debian:Certum_Trusted_Network_CA.pem 740s Adding debian:Certum_Trusted_Network_CA_2.pem 740s Adding debian:Certum_Trusted_Root_CA.pem 740s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 740s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 740s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 740s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 740s Adding debian:Comodo_AAA_Services_root.pem 740s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 740s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 740s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 740s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 740s Adding debian:DigiCert_Assured_ID_Root_CA.pem 740s Adding debian:DigiCert_Assured_ID_Root_G2.pem 740s Adding debian:DigiCert_Assured_ID_Root_G3.pem 740s Adding debian:DigiCert_Global_Root_CA.pem 740s Adding debian:DigiCert_Global_Root_G2.pem 740s Adding debian:DigiCert_Global_Root_G3.pem 740s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 740s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 740s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 741s Adding debian:DigiCert_Trusted_Root_G4.pem 741s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 741s Adding debian:Entrust_Root_Certification_Authority.pem 741s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 741s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 741s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 741s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 741s Adding debian:GLOBALTRUST_2020.pem 741s Adding debian:GTS_Root_R1.pem 741s Adding debian:GTS_Root_R2.pem 741s Adding debian:GTS_Root_R3.pem 741s Adding debian:GTS_Root_R4.pem 741s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 741s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 741s Adding debian:GlobalSign_Root_CA.pem 741s Adding debian:GlobalSign_Root_CA_-_R3.pem 741s Adding debian:GlobalSign_Root_CA_-_R6.pem 741s Adding debian:GlobalSign_Root_E46.pem 741s Adding debian:GlobalSign_Root_R46.pem 741s Adding debian:Go_Daddy_Class_2_CA.pem 741s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 741s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 741s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 741s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 741s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 741s Adding debian:HiPKI_Root_CA_-_G1.pem 741s Adding debian:Hongkong_Post_Root_CA_3.pem 741s Adding debian:ISRG_Root_X1.pem 741s Adding debian:ISRG_Root_X2.pem 741s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 741s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 741s Adding debian:Izenpe.com.pem 741s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 741s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 741s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 741s Adding debian:NAVER_Global_Root_Certification_Authority.pem 741s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 741s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 741s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 741s Adding debian:QuoVadis_Root_CA_1_G3.pem 741s Adding debian:QuoVadis_Root_CA_2.pem 741s Adding debian:QuoVadis_Root_CA_2_G3.pem 741s Adding debian:QuoVadis_Root_CA_3.pem 741s Adding debian:QuoVadis_Root_CA_3_G3.pem 741s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 741s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 741s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 741s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 741s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 741s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 741s Adding debian:SZAFIR_ROOT_CA2.pem 741s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 741s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 741s Adding debian:SecureSign_RootCA11.pem 741s Adding debian:SecureTrust_CA.pem 741s Adding debian:Secure_Global_CA.pem 741s Adding debian:Security_Communication_ECC_RootCA1.pem 741s Adding debian:Security_Communication_RootCA2.pem 741s Adding debian:Security_Communication_RootCA3.pem 741s Adding debian:Security_Communication_Root_CA.pem 741s Adding debian:Starfield_Class_2_CA.pem 741s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 741s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 741s Adding debian:SwissSign_Gold_CA_-_G2.pem 741s Adding debian:SwissSign_Silver_CA_-_G2.pem 741s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 741s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 741s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 741s Adding debian:TWCA_Global_Root_CA.pem 741s Adding debian:TWCA_Root_Certification_Authority.pem 741s Adding debian:TeliaSonera_Root_CA_v1.pem 741s Adding debian:Telia_Root_CA_v2.pem 741s Adding debian:TrustAsia_Global_Root_CA_G3.pem 741s Adding debian:TrustAsia_Global_Root_CA_G4.pem 741s Adding debian:Trustwave_Global_Certification_Authority.pem 741s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 741s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 741s Adding debian:TunTrust_Root_CA.pem 741s Adding debian:UCA_Extended_Validation_Root.pem 741s Adding debian:UCA_Global_G2_Root.pem 741s Adding debian:USERTrust_ECC_Certification_Authority.pem 741s Adding debian:USERTrust_RSA_Certification_Authority.pem 741s Adding debian:XRamp_Global_CA_Root.pem 741s Adding debian:certSIGN_ROOT_CA.pem 741s Adding debian:certSIGN_Root_CA_G2.pem 741s Adding debian:e-Szigno_Root_CA_2017.pem 741s Adding debian:ePKI_Root_Certification_Authority.pem 741s Adding debian:emSign_ECC_Root_CA_-_C3.pem 741s Adding debian:emSign_ECC_Root_CA_-_G3.pem 741s Adding debian:emSign_Root_CA_-_C1.pem 741s Adding debian:emSign_Root_CA_-_G1.pem 741s Adding debian:vTrus_ECC_Root_CA.pem 741s Adding debian:vTrus_Root_CA.pem 741s done. 741s Setting up bbmap (39.06+dfsg-1) ... 741s Setting up autopkgtest-satdep (0) ... 746s (Reading database ... 77220 files and directories currently installed.) 746s Removing autopkgtest-satdep (0) ... 746s autopkgtest [16:24:45]: test run-unit-test: [----------------------- 747s 747s # bbmap 747s bbmap.sh --version 747s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 747s java -ea -Xmx2770m -Xms2770m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 747s BBMap version 39.06 747s For help, please run the shellscript with no parameters, or look in /docs/. 747s bbmap.sh --help 747s 747s BBMap 747s Written by Brian Bushnell, from Dec. 2010 - present 747s Last modified September 15, 2022 747s 747s Description: Fast and accurate splice-aware read aligner. 747s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 747s 747s To index: bbmap.sh ref= 747s To map: bbmap.sh in= out= 747s To map without writing an index: 747s bbmap.sh ref= in= out= nodisk 747s 747s in=stdin will accept reads from standard in, and out=stdout will write to 747s standard out, but file extensions are still needed to specify the format of the 747s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 747s standard in; out=stdout.sam.gz will write gzipped sam. 747s 747s Indexing Parameters (required when building the index): 747s nodisk=f Set to true to build index in memory and write nothing 747s to disk except output. 747s ref= Specify the reference sequence. Only do this ONCE, 747s when building the index (unless using 'nodisk'). 747s build=1 If multiple references are indexed in the same directory, 747s each needs a unique numeric ID (unless using 'nodisk'). 747s k=13 Kmer length, range 8-15. Longer is faster but uses 747s more memory. Shorter is more sensitive. 747s If indexing and mapping are done in two steps, K should 747s be specified each time. 747s path=<.> Specify the location to write the index, if you don't 747s want it in the current working directory. 747s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 747s number (reduces RAM by 50% and sensitivity slightly). 747s Should be enabled both when building the index AND 747s when mapping. 747s rebuild=f Force a rebuild of the index (ref= should be set). 747s 747s Input Parameters: 747s build=1 Designate index to use. Corresponds to the number 747s specified when building the index. 747s in= Primary reads input; required parameter. 747s in2= For paired reads in two files. 747s interleaved=auto True forces paired/interleaved input; false forces 747s single-ended mapping. If not specified, interleaved 747s status will be autodetected from read names. 747s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 747s BBMap and 6000 for BBMapPacBio. Only works for FASTA 747s input (use 'maxlen' for FASTQ input). The default for 747s bbmap.sh is 500, and for mapPacBio.sh is 6000. 747s unpigz=f Spawn a pigz (parallel gzip) process for faster 747s decompression than using Java. 747s Requires pigz to be installed. 747s touppercase=t (tuc) Convert lowercase letters in reads to upper case 747s (otherwise they will not match the reference). 747s 747s Sampling Parameters: 747s 747s reads=-1 Set to a positive number N to only process the first N 747s reads (or pairs), then quit. -1 means use all reads. 747s samplerate=1 Set to a number from 0 to 1 to randomly select that 747s fraction of reads for mapping. 1 uses all reads. 747s skipreads=0 Set to a number N to skip the first N reads (or pairs), 747s then map the rest. 747s 747s Mapping Parameters: 747s fast=f This flag is a macro which sets other paramters to run 747s faster, at reduced sensitivity. Bad for RNA-seq. 747s slow=f This flag is a macro which sets other paramters to run 747s slower, at greater sensitivity. 'vslow' is even slower. 747s maxindel=16000 Don't look for indels longer than this. Lower is faster. 747s Set to >=100k for RNAseq with long introns like mammals. 747s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 747s By default these are not sought, but may be found anyway. 747s tipsearch=100 Look this far for read-end deletions with anchors 747s shorter than K, using brute force. 747s minid=0.76 Approximate minimum alignment identity to look for. 747s Higher is faster and less sensitive. 747s minhits=1 Minimum number of seed hits required for candidate sites. 747s Higher is faster. 747s local=f Set to true to use local, rather than global, alignments. 747s This will soft-clip ugly ends of poor alignments. 747s perfectmode=f Allow only perfect mappings when set to true (very fast). 747s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 747s N's in the reference) mappings. 747s threads=auto (t) Set to number of threads desired. By default, uses 747s all cores available. 747s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 747s multiple top-scoring mapping locations). 747s best (use the first best site) 747s toss (consider unmapped) 747s random (select one top-scoring site randomly) 747s all (retain all top-scoring sites) 747s samestrandpairs=f (ssp) Specify whether paired reads should map to the 747s same strand or opposite strands. 747s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 747s orientation. Set to false for long-mate-pair libraries. 747s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 747s insert size or orientation, the read with the lower 747s mapping quality is marked unmapped. 747s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 747s be sent to 'outu' but not 'outm'. 747s rcomp=f Reverse complement both reads prior to mapping (for LMP 747s outward-facing libraries). 747s rcompmate=f Reverse complement read2 prior to mapping. 747s pairlen=32000 Set max allowed distance between paired reads. 747s (insert size)=(pairlen)+(read1 length)+(read2 length) 747s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 747s greater than this. Lower is faster. 747s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 747s is faster. 747s averagepairdist=100 (apd) Initial average distance between paired reads. 747s Varies dynamically; does not need to be specified. 747s deterministic=f Run in deterministic mode. In this case it is good 747s to set averagepairdist. BBMap is deterministic 747s without this flag if using single-ended reads, 747s or run singlethreaded. 747s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 747s fraction of read length. Faster but less accurate. 747s bandwidth=0 (bw) Set the bandwidth directly. 747s fraction of read length. Faster but less accurate. 747s usejni=f (jni) Do alignments faster, in C code. Requires 747s compiling the C code; details are in /jni/README.txt. 747s maxsites2=800 Don't analyze (or print) more than this many alignments 747s per read. 747s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 747s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 747s will ignore the most common 3% of kmers. 747s greedy=t Use a greedy algorithm to discard the least-useful 747s kmers on a per-read basis. 747s kfilter=0 If positive, potential mapping sites must have at 747s least this many consecutive exact matches. 747s 747s 747s Quality and Trimming Parameters: 747s qin=auto Set to 33 or 64 to specify input quality value ASCII 747s offset. 33 is Sanger, 64 is old Solexa. 747s qout=auto Set to 33 or 64 to specify output quality value ASCII 747s offset (only if output format is fastq). 747s qtrim=f Quality-trim ends before mapping. Options are: 747s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 747s untrim=f Undo trimming after mapping. Untrimmed bases will be 747s soft-clipped in cigar strings. 747s trimq=6 Trim regions with average quality below this 747s (phred algorithm). 747s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 747s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 747s quality strings for fasta input reads. 747s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 747s out-of-range quality values. 747s usequality=t Use quality scores when determining which read kmers 747s to use as seeds. 747s minaveragequality=0 (maq) Do not map reads with average quality below this. 747s maqb=0 If positive, calculate maq from this many initial bases. 747s 747s Output Parameters: 747s out= Write all reads to this file. 747s outu= Write only unmapped reads to this file. Does not 747s include unmapped paired reads with a mapped mate. 747s outm= Write only mapped reads to this file. Includes 747s unmapped paired reads with a mapped mate. 747s mappedonly=f If true, treats 'out' like 'outm'. 747s bamscript= (bs) Write a shell script to that will turn 747s the sam output into a sorted, indexed bam file. 747s ordered=f Set to true to output reads in same order as input. 747s Slower and uses more memory. 747s overwrite=f (ow) Allow process to overwrite existing files. 747s secondary=f Print secondary alignments. 747s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 747s with score of at least this fraction of primary. 747s ssao=f (secondarysiteasambiguousonly) Only print secondary 747s alignments for ambiguously-mapped reads. 747s maxsites=5 Maximum number of total alignments to print per read. 747s Only relevant when secondary=t. 747s quickmatch=f Generate cigar strings more quickly. 747s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 747s assuming that the remainder is a comment or description. 747s ziplevel=2 (zl) Compression level for zip or gzip output. 747s pigz=f Spawn a pigz (parallel gzip) process for faster 747s compression than Java. Requires pigz to be installed. 747s machineout=f Set to true to output statistics in machine-friendly 747s 'key=value' format. 747s printunmappedcount=f Print the total number of unmapped reads and bases. 747s If input is paired, the number will be of pairs 747s for which both reads are unmapped. 747s showprogress=0 If positive, print a '.' every X reads. 747s showprogress2=0 If positive, print the number of seconds since the 747s last progress update (instead of a '.'). 747s renamebyinsert=f Renames reads based on their mapped insert size. 747s 747s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 747s bloom=f Use a Bloom filter to ignore reads not sharing kmers 747s with the reference. This uses more memory, but speeds 747s mapping when most reads don't match the reference. 747s bloomhashes=2 Number of hash functions. 747s bloomminhits=3 Number of consecutive hits to be considered matched. 747s bloomk=31 Bloom filter kmer length. 747s bloomserial=t Use the serialized Bloom filter for greater loading 747s speed, if available. If not, generate and write one. 747s 747s Post-Filtering Parameters: 747s idfilter=0 Independant of minid; sets exact minimum identity 747s allowed for alignments to be printed. Range 0 to 1. 747s subfilter=-1 Ban alignments with more than this many substitutions. 747s insfilter=-1 Ban alignments with more than this many insertions. 747s delfilter=-1 Ban alignments with more than this many deletions. 747s indelfilter=-1 Ban alignments with more than this many indels. 747s editfilter=-1 Ban alignments with more than this many edits. 747s inslenfilter=-1 Ban alignments with an insertion longer than this. 747s dellenfilter=-1 Ban alignments with a deletion longer than this. 747s nfilter=-1 Ban alignments with more than this many ns. This 747s includes nocall, noref, and off scaffold ends. 747s 747s Sam flags and settings: 747s noheader=f Disable generation of header lines. 747s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 747s with = and X, or 1.3 to use M. 747s saa=t (secondaryalignmentasterisks) Use asterisks instead of 747s bases for sam secondary alignments. 747s cigar=t Set to 'f' to skip generation of cigar strings (faster). 747s keepnames=f Keep original names of paired reads, rather than 747s ensuring both reads have the same name. 747s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 747s cigar strings for deletions of at least that length. 747s rgid= Set readgroup ID. All other readgroup fields 747s can be set similarly, with the flag rgXX= 747s If you set a readgroup flag to the word 'filename', 747s e.g. rgid=filename, the input file name will be used. 747s mdtag=f Write MD tags. 747s nhtag=f Write NH tags. 747s xmtag=f Write XM tags (may only work correctly with ambig=all). 747s amtag=f Write AM tags. 747s nmtag=f Write NM tags. 747s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 747s for RNAseq using firststrand, secondstrand, or 747s unstranded libraries. Needed by Cufflinks. 747s JGI mainly uses 'firststrand'. 747s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 747s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 747s prefixed by YL:Z: 747s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 747s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 747s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 747s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 747s boundstag=f Write a tag indicating whether either read in the pair 747s goes off the end of the reference, prefixed by XB:Z: 747s notags=f Turn off all optional tags. 747s 747s Histogram and statistics output parameters: 747s scafstats= Statistics on how many reads mapped to which scaffold. 747s refstats= Statistics on how many reads mapped to which reference 747s file; only for BBSplit. 747s sortscafs=t Sort scaffolds or references by read count. 747s bhist= Base composition histogram by position. 747s qhist= Quality histogram by position. 747s aqhist= Histogram of average read quality. 747s bqhist= Quality histogram designed for box plots. 747s lhist= Read length histogram. 747s ihist= Write histogram of insert sizes (for paired reads). 747s ehist= Errors-per-read histogram. 747s qahist= Quality accuracy histogram of error rates versus 747s quality score. 747s indelhist= Indel length histogram. 747s mhist= Histogram of match, sub, del, and ins rates by 747s read location. 747s gchist= Read GC content histogram. 747s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 747s gcpairs=t Use average GC of paired reads. 747s idhist= Histogram of read count versus percent identity. 747s idbins=100 Number idhist bins. Set to 'auto' to use read length. 747s statsfile=stderr Mapping statistics are printed here. 747s 747s Coverage output parameters (these may reduce speed and use more RAM): 747s covstats= Per-scaffold coverage info. 747s rpkm= Per-scaffold RPKM/FPKM counts. 747s covhist= Histogram of # occurrences of each depth level. 747s basecov= Coverage per base location. 747s bincov= Print binned coverage per location (one line per X bases). 747s covbinsize=1000 Set the binsize for binned coverage output. 747s nzo=t Only print scaffolds with nonzero coverage. 747s twocolumn=f Change to true to print only ID and Avg_fold instead of 747s all 6 columns to the 'out=' file. 747s 32bit=f Set to true if you need per-base coverage over 64k. 747s strandedcov=f Track coverage for plus and minus strand independently. 747s startcov=f Only track start positions of reads. 747s secondarycov=t Include coverage of secondary alignments. 747s physcov=f Calculate physical coverage for paired reads. 747s This includes the unsequenced bases. 747s delcoverage=t (delcov) Count bases covered by deletions as covered. 747s True is faster than false. 747s covk=0 If positive, calculate kmer coverage statistics. 747s 747s Java Parameters: 747s -Xmx This will set Java's memory usage, 747s overriding autodetection. 747s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 747s will specify 800 megs. The max is typically 85% of 747s physical memory. The human genome requires around 24g, 747s or 12g with the 'usemodulo' flag. The index uses 747s roughly 6 bytes per reference base. 747s -eoom This flag will cause the process to exit if an 747s out-of-memory exception occurs. Requires Java 8u92+. 747s -da Disable assertions. 747s 747s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 747s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 747s 747s bbmap.sh ref=example.fasta 747s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 747s java -ea -Xmx2771m -Xms2771m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 747s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 747s Version 39.06 747s 748s No output file. 748s Writing reference. 748s Executing dna.FastaToChromArrays2 [example.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false] 748s 748s Set genScaffoldInfo=true 748s Writing chunk 1 748s Set genome to 1 748s 748s Loaded Reference: 0.008 seconds. 748s Loading index for chunk 1-1, build 1 748s No index available; generating from reference genome: /tmp/autopkgtest.iDd7qY/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 748s Indexing threads started for block 0-1 748s Indexing threads finished for block 0-1 749s Generated Index: 1.067 seconds. 749s No reads to process; quitting. 749s 749s Total time: 1.338 seconds. 749s test -d ref 749s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 749s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 749s java -ea -Xmx2771m -Xms2771m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 749s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 749s Version 39.06 749s 749s Retaining first best site only for ambiguous mappings. 749s Set genome to 1 749s 749s Loaded Reference: 0.045 seconds. 749s Loading index for chunk 1-1, build 1 749s Generated Index: 0.374 seconds. 753s Analyzed Index: 3.074 seconds. 753s Started output stream: 0.039 seconds. 753s Cleared Memory: 0.119 seconds. 753s Processing reads in single-ended mode. 753s Started read stream. 753s Started 4 mapping threads. 753s Detecting finished threads: 0, 1, 2, 3 753s 753s ------------------ Results ------------------ 753s 753s Genome: 1 753s Key Length: 13 753s Max Indel: 16000 753s Minimum Score Ratio: 0.56 753s Mapping Mode: normal 753s Reads Used: 4 (153 bases) 753s 753s Mapping: 0.133 seconds. 753s Reads/sec: 30.11 753s kBases/sec: 1.15 753s 753s 753s Read 1 data: pct reads num reads pct bases num bases 753s 753s mapped: 0.0000% 0 0.0000% 0 753s unambiguous: 0.0000% 0 0.0000% 0 753s ambiguous: 0.0000% 0 0.0000% 0 753s low-Q discards: 25.0000% 1 19.6078% 30 753s 753s perfect best site: 0.0000% 0 0.0000% 0 753s semiperfect site: 0.0000% 0 0.0000% 0 753s 753s Match Rate: NA NA NaN% 0 753s Error Rate: NaN% 0 NaN% 0 753s Sub Rate: NaN% 0 NaN% 0 753s Del Rate: NaN% 0 NaN% 0 753s Ins Rate: NaN% 0 NaN% 0 753s N Rate: NaN% 0 NaN% 0 753s 753s Total time: 3.985 seconds. 753s test -r out.sam 753s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 753s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 753s java -ea -Xmx2771m -Xms2771m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 753s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 753s Version 39.06 753s 753s Retaining first best site only for ambiguous mappings. 753s Executing dna.FastaToChromArrays2 [example.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=false, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=true] 753s 753s Set genScaffoldInfo=true 753s Set genome to 1 753s 753s Loaded Reference: 0.002 seconds. 753s Loading index for chunk 1-1, build 1 753s Indexing threads started for block 0-1 753s Indexing threads finished for block 0-1 754s Generated Index: 0.252 seconds. 760s Analyzed Index: 6.079 seconds. 760s Started output stream: 0.073 seconds. 760s Cleared Memory: 0.120 seconds. 760s Processing reads in single-ended mode. 760s Started read stream. 760s Started 4 mapping threads. 760s Detecting finished threads: 0, 1, 2, 3 760s 760s ------------------ Results ------------------ 760s 760s Genome: 1 760s Key Length: 13 760s Max Indel: 16000 760s Minimum Score Ratio: 0.56 760s Mapping Mode: normal 760s Reads Used: 3 (75 bases) 760s 760s Mapping: 0.117 seconds. 760s Reads/sec: 25.57 760s kBases/sec: 0.64 760s 760s 760s Read 1 data: pct reads num reads pct bases num bases 760s 760s mapped: 100.0000% 3 100.0000% 75 760s unambiguous: 100.0000% 3 100.0000% 75 760s ambiguous: 0.0000% 0 0.0000% 0 760s low-Q discards: 0.0000% 0 0.0000% 0 760s 760s perfect best site: 100.0000% 3 100.0000% 75 760s semiperfect site: 100.0000% 3 100.0000% 75 760s 760s Match Rate: NA NA 100.0000% 75 760s Error Rate: 0.0000% 0 0.0000% 0 760s Sub Rate: 0.0000% 0 0.0000% 0 760s Del Rate: 0.0000% 0 0.0000% 0 760s Ins Rate: 0.0000% 0 0.0000% 0 760s N Rate: 0.0000% 0 0.0000% 0 760s 760s Total time: 6.834 seconds. 760s test -r out2.sam 760s 760s # bbduk 760s bbduk.sh --version 760s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 760s java -ea -Xmx1385m -Xms1385m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 760s BBMap version 39.06 760s For help, please run the shellscript with no parameters, or look in /docs/. 760s bbduk.sh --help 760s 760s Written by Brian Bushnell 760s Last modified November 9, 2023 760s 760s Description: Compares reads to the kmers in a reference dataset, optionally 760s allowing an edit distance. Splits the reads into two outputs - those that 760s match the reference, and those that don't. Can also trim (remove) the matching 760s parts of the reads rather than binning the reads. 760s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 760s 760s Usage: bbduk.sh in= out= ref= 760s 760s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 760s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 760s fasta input, set in=stdin.fa.gz 760s 760s Input parameters: 760s in= Main input. in=stdin.fq will pipe from stdin. 760s in2= Input for 2nd read of pairs in a different file. 760s ref= Comma-delimited list of reference files. 760s In addition to filenames, you may also use the keywords: 760s adapters, artifacts, phix, lambda, pjet, mtst, kapa 760s literal= Comma-delimited list of literal reference sequences. 760s touppercase=f (tuc) Change all bases upper-case. 760s interleaved=auto (int) t/f overrides interleaved autodetection. 760s Must be set mainually when streaming fastq input. 760s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 760s reads=-1 If positive, quit after processing X reads or pairs. 760s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 760s possible unambiguous copies. Intended for short motifs 760s or adapter barcodes, as time/memory use is exponential. 760s samplerate=1 Set lower to only process a fraction of input reads. 760s samref= Optional reference fasta for processing sam files. 760s 760s Output parameters: 760s out= (outnonmatch) Write reads here that do not contain 760s kmers matching the database. 'out=stdout.fq' will pipe 760s to standard out. 760s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 760s different file. 760s outm= (outmatch) Write reads here that fail filters. In default 760s kfilter mode, this means any read with a matching kmer. 760s In any mode, it also includes reads that fail filters such 760s as minlength, mingc, maxgc, entropy, etc. In other words, 760s it includes all reads that do not go to 'out'. 760s outm2= (outmatch2) Use this to write 2nd read of pairs to a 760s different file. 760s outs= (outsingle) Use this to write singleton reads whose mate 760s was trimmed shorter than minlen. 760s stats= Write statistics about which contamininants were detected. 760s refstats= Write statistics on a per-reference-file basis. 760s rpkm= Write RPKM for each reference sequence (for RNA-seq). 760s dump= Dump kmer tables to a file, in fasta format. 760s duk= Write statistics in duk's format. *DEPRECATED* 760s nzo=t Only write statistics about ref sequences with nonzero hits. 760s overwrite=t (ow) Grant permission to overwrite files. 760s showspeed=t (ss) 'f' suppresses display of processing speed. 760s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 760s fastawrap=70 Length of lines in fasta output. 760s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 760s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 760s 5 includes base counts. 760s rename=f Rename reads to indicate which sequences they matched. 760s refnames=f Use names of reference files rather than scaffold IDs. 760s trd=f Truncate read and ref names at the first whitespace. 760s ordered=f Set to true to output reads in same order as input. 760s maxbasesout=-1 If positive, quit after writing approximately this many 760s bases to out (outu/outnonmatch). 760s maxbasesoutm=-1 If positive, quit after writing approximately this many 760s bases to outm (outmatch). 760s json=f Print to screen in json format. 760s 760s Histogram output parameters: 760s bhist= Base composition histogram by position. 760s qhist= Quality histogram by position. 760s qchist= Count of bases with each quality value. 760s aqhist= Histogram of average read quality. 760s bqhist= Quality histogram designed for box plots. 760s lhist= Read length histogram. 760s phist= Polymer length histogram. 760s gchist= Read GC content histogram. 760s enthist= Read entropy histogram. 760s ihist= Insert size histogram, for paired reads in mapped sam. 760s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 760s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 760s more memory. The default is 6000 for some histograms 760s and 80000 for others. 760s 760s Histograms for mapped sam/bam files only: 760s histbefore=t Calculate histograms from reads before processing. 760s ehist= Errors-per-read histogram. 760s qahist= Quality accuracy histogram of error rates versus quality 760s score. 760s indelhist= Indel length histogram. 760s mhist= Histogram of match, sub, del, and ins rates by position. 760s idhist= Histogram of read count versus percent identity. 760s idbins=100 Number idhist bins. Set to 'auto' to use read length. 760s varfile= Ignore substitution errors listed in this file when 760s calculating error rates. Can be generated with 760s CallVariants. 760s vcf= Ignore substitution errors listed in this VCF file 760s when calculating error rates. 760s ignorevcfindels=t Also ignore indels listed in the VCF. 760s 760s Processing parameters: 760s k=27 Kmer length used for finding contaminants. Contaminants 760s shorter than k will not be found. k must be at least 1. 760s rcomp=t Look for reverse-complements of kmers in addition to 760s forward kmers. 760s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 760s increase sensitivity in the presence of errors. This may 760s also be set to a number, e.g. mm=3, to mask that many bp. 760s The default mm=t corresponds to mm=1 for odd-length kmers 760s and mm=2 for even-length kmers (as of v39.04), while 760s mm=f is always equivalent to mm=0. 760s minkmerhits=1 (mkh) Reads need at least this many matching kmers 760s to be considered as matching the reference. 760s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 760s kmers to hit a ref, in order to be considered a match. 760s If this and minkmerhits are set, the greater is used. 760s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 760s bases to be covered by ref kmers to be considered a match. 760s If specified, mcf overrides mkh and mkf. 760s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 760s Memory use is proportional to (3*K)^hdist. 760s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 760s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 760s and indels). Memory use is proportional to (8*K)^edist. 760s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 760s qhdist2=0 Sets qhdist for short kmers, when using mink. 760s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 760s forbidn=f (fn) Forbids matching of read kmers containing N. 760s By default, these will match a reference 'A' if 760s hdist>0 or edist>0, to increase sensitivity. 760s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 760s match (or either is trimmed shorter than minlen). 760s Set to false to require both. 760s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 760s This makes the statistics a bit odd. 760s findbestmatch=f (fbm) If multiple matches, associate read with sequence 760s sharing most kmers. Reduces speed. 760s skipr1=f Don't do kmer-based operations on read 1. 760s skipr2=f Don't do kmer-based operations on read 2. 760s ecco=f For overlapping paired reads only. Performs error- 760s correction with BBMerge prior to kmer operations. 760s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 760s matrices generated by CalcTrueQuality. 760s sam= If recalibration is desired, and matrices have not already 760s been generated, BBDuk will create them from the sam file. 760s amino=f Run in amino acid mode. Some features have not been 760s tested, but kmer-matching works fine. Maximum k is 12. 760s 760s Speed and Memory parameters: 760s threads=auto (t) Set number of threads to use; default is number of 760s logical processors. 760s prealloc=f Preallocate memory in table. Allows faster table loading 760s and more efficient memory usage, for a large reference. 760s monitor=f Kill this process if it crashes. monitor=600,0.01 would 760s kill after 600 seconds under 1% usage. 760s minrskip=1 (mns) Force minimal skip interval when indexing reference 760s kmers. 1 means use all, 2 means use every other kmer, etc. 760s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 760s reference kmers. Normally all are used for scaffolds<100kb, 760s but with longer scaffolds, up to maxrskip-1 are skipped. 760s rskip= Set both minrskip and maxrskip to the same value. 760s If not set, rskip will vary based on sequence length. 760s qskip=1 Skip query kmers to increase speed. 1 means use all. 760s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 760s reads and reference. Increases speed and reduces memory. 760s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 760s 760s Trimming/Filtering/Masking parameters: 760s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 760s All kmer processing modes are mutually exclusive. 760s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 760s 760s ktrim=f Trim reads to remove bases matching reference kmers, plus 760s all bases to the left or right. 760s Values: 760s f (don't trim), 760s r (trim to the right), 760s l (trim to the left) 760s ktrimtips=0 Set this to a positive number to perform ktrim on both 760s ends, examining only the outermost X bases. 760s kmask= Replace bases matching ref kmers with another symbol. 760s Allows any non-whitespace character, and processes short 760s kmers on both ends if mink is set. 'kmask=lc' will 760s convert masked bases to lowercase. 760s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 760s ksplit=f For single-ended reads only. Reads will be split into 760s pairs around the kmer. If the kmer is at the end of the 760s read, it will be trimmed instead. Singletons will go to 760s out, and pairs will go to outm. Do not use ksplit with 760s other operations such as quality-trimming or filtering. 760s mink=0 Look for shorter kmers at read tips down to this length, 760s when k-trimming or masking. 0 means disabled. Enabling 760s this will disable maskmiddle. 760s qtrim=f Trim read ends to remove bases with quality below trimq. 760s Performed AFTER looking for kmers. Values: 760s rl (trim both ends), 760s f (neither end), 760s r (right end only), 760s l (left end only), 760s w (sliding window). 760s trimq=6 Regions with average quality BELOW this will be trimmed, 760s if qtrim is set to something other than f. Can be a 760s floating-point number like 7.3. 760s trimclip=f Trim soft-clipped bases from sam files. 760s minlength=10 (ml) Reads shorter than this after trimming will be 760s discarded. Pairs will be discarded if both are shorter. 760s mlf=0 (minlengthfraction) Reads shorter than this fraction of 760s original length after trimming will be discarded. 760s maxlength= Reads longer than this after trimming will be discarded. 760s minavgquality=0 (maq) Reads with average quality (after trimming) below 760s this will be discarded. 760s maqb=0 If positive, calculate maq from this many initial bases. 760s minbasequality=0 (mbq) Reads with any base below this quality (after 760s trimming) will be discarded. 760s maxns=-1 If non-negative, reads with more Ns than this 760s (after trimming) will be discarded. 760s mcb=0 (minconsecutivebases) Discard reads without at least 760s this many consecutive called bases. 760s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 760s than minlength to outm rather than discarding. 760s tp=0 (trimpad) Trim this much extra around matching kmers. 760s tbo=f (trimbyoverlap) Trim adapters based on where paired 760s reads overlap. 760s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 760s minoverlap=14 Require this many bases of overlap for detection. 760s mininsert=40 Require insert size of at least this for overlap. 760s Should be reduced to 16 for small RNA sequencing. 760s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 760s reads to the minimum length of either. 760s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 760s (exclusive, 0-based). 760s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 760s (exclusive, 0-based). 760s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 760s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 760s modulo this number. 760s restrictleft=0 If positive, only look for kmer matches in the 760s leftmost X bases. 760s restrictright=0 If positive, only look for kmer matches in the 760s rightmost X bases. 760s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 760s both ends is desired, use ktrimtips. 760s mingc=0 Discard reads with GC content below this. 760s maxgc=1 Discard reads with GC content above this. 760s gcpairs=t Use average GC of paired reads. 760s Also affects gchist. 760s tossjunk=f Discard reads with invalid characters as bases. 760s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 760s 760s Header-parsing parameters - these require Illumina headers: 760s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 760s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 760s or barcodes containing 'N' otherwise. A barcode must be 760s the last part of the read header. Values: 760s t: Remove reads with bad barcodes. 760s f: Ignore barcodes. 760s crash: Crash upon encountering bad barcodes. 760s barcodes= Comma-delimited list of barcodes or files of barcodes. 760s xmin=-1 If positive, discard reads with a lesser X coordinate. 760s ymin=-1 If positive, discard reads with a lesser Y coordinate. 760s xmax=-1 If positive, discard reads with a greater X coordinate. 760s ymax=-1 If positive, discard reads with a greater Y coordinate. 760s 760s Polymer trimming: 760s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 760s at least this length on either end of reads. 760s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 760s length on the left end of reads. Does not trim poly-C. 760s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 760s length on the right end of reads. Does not trim poly-C. 760s trimpolyg=0 This sets both left and right at once. 760s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 760s at least this length (on the left). 760s Note: there are also equivalent poly-C flags. 760s 760s Polymer tracking: 760s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 760s plen=20 Length of homopolymers to count. 760s 760s Entropy/Complexity parameters: 760s entropy=-1 Set between 0 and 1 to filter reads with entropy below 760s that value. Higher is more stringent. 760s entropywindow=50 Calculate entropy using a sliding window of this length. 760s entropyk=5 Calculate entropy using kmers of this length. 760s minbasefrequency=0 Discard reads with a minimum base frequency below this. 760s entropytrim=f Values: 760s f: (false) Do not entropy-trim. 760s r: (right) Trim low entropy on the right end only. 760s l: (left) Trim low entropy on the left end only. 760s rl: (both) Trim low entropy on both ends. 760s entropymask=f Values: 760s f: (filter) Discard low-entropy sequences. 760s t: (true) Mask low-entropy parts of sequences with N. 760s lc: Change low-entropy parts of sequences to lowercase. 760s entropymark=f Mark each base with its entropy value. This is on a scale 760s of 0-41 and is reported as quality scores, so the output 760s should be fastq or fasta+qual. 760s NOTE: If set, entropytrim overrides entropymask. 760s 760s Cardinality estimation: 760s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 760s cardinalityout=f (loglogout) Count unique kmers in output reads. 760s loglogk=31 Use this kmer length for counting. 760s loglogbuckets=2048 Use this many buckets for counting. 760s khist= Kmer frequency histogram; plots number of kmers versus 760s kmer depth. This is approximate. 760s khistout= Kmer frequency histogram for output reads. 760s 760s Java Parameters: 760s 760s -Xmx This will set Java's memory usage, overriding autodetection. 760s -Xmx20g will 760s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 760s The max is typically 85% of physical memory. 760s -eoom This flag will cause the process to exit if an 760s out-of-memory exception occurs. Requires Java 8u92+. 760s -da Disable assertions. 760s 760s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 760s 760s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 760s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 760s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 760s java -ea -Xmx1385m -Xms1385m -cp /usr/share/java/bbmap.jar jgi.BBDuk in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 761s Executing jgi.BBDuk [in1=misc_dna_as_illumina.fastq, in2=misc_rna_as_illumina.fastq, qtrim=rl, trimq=15, minlen=75, out=out.fastq.gz] 761s Version 39.06 761s 761s 0.031 seconds. 761s Initial: 761s Memory: max=1453m, total=1453m, free=1423m, used=30m 761s 761s Input is being processed as paired 761s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 761s Started output streams: 0.032 seconds. 761s Processing time: 0.011 seconds. 761s 761s Input: 8 reads 306 bases. 761s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 761s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 761s Result: 0 reads (0.00%) 0 bases (0.00%) 761s 761s Time: 0.046 seconds. 761s Reads Processed: 8 0.17k reads/sec 761s Bases Processed: 306 0.01m bases/sec 761s test -r out.fastq.gz 761s 761s # bbnorm 761s bbnorm.sh --version 761s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 761s java -ea -Xmx2771m -Xms2771m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 761s BBMap version 39.06 761s For help, please run the shellscript with no parameters, or look in /docs/. 761s bbnorm.sh --help 761s 761s Written by Brian Bushnell 761s Last modified October 19, 2017 761s 761s Description: Normalizes read depth based on kmer counts. 761s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 761s However, Tadpole has superior error-correction to BBNorm. 761s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 761s 761s Usage: bbnorm.sh in= out= outt= hist= 761s 761s Input parameters: 761s in=null Primary input. Use in2 for paired reads in a second file 761s in2=null Second input file for paired reads in two files 761s extra=null Additional files to use for input (generating hash table) but not for output 761s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 761s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 761s kmersample=1 Process every nth kmer, and skip the rest 761s readsample=1 Process every nth read, and skip the rest 761s interleaved=auto May be set to true or false to force the input read file to ovverride autodetection of the input file as paired interleaved. 761s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 761s 761s Output parameters: 761s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 761s outt= (outtoss) File for reads that were excluded from primary output 761s reads=-1 Only process this number of reads, then quit (-1 means all) 761s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 761s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 761s zerobin=f Set to true if you want kmers with a count of 0 to go in the 0 bin instead of the 1 bin in histograms. 761s Default is false, to prevent confusion about how there can be 0-count kmers. 761s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 761s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 761s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 761s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 761s rename=f Rename reads based on their kmer depth. 761s 761s Hashing parameters: 761s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 761s bits=32 Bits per cell in bloom filter; must be 2, 4, 8, 16, or 32. Maximum kmer depth recorded is 2^cbits. Automatically reduced to 16 in 2-pass. 761s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 761s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 761s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 761s prefilter=f True is slower, but generally more accurate; filters out low-depth kmers from the main hashtable. The prefilter is more memory-efficient because it uses 2-bit cells. 761s prehashes=2 Number of hashes for prefilter. 761s prefilterbits=2 (pbits) Bits per cell in prefilter. 761s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 761s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 761s minq=6 Ignore kmers containing bases with quality below this 761s minprob=0.5 Ignore kmers with overall probability of correctness below this 761s threads=auto (t) Spawn exactly X hashing threads (default is number of logical processors). Total active threads may exceed X due to I/O threads. 761s rdk=t (removeduplicatekmers) When true, a kmer's count will only be incremented once per read pair, even if that kmer occurs more than once. 761s 761s Normalization parameters: 761s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 761s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 761s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 761s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 761s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 761s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 761s percentile=54.0 (dp) Read depth is by default inferred from the 54th percentile of kmer depth, but this may be changed to any number 1-100. 761s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 761s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 761s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 761s 761s Error detection parameters: 761s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 761s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 761s tossbadreads=f (tbr) Throw away reads detected as containing errors. 761s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 761s errordetectratio=125 (edr) Reads with a ratio of at least this much between their high and low depth kmers will be classified as error reads. 761s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 761s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 761s 761s Error correction parameters: 761s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 761s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 761s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 761s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 761s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 761s eccmaxqual=127 Do not correct bases with quality above this value. 761s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 761s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 761s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 761s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 761s overlap=f (ecco) Error correct by read overlap. 761s 761s Depth binning parameters: 761s lowbindepth=10 (lbd) Cutoff for low depth bin. 761s highbindepth=80 (hbd) Cutoff for high depth bin. 761s outlow= Pairs in which both reads have a median below lbd go into this file. 761s outhigh= Pairs in which both reads have a median above hbd go into this file. 761s outmid= All other pairs go into this file. 761s 761s Histogram parameters: 761s hist= Specify a file to write the input kmer depth histogram. 761s histout= Specify a file to write the output kmer depth histogram. 761s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 761s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 761s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 761s 761s Peak calling parameters: 761s peaks= Write the peaks to this file. Default is stdout. 761s minHeight=2 (h) Ignore peaks shorter than this. 761s minVolume=5 (v) Ignore peaks with less area than this. 761s minWidth=3 (w) Ignore peaks narrower than this. 761s minPeak=2 (minp) Ignore peaks with an X-value below this. 761s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 761s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 761s 761s Java Parameters: 761s -Xmx This will set Java's memory usage, overriding autodetection. 761s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 761s The max is typically 85% of physical memory. 761s -eoom This flag will cause the process to exit if an 761s out-of-memory exception occurs. Requires Java 8u92+. 761s -da Disable assertions. 761s 761s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 761s 761s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 761s out=out3.fastq outt=outt.fastq hist=hist.plt 761s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 761s java -ea -Xmx2771m -Xms2771m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=sanger_full_range_original_sanger.fastq qin=33 out=out3.fastq outt=outt.fastq hist=hist.plt 761s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 761s 761s 761s *********** Pass 1 ********** 761s 761s 761s Settings: 761s threads: 4 761s k: 31 761s deterministic: true 761s toss error reads: false 761s passes: 1 761s bits per cell: 16 761s cells: 1025.36M 761s hashes: 3 761s base min quality: 5 761s kmer min prob: 0.5 761s 761s target depth: 400 761s min depth: 3 761s max depth: 500 761s min good kmers: 15 761s depth percentile: 64.8 761s ignore dupe kmers: true 761s fix spikes: false 761s histogram length: 65536 761s print zero cov: false 761s 762s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 762s 762s Estimated unique kmers: 7 762s 762s Table creation time: 1.038 seconds. 762s Started output threads. 763s Started output threads. 763s Table read time: 0.124 seconds. 1.51 kb/sec 763s Total reads in: 2 0.000% Kept 763s Total bases in: 188 0.000% Kept 763s Error reads in: 2 100.000% 763s Error type 1: 2 100.000% 763s Error type 2: 0 0.000% 763s Error type 3: 0 0.000% 763s 763s Wrote histogram to hist.plt 763s Total kmers counted: 128 763s Total unique kmer count: 128 763s Includes forward kmers only. 763s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 763s The most accurate value is the greater of the two. 763s 763s Percent unique: 100.00% 763s Depth average: 1.00 (unique kmers) 763s Depth median: 1 (unique kmers) 763s Depth standard deviation: 0.00 (unique kmers) 763s Corrected depth average: 0.00 763s 763s Depth average: 1.00 (all kmers) 763s Depth median: 1 (all kmers) 763s Depth standard deviation: 0.00 (all kmers) 763s 763s Approx. read depth median: 1.47 763s 763s *********** Pass 2 ********** 763s 763s 763s Settings: 763s threads: 4 763s k: 31 763s deterministic: true 763s toss error reads: false 763s passes: 1 763s bits per cell: 16 763s cells: 1025.36M 763s hashes: 3 763s base min quality: 5 763s kmer min prob: 0.5 763s 763s target depth: 100 763s min depth: 5 763s max depth: 100 763s min good kmers: 15 763s depth percentile: 54.0 763s ignore dupe kmers: true 763s fix spikes: false 763s histogram length: 65536 763s 763s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 763s 763s Estimated unique kmers: 0 763s 763s Table creation time: 0.381 seconds. 763s Started output threads. 763s Started output threads. 763s Table read time: 0.002 seconds. 0.00 kb/sec 763s Total reads in: 0 NaN% Kept 763s Total bases in: 0 NaN% Kept 763s Error reads in: 0 NaN% 763s Error type 1: 0 NaN% 763s Error type 2: 0 NaN% 763s Error type 3: 0 NaN% 763s Total kmers counted: 0 763s Total unique kmer count: 0 763s Includes forward kmers only. 763s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 763s The most accurate value is the greater of the two. 763s 763s Percent unique: NaN% 763s Depth average: NaN (unique kmers) 763s Depth median: 0 (unique kmers) 763s Depth standard deviation: NaN (unique kmers) 763s Corrected depth average: NaN 763s 763s Depth average: NaN (all kmers) 763s Depth median: 0 (all kmers) 763s Depth standard deviation: 0.00 (all kmers) 763s 763s Approx. read depth median: NaN 763s 763s Removing temp files. 763s 763s Total time: 1.823 seconds. 0.10 kb/sec 763s test -r out3.fastq 763s test -r outt.fastq 763s test -r hist.plt 763s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 763s out=out4.fastq outt=outt2.fastq hist=hist2.plt 763s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 763s java -ea -Xmx2771m -Xms2771m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=illumina_full_range_original_illumina.fastq qin=64 out=out4.fastq outt=outt2.fastq hist=hist2.plt 764s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 764s 764s 764s *********** Pass 1 ********** 764s 764s 764s Settings: 764s threads: 4 764s k: 31 764s deterministic: true 764s toss error reads: false 764s passes: 1 764s bits per cell: 16 764s cells: 1025.36M 764s hashes: 3 764s base min quality: 5 764s kmer min prob: 0.5 764s 764s target depth: 400 764s min depth: 3 764s max depth: 500 764s min good kmers: 15 764s depth percentile: 64.8 764s ignore dupe kmers: true 764s fix spikes: false 764s histogram length: 65536 764s print zero cov: false 764s 765s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 765s 765s Estimated unique kmers: 7 765s 765s Table creation time: 1.055 seconds. 765s Started output threads. 765s Started output threads. 765s Table read time: 0.011 seconds. 11.57 kb/sec 765s Total reads in: 2 0.000% Kept 765s Total bases in: 126 0.000% Kept 765s Error reads in: 2 100.000% 765s Error type 1: 2 100.000% 765s Error type 2: 0 0.000% 765s Error type 3: 0 0.000% 765s 765s Wrote histogram to hist2.plt 765s Total kmers counted: 66 765s Total unique kmer count: 66 765s Includes forward kmers only. 765s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 765s The most accurate value is the greater of the two. 765s 765s Percent unique: 100.00% 765s Depth average: 1.00 (unique kmers) 765s Depth median: 1 (unique kmers) 765s Depth standard deviation: 0.00 (unique kmers) 765s Corrected depth average: 0.00 765s 765s Depth average: 1.00 (all kmers) 765s Depth median: 1 (all kmers) 765s Depth standard deviation: 0.00 (all kmers) 765s 765s Approx. read depth median: 1.91 765s 765s *********** Pass 2 ********** 765s 765s 765s Settings: 765s threads: 4 765s k: 31 765s deterministic: true 765s toss error reads: false 765s passes: 1 765s bits per cell: 16 765s cells: 1025.36M 765s hashes: 3 765s base min quality: 5 765s kmer min prob: 0.5 765s 765s target depth: 100 765s min depth: 5 765s max depth: 100 765s min good kmers: 15 765s depth percentile: 54.0 765s ignore dupe kmers: true 765s fix spikes: false 765s histogram length: 65536 765s 765s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 765s 765s Estimated unique kmers: 0 765s 765s Table creation time: 0.368 seconds. 765s Started output threads. 765s Started output threads. 765s Table read time: 0.002 seconds. 0.00 kb/sec 765s Total reads in: 0 NaN% Kept 765s Total bases in: 0 NaN% Kept 765s Error reads in: 0 NaN% 765s Error type 1: 0 NaN% 765s Error type 2: 0 NaN% 765s Error type 3: 0 NaN% 765s Total kmers counted: 0 765s Total unique kmer count: 0 765s Includes forward kmers only. 765s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 765s The most accurate value is the greater of the two. 765s 765s Percent unique: NaN% 765s Depth average: NaN (unique kmers) 765s Depth median: 0 (unique kmers) 765s Depth standard deviation: NaN (unique kmers) 765s Corrected depth average: NaN 765s 765s Depth average: NaN (all kmers) 765s Depth median: 0 (all kmers) 765s Depth standard deviation: 0.00 (all kmers) 765s 765s Approx. read depth median: NaN 765s 765s Removing temp files. 765s 765s Total time: 1.550 seconds. 0.08 kb/sec 765s test -r out4.fastq 765s test -r outt2.fastq 765s test -r hist2.plt 766s autopkgtest [16:25:05]: test run-unit-test: -----------------------] 766s run-unit-test PASS 766s autopkgtest [16:25:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 767s autopkgtest [16:25:06]: @@@@@@@@@@@@@@@@@@@@ summary 767s run-unit-test PASS