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Task #2566

closed

Idea #2039: New user sees a list of completed pipeline instances on Workbench dashboard, and can inspect the pipelines and data.  (Permissions/presentation)

Make the GATK pipeline produce output

Added by Tom Clegg about 10 years ago. Updated almost 10 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Tom Clegg
Target version:
-
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 #1

Updated by Tom Clegg about 10 years ago

  • Status changed from New to In Progress
  • Start date set to 04/09/2014
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 #2

Updated by Tom Clegg about 10 years ago 

2014-04-01_07:01:27 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr INFO  07:02:13,914 ProgressMeter - Total runtime 2205.73 secs, 36.76 min, 0.61 hours 
2014-04-01_07:01:27 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr INFO  07:02:13,914 MicroScheduler - 1258974 reads were filtered out during traversal out of 154989036 total (0.81%) 
2014-04-01_07:01:27 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr INFO  07:02:13,914 MicroScheduler -   -> 1258974 reads (0.81% of total) failing UnmappedReadFilter 
2014-04-01_07:01:27 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr INFO  07:02:13,915 NSRuntimeProfile - Input   time:   11.1 m (32.20%) 
2014-04-01_07:01:27 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr INFO  07:02:13,915 NSRuntimeProfile - Map     time:   20.6 m (59.99%) 
2014-04-01_07:01:27 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr INFO  07:02:13,915 NSRuntimeProfile - Reduce  time:   46.3 s ( 2.25%) 
2014-04-01_07:01:27 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr INFO  07:02:13,915 NSRuntimeProfile - Outside time:  114.6 s ( 5.56%) 
2014-04-01_07:01:28 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr INFO  07:02:14,530 GATKRunReport - Uploaded run statistics report to AWS S3 
2014-04-01_07:01:28 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 stderr srun: error: compute13: task 0: Exited with exit code 1
2014-04-01_07:01:28 qr1hi-8i9sb-9hnod7419iyp86h 29957 0 child 30035 on compute13.1 exit 1 signal 0 success=
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 #3

Updated by Tom Clegg about 10 years ago

  • Status changed from In Progress to Resolved
  • Remaining (hours) changed from 2.0 to 0.0
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