{"action":"closed","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1689","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1689/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1689/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1689/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1689","id":195305801,"number":1689,"title":"gatk error after last night's (successful) upgrade","user":{"login":"naumenko-sa","id":13981803,"avatar_url":"https://avatars.githubusercontent.com/u/13981803?v=3","gravatar_id":"","url":"https://api.github.com/users/naumenko-sa","html_url":"https://github.com/naumenko-sa","followers_url":"https://api.github.com/users/naumenko-sa/followers","following_url":"https://api.github.com/users/naumenko-sa/following{/other_user}","gists_url":"https://api.github.com/users/naumenko-sa/gists{/gist_id}","starred_url":"https://api.github.com/users/naumenko-sa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/naumenko-sa/subscriptions","organizations_url":"https://api.github.com/users/naumenko-sa/orgs","repos_url":"https://api.github.com/users/naumenko-sa/repos","events_url":"https://api.github.com/users/naumenko-sa/events{/privacy}","received_events_url":"https://api.github.com/users/naumenko-sa/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-13T16:47:01Z","updated_at":"2016-12-13T18:28:25Z","closed_at":"2016-12-13T18:28:25Z","body":"Hello!\r\n\r\nAfter successful upgrade last night with\r\n`bcbio_nextgen.py upgrade -u development --tools --data`\r\n\r\nI have an error:\r\n`gatk -R ~/work/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T VariantsToTable -V 394-gatk-haplotype.decomposed.vcf.gz -F CHROM -F POS -F REF -F ALT -F DP -GF DP -GF AD -o test.table --allowMissingData`\r\n```\r\n'import site' failed; use -v for traceback\r\nTraceback (most recent call last):\r\n  File \"/home/naumenko/work/tools/bin/gatk\", line 9, in <module>\r\n    import os\r\n  File \"/home/naumenko/work/tools/bcbio/anaconda/lib/python2.7/os.py\", line 400, in <module>\r\n    import UserDict\r\n  File \"/home/naumenko/work/tools/bcbio/anaconda/lib/python2.7/UserDict.py\", line 116, in <module>\r\n    import _abcoll\r\n  File \"/home/naumenko/work/tools/bcbio/anaconda/lib/python2.7/_abcoll.py\", line 456, in <module>\r\n    KeysView.register(type({}.viewkeys()))\r\nAttributeError: 'dict' object has no attribute 'viewkeys'\r\n```\r\n\r\nWithout wrapper it works:\r\n`java -Xmx1g -jar ~/work/tools/bcbio/toolplus/gatk/3.6-0-g89b7209/GenomeAnalysisTK.jar -R ~/work/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T VariantsToTable -V 394-gatk-haplotype.decomposed.vcf.gz -F CHROM -F POS -F REF -F ALT -F DP -GF DP -GF AD -o test.table --allowMissingData`\r\n```\r\nINFO  11:41:15,227 HelpFormatter - --------------------------------------------------------------------------------- \r\nINFO  11:41:15,231 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29 \r\nINFO  11:41:15,234 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute \r\nINFO  11:41:15,234 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk \r\nINFO  11:41:15,234 HelpFormatter - [Tue Dec 13 11:41:15 EST 2016] Executing on Linux 2.6.32-642.6.2.el6.x86_64 amd64 \r\nINFO  11:41:15,235 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14 JdkDeflater \r\nINFO  11:41:15,238 HelpFormatter - Program Args: -R /home/naumenko/work/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T VariantsToTable -V 394-gatk-haplotype.decomposed.vcf.gz -F CHROM -F POS -F REF -F ALT -F DP -GF DP -GF AD -o test.table --allowMissingData \r\nINFO  11:41:15,264 HelpFormatter - Executing as naumenko@qlogin1 on Linux 2.6.32-642.6.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14. \r\nINFO  11:41:15,265 HelpFormatter - Date/Time: 2016/12/13 11:41:15 \r\nINFO  11:41:15,265 HelpFormatter - --------------------------------------------------------------------------------- \r\nINFO  11:41:15,266 HelpFormatter - --------------------------------------------------------------------------------- \r\nINFO  11:41:15,298 GenomeAnalysisEngine - Strictness is SILENT \r\nINFO  11:41:15,734 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 \r\nWARN  11:41:15,977 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation \r\nINFO  11:41:16,178 GenomeAnalysisEngine - Preparing for traversal \r\nINFO  11:41:16,192 GenomeAnalysisEngine - Done preparing for traversal \r\nINFO  11:41:16,194 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] \r\nINFO  11:41:16,194 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining \r\nINFO  11:41:16,194 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime \r\nINFO  11:41:36,677 ProgressMeter -            done    369157.0    20.0 s      55.0 s      100.0%    20.0 s       0.0 s \r\nINFO  11:41:36,678 ProgressMeter - Total runtime 20.48 secs, 0.34 min, 0.01 hours \r\n------------------------------------------------------------------------------------------\r\nDone. There were 1 WARN messages, the first 1 are repeated below.\r\nWARN  11:41:15,977 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation \r\n```\r\n\r\nBefore the update I used the wrapper for many times. \r\nCould you please point out what is happening?\r\nMay this cause problems with variant calling in the variant2 pipeline?\r\n\r\nThanks!\r\nSergey"}}
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