Workflow failed

QiangHu

Hello,

I am submitting jobs in the firecloud with the five-dollar-genome-analysis-pipeline. One of my job failed in the germline_single_sample_workflow.SplitRG step. Here is the error message.

message: Call input and runtime attributes evaluation failed for GatherMonolithicBamFile
causedBy:
message: No coercion defined from '257' of type 'Int' to 'Float'.

Could anyone help to check this error?

Thanks,
Qiang

QiangHu

I submitted another job with Germline-SNPs-Indels-GATK4-hg38 workflow. The job failed again in the PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem step. The error message shows "No space left on device", so space is full? Any suggestion?? Thanks!

Here are the error messages from SamToFastqAndBwaMem-0-stderr.log:

[M::mem_process_seqs] Processed 664720 reads in 708.240 CPU sec, 45.352 real sec
[M::process] 0 single-end sequences; 664706 paired-end sequences
[E::bgzf_flush] hwrite error (wrong size)
samtools view: writing to standard output failed: No space left on device
[E::bgzf_close] file write error
samtools view: error closing standard output: -1
[Fri Mar 16 04:05:27 UTC 2018] picard.sam.SamToFastq done. Elapsed time: 654.37 minutes.
Runtime.totalMemory()=3145203712
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Error in writing fastq file /dev/stdout
at htsjdk.samtools.fastq.BasicFastqWriter.write(BasicFastqWriter.java:66)
at picard.sam.SamToFastq.writeRecord(SamToFastq.java:351)
at picard.sam.SamToFastq.doWork(SamToFastq.java:206)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

KateN

To address your second bug first, the issue there is that you've ran out of disk space. In your method configuration, in the SamToFastqAndBwaMem task, you should increase the value of mem_size.

For your first bug, are you still experiencing the error message? If so, would you please share the workspace with [email protected]? I will also need the submission ID and workflow ID for the run where you encountered the error message.

QiangHu

Thank you for your reply. I just sent email to GROUP_support. Thanks!

KateN

Ah, slight miscommunication there. I need you to share the workspace in FireCloud with [email protected]. You'll go to the workspace, click share on the left-hand side of the page, then add the above email address as a Reader of the workspace. Could you also give the name of the workspace here? I neglected to ask for that.

Additionally, I've been told that mem_size is the wrong attribute to change. (It refers to RAM rather than disk size) The correct one for SamToFastqAndBwaMem is flowcell_medium_disk. You'll need to increase that value in order to increase the disk size.

QiangHu

Just shared my workspace to GROUP_support. Here is workspace name:
fccredits-curium-orange-2937/five-dollar-genome-analysis-pipeline_copy
Thanks!

KateN

Alright, as it turns out the coercion error you were seeing was due to a small issue where splitRG.GatherMonolithicBamFile being given a Int type for the disk size when it was expecting a Float. After fixing that, the method author found another problem with an indexing step in the GatherBamFiles task.

As a result, they are currently working on a fix, and will soon release a new snapshot of the method and its method configuration. I will report back here when they have the fix live, but you can always check the featured method on FireCloud to look for updates in the meantime.

QiangHu

Great. Looking forward to your update. Thanks!

bshifaw

@QiangHu , a new snapshot of the method is now available.