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Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
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Manta never finish on a merged bam file. #199

Closed AJ2802 closed 4 years ago

AJ2802 commented 4 years ago

Hello, I merge 3 bam files from the same sample together and then run manta on the merged file. However, manta never finishes the following instructions. I am not sure it is because of a bug or the size of bam file.

[2019-10-14T18:06:57.823699Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [TaskManager] Launching command task: 'generateCandidateSV_0000' from master workflow [2019-10-14T18:06:57.901957Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [TaskRunner:generateCandidateSV_0000] Task initiated on local node [2019-10-14T18:12:07.779535Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] ===== MantaWorkflow StatusUpdate ===== [2019-10-14T18:12:07.826284Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Workflow specification is complete?: False [2019-10-14T18:12:07.840179Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Task status (waiting/queued/running/complete/error): 9/0/1/384/0 [2019-10-14T18:12:07.864777Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task time (hrs): 0.0000 [2019-10-14T18:12:07.866293Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task name: '' [2019-10-14T18:12:07.867756Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task time (hrs): 0.0858 [2019-10-14T18:12:07.869393Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task name: 'generateCandidateSV_0000' [2019-10-14T19:12:08.215685Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] ===== MantaWorkflow StatusUpdate ===== [2019-10-14T19:12:08.270986Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Workflow specification is complete?: False [2019-10-14T19:12:08.307943Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Task status (waiting/queued/running/complete/error): 9/0/1/384/0 [2019-10-14T19:12:08.310557Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task time (hrs): 0.0000 [2019-10-14T19:12:08.312002Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task name: '' [2019-10-14T19:12:08.313514Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task time (hrs): 1.0861 [2019-10-14T19:12:08.314879Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task name: 'generateCandidateSV_0000' [2019-10-14T20:12:08.424456Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] ===== MantaWorkflow StatusUpdate ===== [2019-10-14T20:12:08.456360Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Workflow specification is complete?: False [2019-10-14T20:12:08.483704Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Task status (waiting/queued/running/complete/error): 9/0/1/384/0 [2019-10-14T20:12:08.487534Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task time (hrs): 0.0000 [2019-10-14T20:12:08.489295Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task name: '' [2019-10-14T20:12:08.492162Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task time (hrs): 2.0861 [2019-10-14T20:12:08.493631Z] [ptong-cnv-research-2.c.cgsdevelopment-1216.internal] [26317_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task name: 'generateCandidateSV_0000'

002-two commented 1 year ago

Hello，I wonder if this problem has been solved！

serge2016 commented 1 year ago

Similar question here...