Build #256

Environment variables

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ghprbActualCommit734ed70a5caf8190091341886a69147ddfdbffa9
ghprbActualCommitAuthorMichael L Heuer
ghprbActualCommitAuthorEmailheuermh@acm.org
ghprbAuthorRepoGitUrlhttps://github.com/heuermh/cannoli.git
ghprbCommentBodynull
ghprbCredentialsIdb7d94526-9e9b-435f-9275-d7dbf209f4a3
ghprbGhRepositorybigdatagenomics/cannoli
ghprbPullAuthorLoginheuermh
ghprbPullAuthorLoginMention@heuermh
ghprbPullDescriptionGitHub pull request #203 of commit 734ed70a5caf8190091341886a69147ddfdbffa9, no merge conflicts.
ghprbPullId203
ghprbPullLinkhttps://github.com/bigdatagenomics/cannoli/pull/203
ghprbPullLongDescriptionWork in progress, not working\r\n```\r\n$ ./bin/cannoli-submit sambambaMarkdup \\r\n  NA12878.alignedHg38.duplicateMarked.baseRealigned.bam \\r\n  NA12878.alignedHg38.duplicateMarked.baseRealigned.markdup.alignments.adam\r\n\r\n...\r\n19/10/04 11:45:49 INFO SambambaMarkdup: Piping RDDBoundAlignmentRecordDataset\r\nwith 3366 reference sequences, 3 read groups, and 3 processing steps to sambamba\r\nwith command: [sambamba, markdup, /dev/stdin, /dev/stdout] files: []\r\n...\r\n19/10/04 11:46:19 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 0 ms\r\n\r\nsambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018\r\n    LDC 1.11.0 / DMD v2.081.2 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)\r\n\r\nfinding positions of the duplicate reads in the file...\r\n  sorted 0 end pairs\r\n     and 0 single ends (among them 0 unmatched pairs)\r\n  collecting indices of duplicate reads...   done in 0 ms\r\n  found 0 duplicates\r\ncollected list of positions in 0 min 0 sec\r\nsambamba-markdup: not enough data in stream\r\n```\r\n\r\nSimilar issues when calling directly\r\n```\r\n$ cat NA12878.alignedHg38.duplicateMarked.baseRealigned.bam \\r\n  | sambamba markdup /dev/stdin /dev/stdout \\r\n  > NA12878.alignedHg38.duplicateMarked.baseRealigned.markdup.bam\r\n\r\nsambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018\r\n    LDC 1.11.0 / DMD v2.081.2 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)\r\n\r\nfinding positions of the duplicate reads in the file...\r\n  sorted 29356 end pairs\r\n     and 423 single ends (among them 0 unmatched pairs)\r\n  collecting indices of duplicate reads...   done in 5 ms\r\n  found 48 duplicates\r\ncollected list of positions in 0 min 0 sec\r\nsambamba-markdup: not enough data in stream\r\n```\r\n\r\nSeems to work ok without `/dev/stdin` and `/dev/stdout`\r\n```\r\n$ sambamba markdup \\r\n  NA12878.alignedHg38.duplicateMarked.baseRealigned.bam \\r\n  NA12878.alignedHg38.duplicateMarked.baseRealigned.markdup.bam\r\n\r\nsambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018\r\n    LDC 1.11.0 / DMD v2.081.2 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)\r\n\r\nfinding positions of the duplicate reads in the file...\r\n  sorted 29356 end pairs\r\n     and 423 single ends (among them 0 unmatched pairs)\r\n  collecting indices of duplicate reads...   done in 4 ms\r\n  found 48 duplicates\r\ncollected list of positions in 0 min 0 sec\r\nmarking duplicates...\r\ncollected list of positions in 0 min 2 sec\r\n```
ghprbPullTitleAdd Sambamba markdup for marking duplicate reads
ghprbSourceBranchsambamba-markdup
ghprbTargetBranchmaster
sha1origin/pr/203/merge