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PublicPairedSingleSampleWf_160927 Error while running locally @ SamToFastqAndBwaMem
i tried to run your PublicPairedSingleSampleWf locally but run in some trouble...
The pipeline stopps with java.lang.Exception: Call PairedEndSingleSampleWorkflow.SamToFastqAndBwaMem: return code was 1,
When i look at the stderr in call-SamToFastqAndBwaMem execution Folder i find the following lines:
/bin/bash: line 16: /data/reference/TestData/hiseq2500/NA12878/H06HDADXX130110.1.ATCACGAT.20k_reads.unmerged.bam: No such file or directory<br />
tee: /data/reference/TestData/hiseq2500/NA12878/H06HDADXX130110.1.ATCACGAT.20k_reads.unmerged.bwa.stderr.log: No such file or directory<br />
And also an Error from picard:
Exception in thread "main" htsjdk.samtools.SAMException: Error in writing fastq file /dev/stdout<br />
at htsjdk.samtools.fastq.BasicFastqWriter.write(BasicFastqWriter.java:68)<br />
at picard.sam.SamToFastq.writeRecord(SamToFastq.java:350)<br />
at picard.sam.SamToFastq.doWork(SamToFastq.java:195)<br />
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)<br />
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)<br />
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)<br />
It seems that SamTOFastq he isnt able to write the output into stdout. But I dunno why, any clue ?
Thanks for your help,