0s autopkgtest [21:09:27]: starting date and time: 2024-03-21 21:09:27+0000 0s autopkgtest [21:09:27]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [21:09:27]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4zxl47mx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:openjdk-17,src:alsa-lib,src:at-spi2-core,src:cups,src:glib2.0,src:gnutls28,src:gtk+2.0,src:gtk+3.0,src:libpng1.6,src:nettle,src:wp2latex --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-17/17.0.11~7ea-1 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+2.0/2.24.33-3.1ubuntu3 gtk+3.0/3.24.41-1.1ubuntu3 libpng1.6/1.6.43-3 nettle/3.9.1-2.2 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-3@bos03-arm64-4.secgroup --name adt-noble-arm64-bbmap-20240321-210927-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 381s Creating nova instance adt-noble-arm64-bbmap-20240321-210927-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240321.img (UUID 28ecccfc-4cb0-4cc6-a280-209e2d140e10)... 381s nova boot failed (attempt #1): 381s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader') 381s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader') 381s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken') 381s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth') 381s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password') 381s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token') 381s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password') 381s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP') 381s 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" 381s DEBUG (connectionpool:962) Starting new HTTPS connection (1): keystone.ps6.canonical.com:5000 381s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "GET /v3 HTTP/1.1" 200 267 381s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 267 Content-Type: application/json Date: Thu, 21 Mar 2024 21:09:58 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) Vary: X-Auth-Token x-openstack-request-id: req-ee1fc49d-ec1c-414f-9a9e-0e95e6ac5ff4 381s 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"}]}} 381s DEBUG (session:946) GET call to https://keystone.ps6.canonical.com:5000/v3 used request id req-ee1fc49d-ec1c-414f-9a9e-0e95e6ac5ff4 381s DEBUG (base:182) Making authentication request to https://keystone.ps6.canonical.com:5000/v3/auth/tokens 381s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "POST /v3/auth/tokens HTTP/1.1" 201 12445 381s 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": ["k6RDc5BoQXmbJ5GqA5nhFQ"], "expires_at": "2024-03-22T21:09:59.000000Z", "issued_at": "2024-03-21T21:09:59.000000Z", "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"}]}} 381s 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}8803a372abef82f06762c585705d585d7ad5cb94c22a0ac8f1b9e2f3d0ea9a22" 381s 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}8803a372abef82f06762c585705d585d7ad5cb94c22a0ac8f1b9e2f3d0ea9a22" 381s DEBUG (connectionpool:962) Starting new HTTPS connection (1): nova.ps6.canonical.com:8774 381s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1 HTTP/1.1" 302 0 381s RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Thu, 21 Mar 2024 21:09:59 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-82b7abea-0db2-4b37-8bf1-3a0534f43471 x-openstack-request-id: req-82b7abea-0db2-4b37-8bf1-3a0534f43471 381s DEBUG (session:548) RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Thu, 21 Mar 2024 21:09:59 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-82b7abea-0db2-4b37-8bf1-3a0534f43471 x-openstack-request-id: req-82b7abea-0db2-4b37-8bf1-3a0534f43471 381s RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged. 381s DEBUG (session:580) RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged. 381s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/ HTTP/1.1" 200 397 381s RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Thu, 21 Mar 2024 21:09:59 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-a27d8cf0-9dd9-4bd2-b8fe-c69949b1820c x-openstack-request-id: req-a27d8cf0-9dd9-4bd2-b8fe-c69949b1820c 381s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Thu, 21 Mar 2024 21:09:59 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-a27d8cf0-9dd9-4bd2-b8fe-c69949b1820c x-openstack-request-id: req-a27d8cf0-9dd9-4bd2-b8fe-c69949b1820c 381s 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"}]}} 381s 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"}]}} 381s GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-a27d8cf0-9dd9-4bd2-b8fe-c69949b1820c 381s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-a27d8cf0-9dd9-4bd2-b8fe-c69949b1820c 381s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader') 381s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader') 381s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken') 381s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth') 381s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password') 381s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token') 381s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password') 381s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth') 381s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP') 381s DEBUG (session:517) REQ: curl -g -i -X GET https://glance.ps6.canonical.com:9292/v2/images/28ecccfc-4cb0-4cc6-a280-209e2d140e10 -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}8803a372abef82f06762c585705d585d7ad5cb94c22a0ac8f1b9e2f3d0ea9a22" -H "X-OpenStack-Nova-API-Version: 2.87" 381s DEBUG (connectionpool:962) Starting new HTTPS connection (1): glance.ps6.canonical.com:9292 381s DEBUG (connectionpool:429) https://glance.ps6.canonical.com:9292 "GET /v2/images/28ecccfc-4cb0-4cc6-a280-209e2d140e10 HTTP/1.1" 200 1935 381s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 1935 Content-Type: application/json Date: Thu, 21 Mar 2024 21:10:00 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) X-Openstack-Request-Id: req-46ef0d60-256d-456e-ab58-31b7f09ccace 381s DEBUG (session:580) RESP BODY: {"base_image_ref": "09c3944a-cd0d-425d-b22f-cde7ec51d155", "boot_roles": "reader,member", "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": "543499e0-aeb9-4922-8880-c51a4fc18bf8", "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-20240321.img", "disk_format": "qcow2", "container_format": "bare", "visibility": "private", "size": 2306342912, "virtual_size": 21474836480, "status": "active", "checksum": "8198422d2c7534f56b5a2a46874755ab", "protected": false, "min_ram": 0, "min_disk": 20, "owner": "bd8b3df3f03d43a0a9303b7c0434fdab", "os_hidden": false, "os_hash_algo": "sha512", "os_hash_value": "c59ccc5319301a5ec5077e547fd66aac380403815cc5c00e980d9dce3efa9cc417db45604d4bf4c4e1913c2a5af61917b84fdf003c36adeb77990adb487af4ed", "id": "28ecccfc-4cb0-4cc6-a280-209e2d140e10", "created_at": "2024-03-21T11:24:35Z", "updated_at": "2024-03-21T11:25:04Z", "locations": [{"url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/28ecccfc-4cb0-4cc6-a280-209e2d140e10/snap", "metadata": {"store": "ceph"}}], "direct_url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/28ecccfc-4cb0-4cc6-a280-209e2d140e10/snap", "tags": [], "self": "/v2/images/28ecccfc-4cb0-4cc6-a280-209e2d140e10", "file": "/v2/images/28ecccfc-4cb0-4cc6-a280-209e2d140e10/file", "schema": "/v2/schemas/image", "stores": "ceph"} 381s DEBUG (session:936) GET call to image for https://glance.ps6.canonical.com:9292/v2/images/28ecccfc-4cb0-4cc6-a280-209e2d140e10 used request id req-46ef0d60-256d-456e-ab58-31b7f09ccace 381s 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}8803a372abef82f06762c585705d585d7ad5cb94c22a0ac8f1b9e2f3d0ea9a22" -H "X-OpenStack-Nova-API-Version: 2.87" 381s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/autopkgtest-big HTTP/1.1" 404 88 381s DEBUG (session:548) RESP: [404] Connection: Keep-Alive Content-Length: 88 Content-Type: application/json; charset=UTF-8 Date: Thu, 21 Mar 2024 21:10:00 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-0a8a0da6-840b-4a07-8525-331a9370c02a x-openstack-request-id: req-0a8a0da6-840b-4a07-8525-331a9370c02a 381s DEBUG (session:580) RESP BODY: {"itemNotFound": {"code": 404, "message": "Flavor autopkgtest-big could not be found."}} 381s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest-big used request id req-0a8a0da6-840b-4a07-8525-331a9370c02a 381s 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}8803a372abef82f06762c585705d585d7ad5cb94c22a0ac8f1b9e2f3d0ea9a22" -H "X-OpenStack-Nova-API-Version: 2.87" 381s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors?is_public=None HTTP/1.1" 200 1739 381s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 1739 Content-Type: application/json Date: Thu, 21 Mar 2024 21:10:00 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-12382bd6-7813-47eb-8612-f6c9c22d4a7d x-openstack-request-id: req-12382bd6-7813-47eb-8612-f6c9c22d4a7d 381s 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}]} 381s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors?is_public=None used request id req-12382bd6-7813-47eb-8612-f6c9c22d4a7d 381s 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}8803a372abef82f06762c585705d585d7ad5cb94c22a0ac8f1b9e2f3d0ea9a22" -H "X-OpenStack-Nova-API-Version: 2.87" 381s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/a8256f9e-53ee-4584-ad7f-60e088825b83 HTTP/1.1" 200 618 381s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 618 Content-Type: application/json Date: Thu, 21 Mar 2024 21:10:00 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-42853d88-695e-44b0-b24b-7eb89325a4f1 x-openstack-request-id: req-42853d88-695e-44b0-b24b-7eb89325a4f1 381s 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"}}} 381s 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-42853d88-695e-44b0-b24b-7eb89325a4f1 381s 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}8803a372abef82f06762c585705d585d7ad5cb94c22a0ac8f1b9e2f3d0ea9a22" -H "X-OpenStack-Nova-API-Version: 2.87" -d '{"server": {"name": "adt-noble-arm64-bbmap-20240321-210927-juju-7f2275-prod-proposed-migration-environment-3", "imageRef": "28ecccfc-4cb0-4cc6-a280-209e2d140e10", "flavorRef": "a8256f9e-53ee-4584-ad7f-60e088825b83", "user_data": "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", "key_name": "testbed-juju-7f2275-prod-proposed-migration-environment-3", "min_count": 1, "max_count": 1, "security_groups": [{"name": "autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-4.secgroup"}], "networks": [{"uuid": "6ea4839c-9760-4b54-ab7d-70a6312667d1"}]}}' 381s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "POST /v2.1/servers HTTP/1.1" 403 115 381s DEBUG (session:548) RESP: [403] Connection: Keep-Alive Content-Length: 115 Content-Type: application/json; charset=UTF-8 Date: Thu, 21 Mar 2024 21:10:00 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-61fefb3e-b7b1-4180-86b4-b420af4ea17e x-openstack-request-id: req-61fefb3e-b7b1-4180-86b4-b420af4ea17e 381s DEBUG (session:580) RESP BODY: {"forbidden": {"code": 403, "message": "Quota exceeded for cores: Requested 4, but already used 142 of 140 cores"}} 381s DEBUG (session:936) POST call to compute for https://nova.ps6.canonical.com:8774/v2.1/servers used request id req-61fefb3e-b7b1-4180-86b4-b420af4ea17e 381s DEBUG (shell:822) Quota exceeded for cores: Requested 4, but already used 142 of 140 cores (HTTP 403) (Request-ID: req-61fefb3e-b7b1-4180-86b4-b420af4ea17e) 381s Traceback (most recent call last): 381s File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 820, in main 381s OpenStackComputeShell().main(argv) 381s File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 742, in main 381s args.func(self.cs, args) 381s File "/usr/lib/python3/dist-packages/novaclient/v2/shell.py", line 971, in do_boot 381s server = cs.servers.create(*boot_args, **boot_kwargs) 381s File "/usr/lib/python3/dist-packages/novaclient/v2/servers.py", line 1477, in create 381s return self._boot(response_key, *boot_args, **boot_kwargs) 381s File "/usr/lib/python3/dist-packages/novaclient/v2/servers.py", line 836, in _boot 381s return self._create('/servers', body, response_key, 381s File "/usr/lib/python3/dist-packages/novaclient/base.py", line 363, in _create 381s resp, body = self.api.client.post(url, body=body) 381s File "/usr/lib/python3/dist-packages/keystoneauth1/adapter.py", line 392, in post 381s return self.request(url, 'POST', **kwargs) 381s File "/usr/lib/python3/dist-packages/novaclient/client.py", line 78, in request 381s raise exceptions.from_response(resp, body, url, method) 381s novaclient.exceptions.Forbidden: Quota exceeded for cores: Requested 4, but already used 142 of 140 cores (HTTP 403) (Request-ID: req-61fefb3e-b7b1-4180-86b4-b420af4ea17e) 381s ERROR (Forbidden): Quota exceeded for cores: Requested 4, but already used 142 of 140 cores (HTTP 403) (Request-ID: req-61fefb3e-b7b1-4180-86b4-b420af4ea17e) 384s autopkgtest [21:15:51]: testbed dpkg architecture: arm64 384s autopkgtest [21:15:51]: testbed apt version: 2.7.12 384s autopkgtest [21:15:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 384s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 385s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 385s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 385s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 385s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3795 kB] 386s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [677 kB] 386s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 386s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 386s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 386s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4179 kB] 387s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 387s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [67.4 kB] 387s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 388s Fetched 9434 kB in 3s (3263 kB/s) 388s Reading package lists... 392s Reading package lists... 392s Building dependency tree... 392s Reading state information... 393s Calculating upgrade... 394s The following packages will be REMOVED: 394s libglib2.0-0 394s The following NEW packages will be installed: 394s libglib2.0-0t64 xdg-user-dirs 394s The following packages will be upgraded: 394s gir1.2-glib-2.0 libglib2.0-data 394s 2 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. 394s Need to get 1774 kB of archives. 394s After this operation, 138 kB of additional disk space will be used. 394s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 395s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 395s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 395s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 395s Fetched 1774 kB in 1s (2352 kB/s) 396s (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 ... 74820 files and directories currently installed.) 396s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 396s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 396s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 396s udisks2 depends on libglib2.0-0 (>= 2.77.0). 396s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 396s python3-gi depends on libglib2.0-0 (>= 2.77.0). 396s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 396s netplan.io depends on libglib2.0-0 (>= 2.70.0). 396s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 396s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 396s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 396s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 396s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 396s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 396s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 396s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 396s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 396s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 396s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 396s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 396s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 396s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 396s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 396s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 396s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 396s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 396s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 396s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 396s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 396s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 396s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 396s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 396s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 396s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 396s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 396s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 396s fwupd depends on libglib2.0-0 (>= 2.79.0). 396s bolt depends on libglib2.0-0 (>= 2.56.0). 396s 396s (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 ... 74820 files and directories currently installed.) 396s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 396s Selecting previously unselected package libglib2.0-0t64:arm64. 396s (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 ... 74795 files and directories currently installed.) 396s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 396s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 396s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 396s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 396s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 396s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 396s Selecting previously unselected package xdg-user-dirs. 396s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 396s Unpacking xdg-user-dirs (0.18-1) ... 396s Setting up xdg-user-dirs (0.18-1) ... 396s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 396s No schema files found: doing nothing. 396s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 396s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 396s Processing triggers for man-db (2.12.0-3) ... 397s Processing triggers for libc-bin (2.39-0ubuntu2) ... 397s Reading package lists... 398s Building dependency tree... 398s Reading state information... 399s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 400s sh: Attempting to set up Debian/Ubuntu apt sources automatically 400s sh: Distribution appears to be Ubuntu 401s Reading package lists... 401s Building dependency tree... 401s Reading state information... 402s eatmydata is already the newest version (131-1). 402s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 402s Reading package lists... 402s Building dependency tree... 402s Reading state information... 404s dbus is already the newest version (1.14.10-4ubuntu1). 404s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 404s Reading package lists... 404s Building dependency tree... 404s Reading state information... 405s rng-tools-debian is already the newest version (2.4). 405s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 405s Reading package lists... 405s Building dependency tree... 405s Reading state information... 407s The following packages will be REMOVED: 407s cloud-init* python3-configobj* python3-debconf* 407s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 407s After this operation, 3252 kB disk space will be freed. 407s (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 ... 74834 files and directories currently installed.) 407s Removing cloud-init (24.1.1-0ubuntu1) ... 408s Removing python3-configobj (5.0.8-3) ... 408s Removing python3-debconf (1.5.86) ... 408s Processing triggers for man-db (2.12.0-3) ... 409s (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 ... 74445 files and directories currently installed.) 409s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 409s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 409s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 409s invoke-rc.d: policy-rc.d denied execution of try-restart. 410s Reading package lists... 410s Building dependency tree... 410s Reading state information... 411s linux-generic is already the newest version (6.8.0-11.11+1). 411s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 412s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 412s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 412s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 414s Reading package lists... 414s Reading package lists... 414s Building dependency tree... 414s Reading state information... 415s Calculating upgrade... 415s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 415s Reading package lists... 416s Building dependency tree... 416s Reading state information... 416s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 417s autopkgtest [21:16:24]: rebooting testbed after setup commands that affected boot 445s autopkgtest [21:16:52]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 448s autopkgtest [21:16:55]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 451s Get:1 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (dsc) [2286 B] 451s Get:2 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (tar) [5343 kB] 451s Get:3 http://ftpmaster.internal/ubuntu noble/universe bbmap 39.06+dfsg-1 (diff) [25.4 kB] 451s gpgv: Signature made Fri Nov 24 11:00:29 2023 UTC 451s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 451s gpgv: issuer "emollier@debian.org" 451s gpgv: Can't check signature: No public key 451s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.06+dfsg-1.dsc: no acceptable signature found 452s autopkgtest [21:16:59]: testing package bbmap version 39.06+dfsg-1 452s autopkgtest [21:16:59]: build not needed 454s autopkgtest [21:17:01]: test run-unit-test: preparing testbed 462s Reading package lists... 462s Building dependency tree... 462s Reading state information... 462s Starting pkgProblemResolver with broken count: 0 462s Starting 2 pkgProblemResolver with broken count: 0 462s Done 463s The following additional packages will be installed: 463s bbmap bbmap-jni ca-certificates-java fontconfig-config fonts-dejavu-core 463s fonts-dejavu-mono java-common libapache-pom-java libasound2 libasound2-data 463s libavahi-client3 libavahi-common-data libavahi-common3 libcommons-cli-java 463s libcommons-codec-java libcommons-io-java libcommons-parent-java libcups2 463s libfontconfig1 libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 463s liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 463s python-biopython-doc 463s Suggested packages: 463s default-jre libasound2-plugins alsa-utils libcommons-io-java-doc cups-common 463s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 463s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 463s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic 463s Recommended packages: 463s pigz alsa-ucm-conf alsa-topology-conf python3-biopython 463s The following NEW packages will be installed: 463s autopkgtest-satdep bbmap bbmap-jni ca-certificates-java fontconfig-config 463s fonts-dejavu-core fonts-dejavu-mono java-common libapache-pom-java 463s libasound2 libasound2-data libavahi-client3 libavahi-common-data 463s libavahi-common3 libcommons-cli-java libcommons-codec-java 463s libcommons-io-java libcommons-parent-java libcups2 libfontconfig1 463s libgraphite2-3 libharfbuzz0b libjpeg-turbo8 libjpeg8 liblcms2-2 463s liblog4j1.2-java libmpj-java libpcsclite1 openjdk-17-jre-headless 463s python-biopython-doc 463s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 463s Need to get 79.2 MB/79.2 MB of archives. 463s After this operation, 238 MB of additional disk space will be used. 463s Get:1 /tmp/autopkgtest.DNrinm/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 463s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 463s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libapache-pom-java all 29-2 [5284 B] 463s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 463s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-codec-java all 1.16.0-1 [306 kB] 463s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libcommons-io-java all 2.11.0-2 [297 kB] 464s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 liblog4j1.2-java all 1.2.17-11 [439 kB] 464s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libmpj-java all 0.44+dfsg-4 [443 kB] 464s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 464s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 464s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 464s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 464s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 464s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 464s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 464s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 464s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 464s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 464s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 464s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 464s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 464s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 464s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 464s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 464s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 464s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 464s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-17-jre-headless arm64 17.0.10+7-1 [47.3 MB] 465s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap all 39.06+dfsg-1 [9768 kB] 465s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 bbmap-jni arm64 39.06+dfsg-1 [26.3 kB] 465s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python-biopython-doc all 1.81+dfsg-3 [17.3 MB] 466s Fetched 79.2 MB in 2s (31.8 MB/s) 466s Selecting previously unselected package libcommons-cli-java. 466s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74390 files and directories currently installed.) 466s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 466s Unpacking libcommons-cli-java (1.6.0-1) ... 466s Selecting previously unselected package libapache-pom-java. 466s Preparing to unpack .../01-libapache-pom-java_29-2_all.deb ... 466s Unpacking libapache-pom-java (29-2) ... 466s Selecting previously unselected package libcommons-parent-java. 466s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 466s Unpacking libcommons-parent-java (56-1) ... 466s Selecting previously unselected package libcommons-codec-java. 466s Preparing to unpack .../03-libcommons-codec-java_1.16.0-1_all.deb ... 466s Unpacking libcommons-codec-java (1.16.0-1) ... 466s Selecting previously unselected package libcommons-io-java. 466s Preparing to unpack .../04-libcommons-io-java_2.11.0-2_all.deb ... 466s Unpacking libcommons-io-java (2.11.0-2) ... 467s Selecting previously unselected package liblog4j1.2-java. 467s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 467s Unpacking liblog4j1.2-java (1.2.17-11) ... 467s Selecting previously unselected package libmpj-java. 467s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 467s Unpacking libmpj-java (0.44+dfsg-4) ... 467s Selecting previously unselected package ca-certificates-java. 467s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 467s Unpacking ca-certificates-java (20240118) ... 467s Selecting previously unselected package java-common. 467s Preparing to unpack .../08-java-common_0.75+exp1_all.deb ... 467s Unpacking java-common (0.75+exp1) ... 467s Selecting previously unselected package libavahi-common-data:arm64. 467s Preparing to unpack .../09-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 467s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 467s Selecting previously unselected package libavahi-common3:arm64. 467s Preparing to unpack .../10-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 467s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 467s Selecting previously unselected package libavahi-client3:arm64. 467s Preparing to unpack .../11-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 467s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 467s Selecting previously unselected package libcups2:arm64. 467s Preparing to unpack .../12-libcups2_2.4.6-0ubuntu3_arm64.deb ... 467s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 467s Selecting previously unselected package liblcms2-2:arm64. 467s Preparing to unpack .../13-liblcms2-2_2.14-2_arm64.deb ... 467s Unpacking liblcms2-2:arm64 (2.14-2) ... 467s Selecting previously unselected package libjpeg-turbo8:arm64. 467s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 467s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 467s Selecting previously unselected package libjpeg8:arm64. 467s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_arm64.deb ... 467s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 467s Selecting previously unselected package fonts-dejavu-mono. 467s Preparing to unpack .../16-fonts-dejavu-mono_2.37-8_all.deb ... 467s Unpacking fonts-dejavu-mono (2.37-8) ... 467s Selecting previously unselected package fonts-dejavu-core. 467s Preparing to unpack .../17-fonts-dejavu-core_2.37-8_all.deb ... 467s Unpacking fonts-dejavu-core (2.37-8) ... 467s Selecting previously unselected package fontconfig-config. 467s Preparing to unpack .../18-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 467s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 468s Selecting previously unselected package libfontconfig1:arm64. 468s Preparing to unpack .../19-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 468s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 468s Selecting previously unselected package libasound2-data. 468s Preparing to unpack .../20-libasound2-data_1.2.10-3build1_all.deb ... 468s Unpacking libasound2-data (1.2.10-3build1) ... 468s Selecting previously unselected package libasound2:arm64. 468s Preparing to unpack .../21-libasound2_1.2.10-3build1_arm64.deb ... 468s Unpacking libasound2:arm64 (1.2.10-3build1) ... 468s Selecting previously unselected package libgraphite2-3:arm64. 468s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_arm64.deb ... 468s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 468s Selecting previously unselected package libharfbuzz0b:arm64. 468s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_arm64.deb ... 468s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 468s Selecting previously unselected package libpcsclite1:arm64. 468s Preparing to unpack .../24-libpcsclite1_2.0.0-1_arm64.deb ... 468s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 468s Selecting previously unselected package openjdk-17-jre-headless:arm64. 468s Preparing to unpack .../25-openjdk-17-jre-headless_17.0.10+7-1_arm64.deb ... 468s Unpacking openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 469s Selecting previously unselected package bbmap. 469s Preparing to unpack .../26-bbmap_39.06+dfsg-1_all.deb ... 469s Unpacking bbmap (39.06+dfsg-1) ... 469s Selecting previously unselected package bbmap-jni. 469s Preparing to unpack .../27-bbmap-jni_39.06+dfsg-1_arm64.deb ... 469s Unpacking bbmap-jni (39.06+dfsg-1) ... 470s Selecting previously unselected package python-biopython-doc. 470s Preparing to unpack .../28-python-biopython-doc_1.81+dfsg-3_all.deb ... 470s Unpacking python-biopython-doc (1.81+dfsg-3) ... 470s Selecting previously unselected package autopkgtest-satdep. 470s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 470s Unpacking autopkgtest-satdep (0) ... 470s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 470s Setting up liblcms2-2:arm64 (2.14-2) ... 470s Setting up java-common (0.75+exp1) ... 470s Setting up libcommons-cli-java (1.6.0-1) ... 470s Setting up liblog4j1.2-java (1.2.17-11) ... 470s Setting up libasound2-data (1.2.10-3build1) ... 470s Setting up libapache-pom-java (29-2) ... 470s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 470s Setting up fonts-dejavu-mono (2.37-8) ... 470s Setting up fonts-dejavu-core (2.37-8) ... 470s Setting up libpcsclite1:arm64 (2.0.0-1) ... 470s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 470s Setting up python-biopython-doc (1.81+dfsg-3) ... 470s Setting up libasound2:arm64 (1.2.10-3build1) ... 470s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 470s Setting up bbmap-jni (39.06+dfsg-1) ... 470s Setting up ca-certificates-java (20240118) ... 470s No JRE found. Skipping Java certificates setup. 470s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 470s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 470s Setting up libcommons-parent-java (56-1) ... 470s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 470s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 470s Setting up libcommons-codec-java (1.16.0-1) ... 470s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 470s Setting up libcommons-io-java (2.11.0-2) ... 470s Setting up libmpj-java (0.44+dfsg-4) ... 470s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 470s Setting up openjdk-17-jre-headless:arm64 (17.0.10+7-1) ... 470s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 470s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 470s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 470s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 470s update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 470s Processing triggers for libc-bin (2.39-0ubuntu2) ... 470s Processing triggers for man-db (2.12.0-3) ... 471s Processing triggers for ca-certificates-java (20240118) ... 472s Adding debian:ACCVRAIZ1.pem 472s Adding debian:AC_RAIZ_FNMT-RCM.pem 472s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 472s Adding debian:ANF_Secure_Server_Root_CA.pem 472s Adding debian:Actalis_Authentication_Root_CA.pem 472s Adding debian:AffirmTrust_Commercial.pem 472s Adding debian:AffirmTrust_Networking.pem 472s Adding debian:AffirmTrust_Premium.pem 472s Adding debian:AffirmTrust_Premium_ECC.pem 472s Adding debian:Amazon_Root_CA_1.pem 472s Adding debian:Amazon_Root_CA_2.pem 472s Adding debian:Amazon_Root_CA_3.pem 472s Adding debian:Amazon_Root_CA_4.pem 472s Adding debian:Atos_TrustedRoot_2011.pem 472s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 472s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 472s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 472s Adding debian:BJCA_Global_Root_CA1.pem 472s Adding debian:BJCA_Global_Root_CA2.pem 472s Adding debian:Baltimore_CyberTrust_Root.pem 472s Adding debian:Buypass_Class_2_Root_CA.pem 472s Adding debian:Buypass_Class_3_Root_CA.pem 472s Adding debian:CA_Disig_Root_R2.pem 472s Adding debian:CFCA_EV_ROOT.pem 472s Adding debian:COMODO_Certification_Authority.pem 472s Adding debian:COMODO_ECC_Certification_Authority.pem 472s Adding debian:COMODO_RSA_Certification_Authority.pem 472s Adding debian:Certainly_Root_E1.pem 472s Adding debian:Certainly_Root_R1.pem 472s Adding debian:Certigna.pem 472s Adding debian:Certigna_Root_CA.pem 472s Adding debian:Certum_EC-384_CA.pem 472s Adding debian:Certum_Trusted_Network_CA.pem 472s Adding debian:Certum_Trusted_Network_CA_2.pem 472s Adding debian:Certum_Trusted_Root_CA.pem 472s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 472s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 472s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 472s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 472s Adding debian:Comodo_AAA_Services_root.pem 472s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 472s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 472s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 472s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 472s Adding debian:DigiCert_Assured_ID_Root_CA.pem 472s Adding debian:DigiCert_Assured_ID_Root_G2.pem 472s Adding debian:DigiCert_Assured_ID_Root_G3.pem 472s Adding debian:DigiCert_Global_Root_CA.pem 472s Adding debian:DigiCert_Global_Root_G2.pem 472s Adding debian:DigiCert_Global_Root_G3.pem 472s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 472s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 472s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 472s Adding debian:DigiCert_Trusted_Root_G4.pem 472s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 472s Adding debian:Entrust_Root_Certification_Authority.pem 472s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 472s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 472s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 472s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 472s Adding debian:GLOBALTRUST_2020.pem 472s Adding debian:GTS_Root_R1.pem 472s Adding debian:GTS_Root_R2.pem 472s Adding debian:GTS_Root_R3.pem 472s Adding debian:GTS_Root_R4.pem 472s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 472s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 472s Adding debian:GlobalSign_Root_CA.pem 472s Adding debian:GlobalSign_Root_CA_-_R3.pem 472s Adding debian:GlobalSign_Root_CA_-_R6.pem 472s Adding debian:GlobalSign_Root_E46.pem 472s Adding debian:GlobalSign_Root_R46.pem 472s Adding debian:Go_Daddy_Class_2_CA.pem 472s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 472s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 472s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 472s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 472s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 472s Adding debian:HiPKI_Root_CA_-_G1.pem 472s Adding debian:Hongkong_Post_Root_CA_3.pem 472s Adding debian:ISRG_Root_X1.pem 472s Adding debian:ISRG_Root_X2.pem 472s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 472s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 472s Adding debian:Izenpe.com.pem 472s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 472s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 472s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 472s Adding debian:NAVER_Global_Root_Certification_Authority.pem 472s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 472s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 472s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 472s Adding debian:QuoVadis_Root_CA_1_G3.pem 472s Adding debian:QuoVadis_Root_CA_2.pem 472s Adding debian:QuoVadis_Root_CA_2_G3.pem 472s Adding debian:QuoVadis_Root_CA_3.pem 472s Adding debian:QuoVadis_Root_CA_3_G3.pem 472s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 472s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 472s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 472s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 472s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 472s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 472s Adding debian:SZAFIR_ROOT_CA2.pem 472s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 472s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 472s Adding debian:SecureSign_RootCA11.pem 472s Adding debian:SecureTrust_CA.pem 472s Adding debian:Secure_Global_CA.pem 472s Adding debian:Security_Communication_ECC_RootCA1.pem 472s Adding debian:Security_Communication_RootCA2.pem 472s Adding debian:Security_Communication_RootCA3.pem 472s Adding debian:Security_Communication_Root_CA.pem 472s Adding debian:Starfield_Class_2_CA.pem 472s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 472s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 472s Adding debian:SwissSign_Gold_CA_-_G2.pem 472s Adding debian:SwissSign_Silver_CA_-_G2.pem 472s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 472s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 472s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 472s Adding debian:TWCA_Global_Root_CA.pem 472s Adding debian:TWCA_Root_Certification_Authority.pem 472s Adding debian:TeliaSonera_Root_CA_v1.pem 472s Adding debian:Telia_Root_CA_v2.pem 472s Adding debian:TrustAsia_Global_Root_CA_G3.pem 472s Adding debian:TrustAsia_Global_Root_CA_G4.pem 472s Adding debian:Trustwave_Global_Certification_Authority.pem 472s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 472s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 472s Adding debian:TunTrust_Root_CA.pem 472s Adding debian:UCA_Extended_Validation_Root.pem 472s Adding debian:UCA_Global_G2_Root.pem 472s Adding debian:USERTrust_ECC_Certification_Authority.pem 472s Adding debian:USERTrust_RSA_Certification_Authority.pem 472s Adding debian:XRamp_Global_CA_Root.pem 472s Adding debian:certSIGN_ROOT_CA.pem 472s Adding debian:certSIGN_Root_CA_G2.pem 472s Adding debian:e-Szigno_Root_CA_2017.pem 472s Adding debian:ePKI_Root_Certification_Authority.pem 472s Adding debian:emSign_ECC_Root_CA_-_C3.pem 472s Adding debian:emSign_ECC_Root_CA_-_G3.pem 472s Adding debian:emSign_Root_CA_-_C1.pem 472s Adding debian:emSign_Root_CA_-_G1.pem 472s Adding debian:vTrus_ECC_Root_CA.pem 472s Adding debian:vTrus_Root_CA.pem 472s done. 472s Setting up bbmap (39.06+dfsg-1) ... 472s Setting up autopkgtest-satdep (0) ... 476s (Reading database ... 77235 files and directories currently installed.) 476s Removing autopkgtest-satdep (0) ... 477s autopkgtest [21:17:24]: test run-unit-test: [----------------------- 477s 477s # bbmap 477s bbmap.sh --version 477s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 477s java -ea -Xmx2770m -Xms2770m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 477s BBMap version 39.06 477s For help, please run the shellscript with no parameters, or look in /docs/. 477s bbmap.sh --help 478s 478s BBMap 478s Written by Brian Bushnell, from Dec. 2010 - present 478s Last modified September 15, 2022 478s 478s Description: Fast and accurate splice-aware read aligner. 478s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 478s 478s To index: bbmap.sh ref= 478s To map: bbmap.sh in= out= 478s To map without writing an index: 478s bbmap.sh ref= in= out= nodisk 478s 478s in=stdin will accept reads from standard in, and out=stdout will write to 478s standard out, but file extensions are still needed to specify the format of the 478s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 478s standard in; out=stdout.sam.gz will write gzipped sam. 478s 478s Indexing Parameters (required when building the index): 478s nodisk=f Set to true to build index in memory and write nothing 478s to disk except output. 478s ref= Specify the reference sequence. Only do this ONCE, 478s when building the index (unless using 'nodisk'). 478s build=1 If multiple references are indexed in the same directory, 478s each needs a unique numeric ID (unless using 'nodisk'). 478s k=13 Kmer length, range 8-15. Longer is faster but uses 478s more memory. Shorter is more sensitive. 478s If indexing and mapping are done in two steps, K should 478s be specified each time. 478s path=<.> Specify the location to write the index, if you don't 478s want it in the current working directory. 478s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 478s number (reduces RAM by 50% and sensitivity slightly). 478s Should be enabled both when building the index AND 478s when mapping. 478s rebuild=f Force a rebuild of the index (ref= should be set). 478s 478s Input Parameters: 478s build=1 Designate index to use. Corresponds to the number 478s specified when building the index. 478s in= Primary reads input; required parameter. 478s in2= For paired reads in two files. 478s interleaved=auto True forces paired/interleaved input; false forces 478s single-ended mapping. If not specified, interleaved 478s status will be autodetected from read names. 478s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 478s BBMap and 6000 for BBMapPacBio. Only works for FASTA 478s input (use 'maxlen' for FASTQ input). The default for 478s bbmap.sh is 500, and for mapPacBio.sh is 6000. 478s unpigz=f Spawn a pigz (parallel gzip) process for faster 478s decompression than using Java. 478s Requires pigz to be installed. 478s touppercase=t (tuc) Convert lowercase letters in reads to upper case 478s (otherwise they will not match the reference). 478s 478s Sampling Parameters: 478s 478s reads=-1 Set to a positive number N to only process the first N 478s reads (or pairs), then quit. -1 means use all reads. 478s samplerate=1 Set to a number from 0 to 1 to randomly select that 478s fraction of reads for mapping. 1 uses all reads. 478s skipreads=0 Set to a number N to skip the first N reads (or pairs), 478s then map the rest. 478s 478s Mapping Parameters: 478s fast=f This flag is a macro which sets other paramters to run 478s faster, at reduced sensitivity. Bad for RNA-seq. 478s slow=f This flag is a macro which sets other paramters to run 478s slower, at greater sensitivity. 'vslow' is even slower. 478s maxindel=16000 Don't look for indels longer than this. Lower is faster. 478s Set to >=100k for RNAseq with long introns like mammals. 478s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 478s By default these are not sought, but may be found anyway. 478s tipsearch=100 Look this far for read-end deletions with anchors 478s shorter than K, using brute force. 478s minid=0.76 Approximate minimum alignment identity to look for. 478s Higher is faster and less sensitive. 478s minhits=1 Minimum number of seed hits required for candidate sites. 478s Higher is faster. 478s local=f Set to true to use local, rather than global, alignments. 478s This will soft-clip ugly ends of poor alignments. 478s perfectmode=f Allow only perfect mappings when set to true (very fast). 478s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 478s N's in the reference) mappings. 478s threads=auto (t) Set to number of threads desired. By default, uses 478s all cores available. 478s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 478s multiple top-scoring mapping locations). 478s best (use the first best site) 478s toss (consider unmapped) 478s random (select one top-scoring site randomly) 478s all (retain all top-scoring sites) 478s samestrandpairs=f (ssp) Specify whether paired reads should map to the 478s same strand or opposite strands. 478s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 478s orientation. Set to false for long-mate-pair libraries. 478s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 478s insert size or orientation, the read with the lower 478s mapping quality is marked unmapped. 478s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 478s be sent to 'outu' but not 'outm'. 478s rcomp=f Reverse complement both reads prior to mapping (for LMP 478s outward-facing libraries). 478s rcompmate=f Reverse complement read2 prior to mapping. 478s pairlen=32000 Set max allowed distance between paired reads. 478s (insert size)=(pairlen)+(read1 length)+(read2 length) 478s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 478s greater than this. Lower is faster. 478s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 478s is faster. 478s averagepairdist=100 (apd) Initial average distance between paired reads. 478s Varies dynamically; does not need to be specified. 478s deterministic=f Run in deterministic mode. In this case it is good 478s to set averagepairdist. BBMap is deterministic 478s without this flag if using single-ended reads, 478s or run singlethreaded. 478s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 478s fraction of read length. Faster but less accurate. 478s bandwidth=0 (bw) Set the bandwidth directly. 478s fraction of read length. Faster but less accurate. 478s usejni=f (jni) Do alignments faster, in C code. Requires 478s compiling the C code; details are in /jni/README.txt. 478s maxsites2=800 Don't analyze (or print) more than this many alignments 478s per read. 478s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 478s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 478s will ignore the most common 3% of kmers. 478s greedy=t Use a greedy algorithm to discard the least-useful 478s kmers on a per-read basis. 478s kfilter=0 If positive, potential mapping sites must have at 478s least this many consecutive exact matches. 478s 478s 478s Quality and Trimming Parameters: 478s qin=auto Set to 33 or 64 to specify input quality value ASCII 478s offset. 33 is Sanger, 64 is old Solexa. 478s qout=auto Set to 33 or 64 to specify output quality value ASCII 478s offset (only if output format is fastq). 478s qtrim=f Quality-trim ends before mapping. Options are: 478s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 478s untrim=f Undo trimming after mapping. Untrimmed bases will be 478s soft-clipped in cigar strings. 478s trimq=6 Trim regions with average quality below this 478s (phred algorithm). 478s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 478s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 478s quality strings for fasta input reads. 478s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 478s out-of-range quality values. 478s usequality=t Use quality scores when determining which read kmers 478s to use as seeds. 478s minaveragequality=0 (maq) Do not map reads with average quality below this. 478s maqb=0 If positive, calculate maq from this many initial bases. 478s 478s Output Parameters: 478s out= Write all reads to this file. 478s outu= Write only unmapped reads to this file. Does not 478s include unmapped paired reads with a mapped mate. 478s outm= Write only mapped reads to this file. Includes 478s unmapped paired reads with a mapped mate. 478s mappedonly=f If true, treats 'out' like 'outm'. 478s bamscript= (bs) Write a shell script to that will turn 478s the sam output into a sorted, indexed bam file. 478s ordered=f Set to true to output reads in same order as input. 478s Slower and uses more memory. 478s overwrite=f (ow) Allow process to overwrite existing files. 478s secondary=f Print secondary alignments. 478s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 478s with score of at least this fraction of primary. 478s ssao=f (secondarysiteasambiguousonly) Only print secondary 478s alignments for ambiguously-mapped reads. 478s maxsites=5 Maximum number of total alignments to print per read. 478s Only relevant when secondary=t. 478s quickmatch=f Generate cigar strings more quickly. 478s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 478s assuming that the remainder is a comment or description. 478s ziplevel=2 (zl) Compression level for zip or gzip output. 478s pigz=f Spawn a pigz (parallel gzip) process for faster 478s compression than Java. Requires pigz to be installed. 478s machineout=f Set to true to output statistics in machine-friendly 478s 'key=value' format. 478s printunmappedcount=f Print the total number of unmapped reads and bases. 478s If input is paired, the number will be of pairs 478s for which both reads are unmapped. 478s showprogress=0 If positive, print a '.' every X reads. 478s showprogress2=0 If positive, print the number of seconds since the 478s last progress update (instead of a '.'). 478s renamebyinsert=f Renames reads based on their mapped insert size. 478s 478s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 478s bloom=f Use a Bloom filter to ignore reads not sharing kmers 478s with the reference. This uses more memory, but speeds 478s mapping when most reads don't match the reference. 478s bloomhashes=2 Number of hash functions. 478s bloomminhits=3 Number of consecutive hits to be considered matched. 478s bloomk=31 Bloom filter kmer length. 478s bloomserial=t Use the serialized Bloom filter for greater loading 478s speed, if available. If not, generate and write one. 478s 478s Post-Filtering Parameters: 478s idfilter=0 Independant of minid; sets exact minimum identity 478s allowed for alignments to be printed. Range 0 to 1. 478s subfilter=-1 Ban alignments with more than this many substitutions. 478s insfilter=-1 Ban alignments with more than this many insertions. 478s delfilter=-1 Ban alignments with more than this many deletions. 478s indelfilter=-1 Ban alignments with more than this many indels. 478s editfilter=-1 Ban alignments with more than this many edits. 478s inslenfilter=-1 Ban alignments with an insertion longer than this. 478s dellenfilter=-1 Ban alignments with a deletion longer than this. 478s nfilter=-1 Ban alignments with more than this many ns. This 478s includes nocall, noref, and off scaffold ends. 478s 478s Sam flags and settings: 478s noheader=f Disable generation of header lines. 478s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 478s with = and X, or 1.3 to use M. 478s saa=t (secondaryalignmentasterisks) Use asterisks instead of 478s bases for sam secondary alignments. 478s cigar=t Set to 'f' to skip generation of cigar strings (faster). 478s keepnames=f Keep original names of paired reads, rather than 478s ensuring both reads have the same name. 478s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 478s cigar strings for deletions of at least that length. 478s rgid= Set readgroup ID. All other readgroup fields 478s can be set similarly, with the flag rgXX= 478s If you set a readgroup flag to the word 'filename', 478s e.g. rgid=filename, the input file name will be used. 478s mdtag=f Write MD tags. 478s nhtag=f Write NH tags. 478s xmtag=f Write XM tags (may only work correctly with ambig=all). 478s amtag=f Write AM tags. 478s nmtag=f Write NM tags. 478s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 478s for RNAseq using firststrand, secondstrand, or 478s unstranded libraries. Needed by Cufflinks. 478s JGI mainly uses 'firststrand'. 478s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 478s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 478s prefixed by YL:Z: 478s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 478s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 478s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 478s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 478s boundstag=f Write a tag indicating whether either read in the pair 478s goes off the end of the reference, prefixed by XB:Z: 478s notags=f Turn off all optional tags. 478s 478s Histogram and statistics output parameters: 478s scafstats= Statistics on how many reads mapped to which scaffold. 478s refstats= Statistics on how many reads mapped to which reference 478s file; only for BBSplit. 478s sortscafs=t Sort scaffolds or references by read count. 478s bhist= Base composition histogram by position. 478s qhist= Quality histogram by position. 478s aqhist= Histogram of average read quality. 478s bqhist= Quality histogram designed for box plots. 478s lhist= Read length histogram. 478s ihist= Write histogram of insert sizes (for paired reads). 478s ehist= Errors-per-read histogram. 478s qahist= Quality accuracy histogram of error rates versus 478s quality score. 478s indelhist= Indel length histogram. 478s mhist= Histogram of match, sub, del, and ins rates by 478s read location. 478s gchist= Read GC content histogram. 478s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 478s gcpairs=t Use average GC of paired reads. 478s idhist= Histogram of read count versus percent identity. 478s idbins=100 Number idhist bins. Set to 'auto' to use read length. 478s statsfile=stderr Mapping statistics are printed here. 478s 478s Coverage output parameters (these may reduce speed and use more RAM): 478s covstats= Per-scaffold coverage info. 478s rpkm= Per-scaffold RPKM/FPKM counts. 478s covhist= Histogram of # occurrences of each depth level. 478s basecov= Coverage per base location. 478s bincov= Print binned coverage per location (one line per X bases). 478s covbinsize=1000 Set the binsize for binned coverage output. 478s nzo=t Only print scaffolds with nonzero coverage. 478s twocolumn=f Change to true to print only ID and Avg_fold instead of 478s all 6 columns to the 'out=' file. 478s 32bit=f Set to true if you need per-base coverage over 64k. 478s strandedcov=f Track coverage for plus and minus strand independently. 478s startcov=f Only track start positions of reads. 478s secondarycov=t Include coverage of secondary alignments. 478s physcov=f Calculate physical coverage for paired reads. 478s This includes the unsequenced bases. 478s delcoverage=t (delcov) Count bases covered by deletions as covered. 478s True is faster than false. 478s covk=0 If positive, calculate kmer coverage statistics. 478s 478s Java Parameters: 478s -Xmx This will set Java's memory usage, 478s overriding autodetection. 478s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 478s will specify 800 megs. The max is typically 85% of 478s physical memory. The human genome requires around 24g, 478s or 12g with the 'usemodulo' flag. The index uses 478s roughly 6 bytes per reference base. 478s -eoom This flag will cause the process to exit if an 478s out-of-memory exception occurs. Requires Java 8u92+. 478s -da Disable assertions. 478s 478s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 478s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 478s 478s bbmap.sh ref=example.fasta 478s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 478s java -ea -Xmx2770m -Xms2770m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 478s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 478s Version 39.06 478s 478s No output file. 478s Writing reference. 478s 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] 478s 478s Set genScaffoldInfo=true 478s Writing chunk 1 478s Set genome to 1 478s 478s Loaded Reference: 0.006 seconds. 478s Loading index for chunk 1-1, build 1 478s No index available; generating from reference genome: /tmp/autopkgtest.DNrinm/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 478s Indexing threads started for block 0-1 478s Indexing threads finished for block 0-1 479s Generated Index: 1.117 seconds. 479s No reads to process; quitting. 479s 479s Total time: 1.357 seconds. 479s test -d ref 479s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 479s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 479s java -ea -Xmx2770m -Xms2770m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 479s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 479s Version 39.06 479s 479s Retaining first best site only for ambiguous mappings. 479s Set genome to 1 479s 479s Loaded Reference: 0.049 seconds. 479s Loading index for chunk 1-1, build 1 480s Generated Index: 0.381 seconds. 483s Analyzed Index: 3.269 seconds. 483s Started output stream: 0.050 seconds. 483s Cleared Memory: 0.119 seconds. 483s Processing reads in single-ended mode. 483s Started read stream. 483s Started 4 mapping threads. 483s Detecting finished threads: 0, 1, 2, 3 483s 483s ------------------ Results ------------------ 483s 483s Genome: 1 483s Key Length: 13 483s Max Indel: 16000 483s Minimum Score Ratio: 0.56 483s Mapping Mode: normal 483s Reads Used: 4 (153 bases) 483s 483s Mapping: 0.111 seconds. 483s Reads/sec: 35.98 483s kBases/sec: 1.38 483s 483s 483s Read 1 data: pct reads num reads pct bases num bases 483s 483s mapped: 0.0000% 0 0.0000% 0 483s unambiguous: 0.0000% 0 0.0000% 0 483s ambiguous: 0.0000% 0 0.0000% 0 483s low-Q discards: 25.0000% 1 19.6078% 30 483s 483s perfect best site: 0.0000% 0 0.0000% 0 483s semiperfect site: 0.0000% 0 0.0000% 0 483s 483s Match Rate: NA NA NaN% 0 483s Error Rate: NaN% 0 NaN% 0 483s Sub Rate: NaN% 0 NaN% 0 483s Del Rate: NaN% 0 NaN% 0 483s Ins Rate: NaN% 0 NaN% 0 483s N Rate: NaN% 0 NaN% 0 483s 483s Total time: 4.114 seconds. 483s test -r out.sam 483s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 484s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 484s java -ea -Xmx2770m -Xms2770m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 484s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 484s Version 39.06 484s 484s Retaining first best site only for ambiguous mappings. 484s 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] 484s 484s Set genScaffoldInfo=true 484s Set genome to 1 484s 484s Loaded Reference: 0.001 seconds. 484s Loading index for chunk 1-1, build 1 484s Indexing threads started for block 0-1 484s Indexing threads finished for block 0-1 484s Generated Index: 0.230 seconds. 487s Analyzed Index: 2.981 seconds. 487s Started output stream: 0.062 seconds. 487s Cleared Memory: 0.113 seconds. 487s Processing reads in single-ended mode. 487s Started read stream. 487s Started 4 mapping threads. 487s Detecting finished threads: 0, 1, 2, 3 487s 487s ------------------ Results ------------------ 487s 487s Genome: 1 487s Key Length: 13 487s Max Indel: 16000 487s Minimum Score Ratio: 0.56 487s Mapping Mode: normal 487s Reads Used: 3 (75 bases) 487s 487s Mapping: 0.119 seconds. 487s Reads/sec: 25.19 487s kBases/sec: 0.63 487s 487s 487s Read 1 data: pct reads num reads pct bases num bases 487s 487s mapped: 100.0000% 3 100.0000% 75 487s unambiguous: 100.0000% 3 100.0000% 75 487s ambiguous: 0.0000% 0 0.0000% 0 487s low-Q discards: 0.0000% 0 0.0000% 0 487s 487s perfect best site: 100.0000% 3 100.0000% 75 487s semiperfect site: 100.0000% 3 100.0000% 75 487s 487s Match Rate: NA NA 100.0000% 75 487s Error Rate: 0.0000% 0 0.0000% 0 487s Sub Rate: 0.0000% 0 0.0000% 0 487s Del Rate: 0.0000% 0 0.0000% 0 487s Ins Rate: 0.0000% 0 0.0000% 0 487s N Rate: 0.0000% 0 0.0000% 0 487s 487s Total time: 3.661 seconds. 488s test -r out2.sam 488s 488s # bbduk 488s bbduk.sh --version 488s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 488s java -ea -Xmx1385m -Xms1385m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 488s BBMap version 39.06 488s For help, please run the shellscript with no parameters, or look in /docs/. 488s bbduk.sh --help 488s 488s Written by Brian Bushnell 488s Last modified November 9, 2023 488s 488s Description: Compares reads to the kmers in a reference dataset, optionally 488s allowing an edit distance. Splits the reads into two outputs - those that 488s match the reference, and those that don't. Can also trim (remove) the matching 488s parts of the reads rather than binning the reads. 488s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 488s 488s Usage: bbduk.sh in= out= ref= 488s 488s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 488s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 488s fasta input, set in=stdin.fa.gz 488s 488s Input parameters: 488s in= Main input. in=stdin.fq will pipe from stdin. 488s in2= Input for 2nd read of pairs in a different file. 488s ref= Comma-delimited list of reference files. 488s In addition to filenames, you may also use the keywords: 488s adapters, artifacts, phix, lambda, pjet, mtst, kapa 488s literal= Comma-delimited list of literal reference sequences. 488s touppercase=f (tuc) Change all bases upper-case. 488s interleaved=auto (int) t/f overrides interleaved autodetection. 488s Must be set mainually when streaming fastq input. 488s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 488s reads=-1 If positive, quit after processing X reads or pairs. 488s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 488s possible unambiguous copies. Intended for short motifs 488s or adapter barcodes, as time/memory use is exponential. 488s samplerate=1 Set lower to only process a fraction of input reads. 488s samref= Optional reference fasta for processing sam files. 488s 488s Output parameters: 488s out= (outnonmatch) Write reads here that do not contain 488s kmers matching the database. 'out=stdout.fq' will pipe 488s to standard out. 488s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 488s different file. 488s outm= (outmatch) Write reads here that fail filters. In default 488s kfilter mode, this means any read with a matching kmer. 488s In any mode, it also includes reads that fail filters such 488s as minlength, mingc, maxgc, entropy, etc. In other words, 488s it includes all reads that do not go to 'out'. 488s outm2= (outmatch2) Use this to write 2nd read of pairs to a 488s different file. 488s outs= (outsingle) Use this to write singleton reads whose mate 488s was trimmed shorter than minlen. 488s stats= Write statistics about which contamininants were detected. 488s refstats= Write statistics on a per-reference-file basis. 488s rpkm= Write RPKM for each reference sequence (for RNA-seq). 488s dump= Dump kmer tables to a file, in fasta format. 488s duk= Write statistics in duk's format. *DEPRECATED* 488s nzo=t Only write statistics about ref sequences with nonzero hits. 488s overwrite=t (ow) Grant permission to overwrite files. 488s showspeed=t (ss) 'f' suppresses display of processing speed. 488s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 488s fastawrap=70 Length of lines in fasta output. 488s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 488s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 488s 5 includes base counts. 488s rename=f Rename reads to indicate which sequences they matched. 488s refnames=f Use names of reference files rather than scaffold IDs. 488s trd=f Truncate read and ref names at the first whitespace. 488s ordered=f Set to true to output reads in same order as input. 488s maxbasesout=-1 If positive, quit after writing approximately this many 488s bases to out (outu/outnonmatch). 488s maxbasesoutm=-1 If positive, quit after writing approximately this many 488s bases to outm (outmatch). 488s json=f Print to screen in json format. 488s 488s Histogram output parameters: 488s bhist= Base composition histogram by position. 488s qhist= Quality histogram by position. 488s qchist= Count of bases with each quality value. 488s aqhist= Histogram of average read quality. 488s bqhist= Quality histogram designed for box plots. 488s lhist= Read length histogram. 488s phist= Polymer length histogram. 488s gchist= Read GC content histogram. 488s enthist= Read entropy histogram. 488s ihist= Insert size histogram, for paired reads in mapped sam. 488s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 488s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 488s more memory. The default is 6000 for some histograms 488s and 80000 for others. 488s 488s Histograms for mapped sam/bam files only: 488s histbefore=t Calculate histograms from reads before processing. 488s ehist= Errors-per-read histogram. 488s qahist= Quality accuracy histogram of error rates versus quality 488s score. 488s indelhist= Indel length histogram. 488s mhist= Histogram of match, sub, del, and ins rates by position. 488s idhist= Histogram of read count versus percent identity. 488s idbins=100 Number idhist bins. Set to 'auto' to use read length. 488s varfile= Ignore substitution errors listed in this file when 488s calculating error rates. Can be generated with 488s CallVariants. 488s vcf= Ignore substitution errors listed in this VCF file 488s when calculating error rates. 488s ignorevcfindels=t Also ignore indels listed in the VCF. 488s 488s Processing parameters: 488s k=27 Kmer length used for finding contaminants. Contaminants 488s shorter than k will not be found. k must be at least 1. 488s rcomp=t Look for reverse-complements of kmers in addition to 488s forward kmers. 488s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 488s increase sensitivity in the presence of errors. This may 488s also be set to a number, e.g. mm=3, to mask that many bp. 488s The default mm=t corresponds to mm=1 for odd-length kmers 488s and mm=2 for even-length kmers (as of v39.04), while 488s mm=f is always equivalent to mm=0. 488s minkmerhits=1 (mkh) Reads need at least this many matching kmers 488s to be considered as matching the reference. 488s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 488s kmers to hit a ref, in order to be considered a match. 488s If this and minkmerhits are set, the greater is used. 488s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 488s bases to be covered by ref kmers to be considered a match. 488s If specified, mcf overrides mkh and mkf. 488s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 488s Memory use is proportional to (3*K)^hdist. 488s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 488s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 488s and indels). Memory use is proportional to (8*K)^edist. 488s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 488s qhdist2=0 Sets qhdist for short kmers, when using mink. 488s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 488s forbidn=f (fn) Forbids matching of read kmers containing N. 488s By default, these will match a reference 'A' if 488s hdist>0 or edist>0, to increase sensitivity. 488s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 488s match (or either is trimmed shorter than minlen). 488s Set to false to require both. 488s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 488s This makes the statistics a bit odd. 488s findbestmatch=f (fbm) If multiple matches, associate read with sequence 488s sharing most kmers. Reduces speed. 488s skipr1=f Don't do kmer-based operations on read 1. 488s skipr2=f Don't do kmer-based operations on read 2. 488s ecco=f For overlapping paired reads only. Performs error- 488s correction with BBMerge prior to kmer operations. 488s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 488s matrices generated by CalcTrueQuality. 488s sam= If recalibration is desired, and matrices have not already 488s been generated, BBDuk will create them from the sam file. 488s amino=f Run in amino acid mode. Some features have not been 488s tested, but kmer-matching works fine. Maximum k is 12. 488s 488s Speed and Memory parameters: 488s threads=auto (t) Set number of threads to use; default is number of 488s logical processors. 488s prealloc=f Preallocate memory in table. Allows faster table loading 488s and more efficient memory usage, for a large reference. 488s monitor=f Kill this process if it crashes. monitor=600,0.01 would 488s kill after 600 seconds under 1% usage. 488s minrskip=1 (mns) Force minimal skip interval when indexing reference 488s kmers. 1 means use all, 2 means use every other kmer, etc. 488s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 488s reference kmers. Normally all are used for scaffolds<100kb, 488s but with longer scaffolds, up to maxrskip-1 are skipped. 488s rskip= Set both minrskip and maxrskip to the same value. 488s If not set, rskip will vary based on sequence length. 488s qskip=1 Skip query kmers to increase speed. 1 means use all. 488s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 488s reads and reference. Increases speed and reduces memory. 488s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 488s 488s Trimming/Filtering/Masking parameters: 488s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 488s All kmer processing modes are mutually exclusive. 488s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 488s 488s ktrim=f Trim reads to remove bases matching reference kmers, plus 488s all bases to the left or right. 488s Values: 488s f (don't trim), 488s r (trim to the right), 488s l (trim to the left) 488s ktrimtips=0 Set this to a positive number to perform ktrim on both 488s ends, examining only the outermost X bases. 488s kmask= Replace bases matching ref kmers with another symbol. 488s Allows any non-whitespace character, and processes short 488s kmers on both ends if mink is set. 'kmask=lc' will 488s convert masked bases to lowercase. 488s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 488s ksplit=f For single-ended reads only. Reads will be split into 488s pairs around the kmer. If the kmer is at the end of the 488s read, it will be trimmed instead. Singletons will go to 488s out, and pairs will go to outm. Do not use ksplit with 488s other operations such as quality-trimming or filtering. 488s mink=0 Look for shorter kmers at read tips down to this length, 488s when k-trimming or masking. 0 means disabled. Enabling 488s this will disable maskmiddle. 488s qtrim=f Trim read ends to remove bases with quality below trimq. 488s Performed AFTER looking for kmers. Values: 488s rl (trim both ends), 488s f (neither end), 488s r (right end only), 488s l (left end only), 488s w (sliding window). 488s trimq=6 Regions with average quality BELOW this will be trimmed, 488s if qtrim is set to something other than f. Can be a 488s floating-point number like 7.3. 488s trimclip=f Trim soft-clipped bases from sam files. 488s minlength=10 (ml) Reads shorter than this after trimming will be 488s discarded. Pairs will be discarded if both are shorter. 488s mlf=0 (minlengthfraction) Reads shorter than this fraction of 488s original length after trimming will be discarded. 488s maxlength= Reads longer than this after trimming will be discarded. 488s minavgquality=0 (maq) Reads with average quality (after trimming) below 488s this will be discarded. 488s maqb=0 If positive, calculate maq from this many initial bases. 488s minbasequality=0 (mbq) Reads with any base below this quality (after 488s trimming) will be discarded. 488s maxns=-1 If non-negative, reads with more Ns than this 488s (after trimming) will be discarded. 488s mcb=0 (minconsecutivebases) Discard reads without at least 488s this many consecutive called bases. 488s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 488s than minlength to outm rather than discarding. 488s tp=0 (trimpad) Trim this much extra around matching kmers. 488s tbo=f (trimbyoverlap) Trim adapters based on where paired 488s reads overlap. 488s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 488s minoverlap=14 Require this many bases of overlap for detection. 488s mininsert=40 Require insert size of at least this for overlap. 488s Should be reduced to 16 for small RNA sequencing. 488s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 488s reads to the minimum length of either. 488s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 488s (exclusive, 0-based). 488s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 488s (exclusive, 0-based). 488s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 488s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 488s modulo this number. 488s restrictleft=0 If positive, only look for kmer matches in the 488s leftmost X bases. 488s restrictright=0 If positive, only look for kmer matches in the 488s rightmost X bases. 488s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 488s both ends is desired, use ktrimtips. 488s mingc=0 Discard reads with GC content below this. 488s maxgc=1 Discard reads with GC content above this. 488s gcpairs=t Use average GC of paired reads. 488s Also affects gchist. 488s tossjunk=f Discard reads with invalid characters as bases. 488s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 488s 488s Header-parsing parameters - these require Illumina headers: 488s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 488s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 488s or barcodes containing 'N' otherwise. A barcode must be 488s the last part of the read header. Values: 488s t: Remove reads with bad barcodes. 488s f: Ignore barcodes. 488s crash: Crash upon encountering bad barcodes. 488s barcodes= Comma-delimited list of barcodes or files of barcodes. 488s xmin=-1 If positive, discard reads with a lesser X coordinate. 488s ymin=-1 If positive, discard reads with a lesser Y coordinate. 488s xmax=-1 If positive, discard reads with a greater X coordinate. 488s ymax=-1 If positive, discard reads with a greater Y coordinate. 488s 488s Polymer trimming: 488s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 488s at least this length on either end of reads. 488s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 488s length on the left end of reads. Does not trim poly-C. 488s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 488s length on the right end of reads. Does not trim poly-C. 488s trimpolyg=0 This sets both left and right at once. 488s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 488s at least this length (on the left). 488s Note: there are also equivalent poly-C flags. 488s 488s Polymer tracking: 488s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 488s plen=20 Length of homopolymers to count. 488s 488s Entropy/Complexity parameters: 488s entropy=-1 Set between 0 and 1 to filter reads with entropy below 488s that value. Higher is more stringent. 488s entropywindow=50 Calculate entropy using a sliding window of this length. 488s entropyk=5 Calculate entropy using kmers of this length. 488s minbasefrequency=0 Discard reads with a minimum base frequency below this. 488s entropytrim=f Values: 488s f: (false) Do not entropy-trim. 488s r: (right) Trim low entropy on the right end only. 488s l: (left) Trim low entropy on the left end only. 488s rl: (both) Trim low entropy on both ends. 488s entropymask=f Values: 488s f: (filter) Discard low-entropy sequences. 488s t: (true) Mask low-entropy parts of sequences with N. 488s lc: Change low-entropy parts of sequences to lowercase. 488s entropymark=f Mark each base with its entropy value. This is on a scale 488s of 0-41 and is reported as quality scores, so the output 488s should be fastq or fasta+qual. 488s NOTE: If set, entropytrim overrides entropymask. 488s 488s Cardinality estimation: 488s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 488s cardinalityout=f (loglogout) Count unique kmers in output reads. 488s loglogk=31 Use this kmer length for counting. 488s loglogbuckets=2048 Use this many buckets for counting. 488s khist= Kmer frequency histogram; plots number of kmers versus 488s kmer depth. This is approximate. 488s khistout= Kmer frequency histogram for output reads. 488s 488s Java Parameters: 488s 488s -Xmx This will set Java's memory usage, overriding autodetection. 488s -Xmx20g will 488s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 488s The max is typically 85% of physical memory. 488s -eoom This flag will cause the process to exit if an 488s out-of-memory exception occurs. Requires Java 8u92+. 488s -da Disable assertions. 488s 488s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 488s 488s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 488s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 488s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 488s 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 488s 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] 488s Version 39.06 488s 488s 0.017 seconds. 488s Initial: 488s Memory: max=1453m, total=1453m, free=1423m, used=30m 488s 488s Input is being processed as paired 488s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 488s Started output streams: 0.021 seconds. 488s Processing time: 0.004 seconds. 488s 488s Input: 8 reads 306 bases. 488s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 488s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 488s Result: 0 reads (0.00%) 0 bases (0.00%) 488s 488s Time: 0.026 seconds. 488s Reads Processed: 8 0.30k reads/sec 488s Bases Processed: 306 0.01m bases/sec 488s test -r out.fastq.gz 488s 488s # bbnorm 488s bbnorm.sh --version 488s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 488s java -ea -Xmx2770m -Xms2770m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 488s BBMap version 39.06 488s For help, please run the shellscript with no parameters, or look in /docs/. 488s bbnorm.sh --help 488s 488s Written by Brian Bushnell 488s Last modified October 19, 2017 488s 488s Description: Normalizes read depth based on kmer counts. 488s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 488s However, Tadpole has superior error-correction to BBNorm. 488s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 488s 488s Usage: bbnorm.sh in= out= outt= hist= 488s 488s Input parameters: 488s in=null Primary input. Use in2 for paired reads in a second file 488s in2=null Second input file for paired reads in two files 488s extra=null Additional files to use for input (generating hash table) but not for output 488s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 488s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 488s kmersample=1 Process every nth kmer, and skip the rest 488s readsample=1 Process every nth read, and skip the rest 488s 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. 488s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 488s 488s Output parameters: 488s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 488s outt= (outtoss) File for reads that were excluded from primary output 488s reads=-1 Only process this number of reads, then quit (-1 means all) 488s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 488s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 488s 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. 488s Default is false, to prevent confusion about how there can be 0-count kmers. 488s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 488s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 488s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 488s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 488s rename=f Rename reads based on their kmer depth. 488s 488s Hashing parameters: 488s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 488s 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. 488s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 488s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 488s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 488s 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. 488s prehashes=2 Number of hashes for prefilter. 488s prefilterbits=2 (pbits) Bits per cell in prefilter. 488s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 488s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 488s minq=6 Ignore kmers containing bases with quality below this 488s minprob=0.5 Ignore kmers with overall probability of correctness below this 488s 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. 488s 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. 488s 488s Normalization parameters: 488s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 488s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 488s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 488s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 488s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 488s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 488s 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. 488s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 488s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 488s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 488s 488s Error detection parameters: 488s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 488s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 488s tossbadreads=f (tbr) Throw away reads detected as containing errors. 488s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 488s 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. 488s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 488s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 488s 488s Error correction parameters: 488s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 488s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 488s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 488s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 488s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 488s eccmaxqual=127 Do not correct bases with quality above this value. 488s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 488s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 488s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 488s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 488s overlap=f (ecco) Error correct by read overlap. 488s 488s Depth binning parameters: 488s lowbindepth=10 (lbd) Cutoff for low depth bin. 488s highbindepth=80 (hbd) Cutoff for high depth bin. 488s outlow= Pairs in which both reads have a median below lbd go into this file. 488s outhigh= Pairs in which both reads have a median above hbd go into this file. 488s outmid= All other pairs go into this file. 488s 488s Histogram parameters: 488s hist= Specify a file to write the input kmer depth histogram. 488s histout= Specify a file to write the output kmer depth histogram. 488s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 488s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 488s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 488s 488s Peak calling parameters: 488s peaks= Write the peaks to this file. Default is stdout. 488s minHeight=2 (h) Ignore peaks shorter than this. 488s minVolume=5 (v) Ignore peaks with less area than this. 488s minWidth=3 (w) Ignore peaks narrower than this. 488s minPeak=2 (minp) Ignore peaks with an X-value below this. 488s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 488s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 488s 488s Java Parameters: 488s -Xmx This will set Java's memory usage, overriding autodetection. 488s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 488s The max is typically 85% of physical memory. 488s -eoom This flag will cause the process to exit if an 488s out-of-memory exception occurs. Requires Java 8u92+. 488s -da Disable assertions. 488s 488s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 488s 488s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 488s out=out3.fastq outt=outt.fastq hist=hist.plt 488s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 488s java -ea -Xmx2770m -Xms2770m -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 489s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 489s 489s 489s *********** Pass 1 ********** 489s 489s 489s Settings: 489s threads: 4 489s k: 31 489s deterministic: true 489s toss error reads: false 489s passes: 1 489s bits per cell: 16 489s cells: 1024.60M 489s hashes: 3 489s base min quality: 5 489s kmer min prob: 0.5 489s 489s target depth: 400 489s min depth: 3 489s max depth: 500 489s min good kmers: 15 489s depth percentile: 64.8 489s ignore dupe kmers: true 489s fix spikes: false 489s histogram length: 65536 489s print zero cov: false 489s 489s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 489s 489s Estimated unique kmers: 7 489s 489s Table creation time: 0.761 seconds. 489s Started output threads. 489s Started output threads. 489s Table read time: 0.011 seconds. 16.98 kb/sec 489s Total reads in: 2 0.000% Kept 489s Total bases in: 188 0.000% Kept 489s Error reads in: 2 100.000% 489s Error type 1: 2 100.000% 489s Error type 2: 0 0.000% 489s Error type 3: 0 0.000% 489s 489s Wrote histogram to hist.plt 489s Total kmers counted: 128 489s Total unique kmer count: 128 489s Includes forward kmers only. 489s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 489s The most accurate value is the greater of the two. 489s 489s Percent unique: 100.00% 489s Depth average: 1.00 (unique kmers) 489s Depth median: 1 (unique kmers) 489s Depth standard deviation: 0.00 (unique kmers) 489s Corrected depth average: 0.00 489s 489s Depth average: 1.00 (all kmers) 489s Depth median: 1 (all kmers) 489s Depth standard deviation: 0.00 (all kmers) 489s 489s Approx. read depth median: 1.47 489s 489s *********** Pass 2 ********** 489s 489s 489s Settings: 489s threads: 4 489s k: 31 489s deterministic: true 489s toss error reads: false 489s passes: 1 489s bits per cell: 16 489s cells: 1024.60M 489s hashes: 3 489s base min quality: 5 489s kmer min prob: 0.5 489s 489s target depth: 100 489s min depth: 5 489s max depth: 100 489s min good kmers: 15 489s depth percentile: 54.0 489s ignore dupe kmers: true 489s fix spikes: false 489s histogram length: 65536 489s 490s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 490s 490s Estimated unique kmers: 0 490s 490s Table creation time: 0.286 seconds. 490s Started output threads. 490s Started output threads. 490s Table read time: 0.001 seconds. 0.00 kb/sec 490s Total reads in: 0 NaN% Kept 490s Total bases in: 0 NaN% Kept 490s Error reads in: 0 NaN% 490s Error type 1: 0 NaN% 490s Error type 2: 0 NaN% 490s Error type 3: 0 NaN% 490s Total kmers counted: 0 490s Total unique kmer count: 0 490s Includes forward kmers only. 490s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 490s The most accurate value is the greater of the two. 490s 490s Percent unique: NaN% 490s Depth average: NaN (unique kmers) 490s Depth median: 0 (unique kmers) 490s Depth standard deviation: NaN (unique kmers) 490s Corrected depth average: NaN 490s 490s Depth average: NaN (all kmers) 490s Depth median: 0 (all kmers) 490s Depth standard deviation: 0.00 (all kmers) 490s 490s Approx. read depth median: NaN 490s 490s Removing temp files. 490s 490s Total time: 1.249 seconds. 0.15 kb/sec 490s test -r out3.fastq 490s test -r outt.fastq 490s test -r hist.plt 490s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 490s out=out4.fastq outt=outt2.fastq hist=hist2.plt 490s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 490s java -ea -Xmx2770m -Xms2770m -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 490s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 490s 490s 490s *********** Pass 1 ********** 490s 490s 490s Settings: 490s threads: 4 490s k: 31 490s deterministic: true 490s toss error reads: false 490s passes: 1 490s bits per cell: 16 490s cells: 1024.60M 490s hashes: 3 490s base min quality: 5 490s kmer min prob: 0.5 490s 490s target depth: 400 490s min depth: 3 490s max depth: 500 490s min good kmers: 15 490s depth percentile: 64.8 490s ignore dupe kmers: true 490s fix spikes: false 490s histogram length: 65536 490s print zero cov: false 490s 491s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 491s 491s Estimated unique kmers: 7 491s 491s Table creation time: 0.701 seconds. 491s Started output threads. 491s Started output threads. 491s Table read time: 0.005 seconds. 25.53 kb/sec 491s Total reads in: 2 0.000% Kept 491s Total bases in: 126 0.000% Kept 491s Error reads in: 2 100.000% 491s Error type 1: 2 100.000% 491s Error type 2: 0 0.000% 491s Error type 3: 0 0.000% 491s 491s Wrote histogram to hist2.plt 491s Total kmers counted: 66 491s Total unique kmer count: 66 491s Includes forward kmers only. 491s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 491s The most accurate value is the greater of the two. 491s 491s Percent unique: 100.00% 491s Depth average: 1.00 (unique kmers) 491s Depth median: 1 (unique kmers) 491s Depth standard deviation: 0.00 (unique kmers) 491s Corrected depth average: 0.00 491s 491s Depth average: 1.00 (all kmers) 491s Depth median: 1 (all kmers) 491s Depth standard deviation: 0.00 (all kmers) 491s 491s Approx. read depth median: 1.91 491s 491s *********** Pass 2 ********** 491s 491s 491s Settings: 491s threads: 4 491s k: 31 491s deterministic: true 491s toss error reads: false 491s passes: 1 491s bits per cell: 16 491s cells: 1024.60M 491s hashes: 3 491s base min quality: 5 491s kmer min prob: 0.5 491s 491s target depth: 100 491s min depth: 5 491s max depth: 100 491s min good kmers: 15 491s depth percentile: 54.0 491s ignore dupe kmers: true 491s fix spikes: false 491s histogram length: 65536 491s 491s Made hash table: hashes = 3 mem = 1.91 GB cells = 1024.56M used = 0.000% 491s 491s Estimated unique kmers: 0 491s 491s Table creation time: 0.300 seconds. 491s Started output threads. 491s Started output threads. 491s Table read time: 0.001 seconds. 0.00 kb/sec 491s Total reads in: 0 NaN% Kept 491s Total bases in: 0 NaN% Kept 491s Error reads in: 0 NaN% 491s Error type 1: 0 NaN% 491s Error type 2: 0 NaN% 491s Error type 3: 0 NaN% 491s Total kmers counted: 0 491s Total unique kmer count: 0 491s Includes forward kmers only. 491s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 491s The most accurate value is the greater of the two. 491s 491s Percent unique: NaN% 491s Depth average: NaN (unique kmers) 491s Depth median: 0 (unique kmers) 491s Depth standard deviation: NaN (unique kmers) 491s Corrected depth average: NaN 491s 491s Depth average: NaN (all kmers) 491s Depth median: 0 (all kmers) 491s Depth standard deviation: 0.00 (all kmers) 491s 491s Approx. read depth median: NaN 491s 491s Removing temp files. 491s 491s Total time: 1.087 seconds. 0.12 kb/sec 492s test -r out4.fastq 492s test -r outt2.fastq 492s test -r hist2.plt 492s autopkgtest [21:17:39]: test run-unit-test: -----------------------] 493s autopkgtest [21:17:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 493s run-unit-test PASS 493s autopkgtest [21:17:40]: @@@@@@@@@@@@@@@@@@@@ summary 493s run-unit-test PASS