bs3 Memory issue

Memory issue

Open demis001 opened this issue 5 years ago • 1 comments

I doubt this is an issue with the snap aligner. Here is the problem, 250G ram, 56 core Linux machine. Out of memory. I did change the temp directory in bashrc to fix if is related to to the temp space, that didn't fix. Changed to single core, still run out of memory.

`bs3-align -i $SAMDIR/full.21421L_S4_R1_001_trimmed.fq.gz -o $SAMDIR/full.21421L_S4_R1_001.bam -f bam -d $GHOME -g hg38_r87.fa --snap-t 10 --snap--b --snap-so

 BS-Seeker3 beta

Welcome to SNAP version 1.0beta.18.

Loading index from directory... Welcome to SNAP version 1.0beta.18.

Loading index from directory... mmap: Cannot allocate memory SNAP exited with exit code 1 from line 394 of file SNAPLib/BigAlloc.cpp `

Oct 19 '18 17:10 demis001

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Memory issue

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