Hi, I am using the DRAGEN Complete Suite and using the AWS CloudStack deployment guide. When I submit a batch job, all the pre-processing steps seems to work (i.e., reference downloaded from S3 bucket, etc...) but when DRAGEN runs, it exits with the following error message:
2024-01-09T09:54:46.188-08:00
ERROR: The following extra command line options are not recognized
My guess is somehow the last parameters are being passed as arguments directly to DRAGEN versus being treated as I/O pipes. Here's the command being run by the DRAGEN stack:
Hi, I am using the DRAGEN Complete Suite and using the AWS CloudStack deployment guide. When I submit a batch job, all the pre-processing steps seems to work (i.e., reference downloaded from S3 bucket, etc...) but when DRAGEN runs, it exits with the following error message:
My guess is somehow the last parameters are being passed as arguments directly to DRAGEN versus being treated as I/O pipes. Here's the command being run by the DRAGEN stack:
Executing /opt/edico/bin/dragen -f -r /ephemeral/DRAGEN/hg38/ -1 s3://XXX/temp/NA24385-AJ-Son-R1-NS_S33_L001_R1_001.fastq.gz -2 s3://XXX/temp/NA24385-AJ-Son-R1-NS_S33_L001_R2_001.fastq.gz --RGID 1 --RGSM Test --enable-bam-indexing true --enable-map-align-output true --enable-sort true --output-file-prefix output --enable-map-align true --output-format BAM --output-directory /ephemeral/9518aff5-e295-4e05-802a-f4365af3b4bd --enable-variant-caller true --output_status_file /ephemeral/9518aff5-e295-4e05-802a-f4365af3b4bd/job-speedometer.log --intermediate-results-dir /ephemeral/ --lic-no-print > /ephemeral/9518aff5-e295-4e05-802a-f4365af3b4bd/dragen_log_1704822886.txt 2>&1
I am not sure how this is happening as I am using all the default settings. Any help would be appreciated.