{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/250","repository_url":"https://api.github.com/repos/arq5x/lumpy-sv","labels_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/250/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/250/comments","events_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/250/events","html_url":"https://github.com/arq5x/lumpy-sv/issues/250","id":333407096,"node_id":"MDU6SXNzdWUzMzM0MDcwOTY=","number":250,"title":"Error for Partial BAM","user":{"login":"sicotte","id":1950475,"node_id":"MDQ6VXNlcjE5NTA0NzU=","avatar_url":"https://avatars1.githubusercontent.com/u/1950475?v=4","gravatar_id":"","url":"https://api.github.com/users/sicotte","html_url":"https://github.com/sicotte","followers_url":"https://api.github.com/users/sicotte/followers","following_url":"https://api.github.com/users/sicotte/following{/other_user}","gists_url":"https://api.github.com/users/sicotte/gists{/gist_id}","starred_url":"https://api.github.com/users/sicotte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sicotte/subscriptions","organizations_url":"https://api.github.com/users/sicotte/orgs","repos_url":"https://api.github.com/users/sicotte/repos","events_url":"https://api.github.com/users/sicotte/events{/privacy}","received_events_url":"https://api.github.com/users/sicotte/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-06-18T19:38:05Z","updated_at":"2018-06-18T19:45:36Z","closed_at":"2018-06-18T19:45:36Z","author_association":"NONE","body":"Hello,\r\n         I tried running lumpy express with a BAM that has been subsetted to ONLY include chromosome 22 reads (the header lists the whole human genome). I also give it an \"-x bed\" exclude bed file that excludes\r\nall chromosomes, but 22 .. and also excludes most of chromosome 22. \r\n\r\nThe search for translocations/deletions/gains works fine using delly, but I get the following error using lumpyexpress with only the -B and -x options.\r\n\r\nlumpyexpress -B  /research/bsi/projects/pharmacogenetics/s206438.CYP2D6/processing/RUNS/WGS/NA19174.chr22.bam -x /research/bsi/projects/pharmacogenetics/s206438.CYP2D6/LPEA_CAD_NGS_CYP2D6/external/NotD6D7D8.bed\r\nSourcing executables from /research/bsi/tools/biotools/lumpy-sv/0.2.13/bin/lumpyexpress.config ...\r\n\r\nChecking for required python modules (/research/bsi/tools/biotools/python/2.7.10/bin/python)...\r\n/research/bsi/projects/pharmacogenetics/s206438.CYP2D6/processing/RUNS/WGS/NA19174.chr22.bam.bai\r\n/research/bsi/tools/biotools/lumpy-sv/0.2.13/bin/lumpyexpress: line 288: --acceptDupMarks: command not found\r\n[W::hts_idx_load2] The index file is older than the data file: /research/bsi/projects/pharmacogenetics/s206438\r\n\r\nTraceback (most recent call last):\r\n  File \"/research/bsi/tools/biotools/lumpy-sv/0.2.13//scripts/bamkit/bamgroupreads.py\", line 162, in <module>\r\n    sys.exit(main())\r\n  File \"/research/bsi/tools/biotools/lumpy-sv/0.2.13//scripts/bamkit/bamgroupreads.py\", line 158, in main\r\n    bamgroupreads(args.input, args.readgroup, args.reset_dups, args.fix_flags, args.S, args.b, args.u)\r\n  File \"/research/bsi/tools/biotools/lumpy-sv/0.2.13//scripts/bamkit/bamgroupreads.py\", line 91, in bamgroupreads\r\n    out_bam.write(al)\r\n  File \"pysam/libcalignmentfile.pyx\", line 1653, in pysam.libcalignmentfile.AlignmentFile.write\r\n  File \"pysam/libcalignmentfile.pyx\", line 1682, in pysam.libcalignmentfile.AlignmentFile.write\r\nIOError: sam_write1 failed with error code -1\r\n/research/bsi/tools/biotools/python/2.7.10/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2909: RuntimeWarning: Mean of empty slice.\r\n  out=out, **kwargs)\r\n/research/bsi/tools/biotools/python/2.7.10/lib/python2.7/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars\r\n  ret = ret.dtype.type(ret / rcount)\r\nTraceback (most recent call last):\r\n  File \"/research/bsi/tools/biotools/lumpy-sv/0.2.13//scripts/pairend_distro.py\", line 106, in <module>\r\n    (removed, upper_cutoff))\r\nTypeError: %d format: a number is required, not numpy.float64\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/comments/398172591","html_url":"https://github.com/arq5x/lumpy-sv/issues/250#issuecomment-398172591","issue_url":"https://api.github.com/repos/arq5x/lumpy-sv/issues/250","id":398172591,"node_id":"MDEyOklzc3VlQ29tbWVudDM5ODE3MjU5MQ==","user":{"login":"sicotte","id":1950475,"node_id":"MDQ6VXNlcjE5NTA0NzU=","avatar_url":"https://avatars1.githubusercontent.com/u/1950475?v=4","gravatar_id":"","url":"https://api.github.com/users/sicotte","html_url":"https://github.com/sicotte","followers_url":"https://api.github.com/users/sicotte/followers","following_url":"https://api.github.com/users/sicotte/following{/other_user}","gists_url":"https://api.github.com/users/sicotte/gists{/gist_id}","starred_url":"https://api.github.com/users/sicotte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sicotte/subscriptions","organizations_url":"https://api.github.com/users/sicotte/orgs","repos_url":"https://api.github.com/users/sicotte/repos","events_url":"https://api.github.com/users/sicotte/events{/privacy}","received_events_url":"https://api.github.com/users/sicotte/received_events","type":"User","site_admin":false},"created_at":"2018-06-18T19:45:36Z","updated_at":"2018-06-18T19:45:36Z","author_association":"NONE","body":"H"}}
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