0

I have been trying to convert my fastq files on google cloud to uBAM files but no success so far. Here is code I used:

dsub \
--project projectID \
--zones "us-central1-*" \
--logging gs://bucket/logging \
--image broadinstitute/picard \
--command 'java -Xmx8G -jar picard.jar FastqToSam FASTQ=gs://bucket/S_1.fq FASTQ2=gs://bucket/S_2.fq OUTPUT=gs://bucket/S_fastqtosam.bam READ_GROUP_NAME=Cancers SAMPLE_NAME=TS LIBRARY_NAME=Solexa-272222 PLATFORM_UNIT=CL100056 PLATFORM=illumina SEQUENCING_CENTER=BI RUN_DATE=2017-08-20T00:00:00-0400'
--wait

I can see the image has been pulled and run successful, but then I got the error message saying the command is incorrect, and please check PicardcommandLine -h

Does anyone have experience in converting fastq to uBAM with google cloud? PLease help. Much appreciated. Thank you.

Sjon
  • 4,989
  • 6
  • 28
  • 46
Bingley
  • 1

1 Answers1

0

The broadinstitute/picard docker image already runs java as its Entrypoint (see [1] for more details). You need to change the command to remove java -Xmx8G -jar picard.jar.

I'm also not sure whether passing cloud storage paths directly to picard would work and you likely need to specify additional arguments (--input and --output) when running dsub. See https://github.com/DataBiosphere/dsub/blob/master/docs/input_output.md for more details.

[1] The Entrypoint is defined as "/usr/picard/docker_helper.sh", which is this file that runs java directly. Each docker image has its own Entrypoint, so it's important to ensure you are using the right commands for each docker image.

Asha Rostamianfar
  • 16
  • 1