{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/45","repository_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer","labels_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/45/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/45/comments","events_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/45/events","html_url":"https://github.com/PacificBiosciences/cDNA_primer/issues/45","id":176452689,"number":45,"title":"IceQuiver.  Runtime Error: Invalid Input?","user":{"login":"puapinyoying","id":14180992,"avatar_url":"https://avatars.githubusercontent.com/u/14180992?v=3","gravatar_id":"","url":"https://api.github.com/users/puapinyoying","html_url":"https://github.com/puapinyoying","followers_url":"https://api.github.com/users/puapinyoying/followers","following_url":"https://api.github.com/users/puapinyoying/following{/other_user}","gists_url":"https://api.github.com/users/puapinyoying/gists{/gist_id}","starred_url":"https://api.github.com/users/puapinyoying/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/puapinyoying/subscriptions","organizations_url":"https://api.github.com/users/puapinyoying/orgs","repos_url":"https://api.github.com/users/puapinyoying/repos","events_url":"https://api.github.com/users/puapinyoying/events{/privacy}","received_events_url":"https://api.github.com/users/puapinyoying/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-09-12T18:45:12Z","updated_at":"2016-09-14T20:06:42Z","closed_at":null,"body":"Hi,\r\n\r\nI am having some trouble with the IceQuiver step on a specific set of data. Two other samples that were demultiplexed from the same set of cells have no issue.  This sample runs fine for the majority of clusters then runs into a RunTime Error.  Do you know what could it be causing it and how I could fix or work around the issue?  I followed the error logs and posted them below.  Please let me know if you need more information.\r\n\r\n**IceQuiver.log**\r\n```\r\n[DEBUG] [IceQuiver] 2016-09-09 12:05:56: [IceQuiver] Concatenating sam files between 25914 and 26033.\r\n[DEBUG] [IceQuiver] 2016-09-09 12:05:59: [IceQuiver] Concatenation done\r\n[DEBUG] [IceQuiver] 2016-09-09 12:05:59: [IceQuiver] Creating quiver cmds for c25914 to c26033\r\n[DEBUG] [IceQuiver] 2016-09-09 12:05:59: [IceQuiver] Creating quiver bash script /home/brian/3-6kb_grp1_edl_8cell/cluster_out/quivered/c25914to26033.sh for c25914 to c26033.\r\n[DEBUG] [IceQuiver] 2016-09-09 12:06:00: [IceQuiver] Submitting todo quiver jobs.\r\n[DEBUG] [IceQuiver] 2016-09-09 12:06:00: [IceQuiver] Running CMD: bash /home/brian/3-6kb_grp1_edl_8cell/cluster_out/quivered/c25914to26033.sh 1>/home/brian/3-6kb_grp1_edl_8cell/cluster_out/log/quivered/c25914to26033.sh.olog 2>/home/brian/3-6kb_grp1_edl_8cell/cluster_out/log/quivered/c25914to26033.sh.elog\r\n[ERROR] [IceQuiver] 2016-09-09 12:12:55: [IceQuiver] CMD exited with a non-zero code: bash /home/brian/cluster_out/quivered/c25914to26033.sh 1>/home/brian/3-6kb_grp1_edl_8cell/cluster_out/log/quivered/c25914to26033.sh.olog 2>/home/brian/3-6kb_grp1_edl_8cell/cluster_out/log/quivered/c25914to26033.sh.elog, \r\nFailed to run Quiver\r\nError log: /home/brian/3-6kb_grp1_edl_8cell/cluster_out/log/quivered/c25914to26033.sh.elog\r\nOut log: /home/brian/3-6kb_grp1_edl_8cell/cluster_out/log/quivered/c25914to26033.sh.olog\r\n```\r\n\r\n\r\n**c25914to26033.sh.elog**\r\n```\r\n[INFO] 2016-09-09T12:06:00 [samtoh5] started.\r\n[INFO] 2016-09-09T12:06:11 [samtoh5] ended.\r\n[INFO] 2016-09-09T12:07:10 [loadPulses] started.\r\n[INFO] 2016-09-09T12:12:45 [loadPulses] ended.\r\n[INFO] h5py version: 2.2.0\r\n[INFO] hdf5 version: 1.8.12\r\n[INFO] ConsensusCore version: 0.8.8\r\n[INFO] Starting.\r\n[INFO] Peeking at CmpH5 file /home/brian/3-6kb_grp1_edl_8cell/cluster_out/quivered/c25914to26033.cmp.h5\r\n[INFO] Input CmpH5 data: numAlnHits=2855\r\n[INFO] Loading reference\r\n[INFO] Loaded 100 of 100 reference groups from /home/brian/3-6kb_grp1_edl_8cell/cluster_out/quivered/c25914to26033.ref.fa \r\n[INFO] Using Quiver parameters file /c1/apps/smrt_analysis/2.3.0/install/smrtanalysis_2.3.0.140936/analysis/lib/python2.7/GenomicConsensus/quiver/resources/2014-09/GenomicConsensus/QuiverParameters.ini\r\n[INFO] Using Quiver parameter set(s): P6-C4.AllQVsMergingByChannelModel\r\n[INFO] Will disable HDF5 chunk cache (large number of datasets)\r\n[INFO] Available CPUs: 16\r\n[INFO] Requested workers: 15\r\n[INFO] Parallel Mode: Process\r\n[INFO] Launched compute slaves.\r\n[INFO] Launched collector slave.\r\n[INFO] Quiver operating on c25915:2995-3374\r\n...\r\n[INFO] Quiver operating on c25917:495-1005\r\n[INFO] Usable coverage in c25917:2-505: [(4, 505)]\r\n...\r\n[INFO] Usable coverage in c25935:2995-3075: [(2995, 3073)]\r\n[INFO] Quiver operating on c25937:18-505\r\n[INFO] Quiver operating on c25937:495-1005\r\n[INFO] Quiver operating on c25937:995-1505\r\n[INFO] Quiver operating on c25937:1495-2005\r\n[INFO] Quiver operating on c25937:1995-2505\r\n[INFO] Quiver operating on c25937:2495-3005\r\n[INFO] Quiver operating on c25937:2995-3505\r\n[INFO] Quiver operating on c25937:3495-3716\r\n[INFO] Quiver operating on c25942:61-505\r\nProcess QuiverWorkerProcess-14:\r\nTraceback (most recent call last):\r\n  File \"/c1/apps/smrt_analysis/2.3.0/current/redist/python2.7/lib/python2.7/multiprocessing/process.py\", line 258, in _bootstrap\r\n    self.run()\r\n  File \"/c1/apps/smrt_analysis/2.3.0/current/redist/python2.7/lib/python2.7/site-packages/GenomicConsensus/Worker.py\", line 91, in run\r\n    self._run()\r\n  File \"/c1/apps/smrt_analysis/2.3.0/current/redist/python2.7/lib/python2.7/site-packages/GenomicConsensus/Worker.py\", line 77, in _run\r\n    result = self.onChunk(datum)\r\n  File \"/c1/apps/smrt_analysis/2.3.0/current/redist/python2.7/lib/python2.7/site-packages/GenomicConsensus/quiver/quiver.py\", line 196, in onChunk\r\n    refContig, options.coverage, self.quiverConfig)\r\n  File \"/c1/apps/smrt_analysis/2.3.0/current/redist/python2.7/lib/python2.7/site-packages/GenomicConsensus/quiver/quiver.py\", line 116, in consensusAndVariantsForWindow\r\n    quiverConfig)\r\n  File \"/c1/apps/smrt_analysis/2.3.0/current/redist/python2.7/lib/python2.7/site-packages/GenomicConsensus/quiver/utils.py\", line 383, in consensusForAlignments\r\n    refineDinucleotideRepeats(mms)\r\n  File \"/c1/apps/smrt_analysis/2.3.0/current/redist/python2.7/lib/python2.7/site-packages/GenomicConsensus/quiver/utils.py\", line 164, in refineDinucleotideRepeats\r\n    return cc.RefineDinucleotideRepeats(mms)\r\nRuntimeError: Invalid input!\r\n[INFO] Quiver operating on c25942:495-1005\r\n[INFO] Quiver operating on c25942:995-1505\r\n[INFO] Quiver operating on c25942:1495-2005\r\n[INFO] Quiver operating on c25942:1995-2505\r\n[INFO] Quiver operating on c25942:2495-3005\r\n[INFO] Quiver operating on c25942:2995-3096\r\n[INFO] Quiver operating on c25943:70-505\r\n[INFO] Quiver operating on c25943:495-1005\r\n[ERROR] Child process exited with exitcode=1.  Aborting.\r\n[ERROR] Aborting\r\n[INFO] Quiver operating on c25943:995-1505\r\n[INFO] Quiver operating on c25943:1495-2005\r\n[INFO] Quiver operating on c25943:1995-2505\r\n```\r\n\r\n**The command I used:**\r\n```\r\npbtranscript.py cluster 3-6kb_grp1_edl_8cell_isoseq_flnc.fasta 3-6kb_grp1_edl_8cell_final_consensus.fasta \\\r\n--nfl_fa 3-6kb_grp1_pooled_8cell_isoseq_nfl.fasta -d cluster_out \\\r\n--bas_fofn 3-6kb_grp1_pooled_8cell_bax.fofn \\\r\n--ccs_fofn 3-6kb_grp1_pooled_8cell_ccs.fofn \\\r\n--cDNA_size above3k \\\r\n--quiver \\\r\n--blasr_nproc 15 \\\r\n--quiver_nproc 15\r\n```\r\nThanks for your help,\r\nBrian"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/comments/247137066","html_url":"https://github.com/PacificBiosciences/cDNA_primer/issues/45#issuecomment-247137066","issue_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/45","id":247137066,"user":{"login":"puapinyoying","id":14180992,"avatar_url":"https://avatars.githubusercontent.com/u/14180992?v=3","gravatar_id":"","url":"https://api.github.com/users/puapinyoying","html_url":"https://github.com/puapinyoying","followers_url":"https://api.github.com/users/puapinyoying/followers","following_url":"https://api.github.com/users/puapinyoying/following{/other_user}","gists_url":"https://api.github.com/users/puapinyoying/gists{/gist_id}","starred_url":"https://api.github.com/users/puapinyoying/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/puapinyoying/subscriptions","organizations_url":"https://api.github.com/users/puapinyoying/orgs","repos_url":"https://api.github.com/users/puapinyoying/repos","events_url":"https://api.github.com/users/puapinyoying/events{/privacy}","received_events_url":"https://api.github.com/users/puapinyoying/received_events","type":"User","site_admin":false},"created_at":"2016-09-14T20:06:42Z","updated_at":"2016-09-14T20:06:42Z","body":"dalexander & Liz,\r\n\r\nSay I take the approach to install the latest version of GenomicConsensus in a virtualenv.  What would be the best strategy to resume where I left off?  \r\n\r\nThe GenomicConsensus README does not recommend I create a single giant cmp.h5 file. Could I combine Liz's approach to split the quiver jobs using cmd_quiver_rerun script along with the new quiver version?  Will it ultimately lead me to output the 'all_quivered_hq.100_30_0.99.fastq' file?\r\n\r\nThanks,\r\nBrian"}}
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