I am trying to use clipbam option in fgbio (installed in conda env) in a bash script for clipping reads using the following commands:
$FGBIO -ClipBam -i $BAM_MD -o $BAM_MD_CLIPPED -r $ref --clip-overlapping-reads -c Hard -m ${base}"_fgbio_metrics.txt"
I am getting an error:
[2024/02/03 04:02:32 | FgBioMain | Info] ClipBam failed. Elapsed time: 0.19 minutes.
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
please suggest
I am trying to use clipbam option in fgbio (installed in conda env) in a bash script for clipping reads using the following commands: $FGBIO -ClipBam -i $BAM_MD -o $BAM_MD_CLIPPED -r $ref --clip-overlapping-reads -c Hard -m ${base}"_fgbio_metrics.txt" I am getting an error: [2024/02/03 04:02:32 | FgBioMain | Info] ClipBam failed. Elapsed time: 0.19 minutes. Exception in thread "main" java.lang.OutOfMemoryError: Java heap space please suggest