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fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.
http://fulcrumgenomics.github.io/fgbio/
MIT License
309 stars 67 forks source link

heap memory error #967

Closed subarna-slg closed 7 months ago

subarna-slg commented 7 months ago

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

nh13 commented 7 months ago

A quick search of previous issues will contain the solution: https://github.com/search?q=repo%3Afulcrumgenomics%2Ffgbio+heap&type=issues