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khuang28jhu / bs3

BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
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Memory issue #16

Open demis001 opened 6 years ago

demis001 commented 6 years ago

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... Welcome to SNAP version 1.0beta.18.

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

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

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

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

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

Loading index from directory... 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 `

demis001 commented 6 years ago

This fixed the error:

--snap-map --snap-pre

Add to the doc