WDL OutOfMemory Issue

[BioinfoMohIL]

Hello,

I have a script to fetch reads from basespace, and execute kraken2 on the reads. I have something like 300 reads (150 R1, 150 R2). The script fail at some point. I tried to set higher memory by still fail.

I'd glad to get help.

Thank you!

The part of code causing the issue:

scatter(sample_name in GetReadsList.samples_name) {

call FetchReads {

input:

basespace_sample_name = sample_name,
basespace_collection_id = basespace_collection_id,
api_server = api_server,
access_token = access_token

}

call Detect_Specie {

input:
read1 = FetchReads.read1,
read2 = FetchReads.read2,
sample_id = sample_name

}
}

The error :

Task Specie_Detection.FetchReads:24:1 failed. The job was stopped before the command finished. PAPI error code 9. Execution failed: generic::failed_precondition: while running "-c grep -E -q 'OutOfMemory|Killed' /cromwell_root/stderr ; echo $? /cromwell_root/memory_retry_rc": unexpected exit status 1 was not ignored [CheckingForMemoryRetry] Unexpected exit status 1 while running "-c grep -E -q 'OutOfMemory|Killed' /cromwell_root/stderr ; echo $? /cromwell_root/memory_retry_rc": sh: write error: No space left on device

[claymcleod]

Hi there! This is the repository for the WDL specification, which is not associated with any of the WDL execution engines. It seems like you're running Cromwell, so I'd encourage you to post this issue over at the Cromwell GitHub.