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MGX-metagenomics / MGX-server

MGX application server
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ConvertToBAM: Conveyor issue #81

Closed sjaenick closed 7 years ago

sjaenick commented 7 years ago

In gitlab by @sjaenick on Jun 21, 2016, 19:48


[samfaipath] build FASTA index...
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
  -@, --threads INT
             Set number of sorting and compression threads [1]
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
node Id:4 () aborted with exception: System.ApplicationException: samtools sort (sort /vol/mgx-data/MGX_terpene_soils/mapping/330.bam.tmp /vol/mgx-data/MGX_terpene_soils/mapping/330) exited with exit code 1
  at Conveyor.ReadMapping.BAMConverter.ConvertToBAM (System.String samFile, System.String refFASTA, System.String bamFile) [0x00171] in /homes/sjaenick/Conveyor-MGX/conveyor/Staging/Conveyor.ReadMapping/SAM/BAMConverter.cs:48 
  at Conveyor.MGX.CreateMapping.Finish () [0x0013e] in /homes/sjaenick/Conveyor-MGX/conveyor/Staging/Conveyor.MGX/NodeTypes/CreateMapping/CreateMapping.cs:87 
  at Conveyor.Processing.Threaded.nodeProcessing () [0x00075] in /homes/sjaenick/Conveyor-MGX/conveyor/Conveyor.Processing/Conveyor.Processing/Execution/Threaded.cs:235
sjaenick commented 7 years ago

In gitlab by @sjaenick on Jun 25, 2016, 10:37

fixed