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jbisanz / StrainR

Quantification of highly related strains in shotgun metagenomics
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bbmap error #2

Open allifc opened 1 year ago

allifc commented 1 year ago

PreProcessR.R is throwing an error at the bbmap step:

`Max memory cannot be determined. Attempting to use 3200 MB. If this fails, please add the -Xmx flag (e.g. -Xmx24g) to your command, or run this program qsubbed or from a qlogin session on Genepool, or set ulimit to an appropriate value. java -ea -Xmx3200m -Xms3200m -cp /Users/allison/opt/anaconda3/envs/strainR/opt/bbmap-39.01-0/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=TestPre/BBindex/BBIndex.fasta path=TestPre/BBindex/ Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=TestPre/BBindex/BBIndex.fasta, path=TestPre/BBindex/] Version 39.01

No output file. Writing reference. Executing dna.FastaToChromArrays2 [TestPre/BBindex/BBIndex.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false]

Set genScaffoldInfo=true Writing chunk 1 Set genome to 1

Loaded Reference: 0.040 seconds. Loading index for chunk 1-1, build 1 No index available; generating from reference genome: /Bioinformatics/StrainR/TestPre/BBindex/ref/index/1/chr1_index_k13_c4_b1.block Indexing threads started for block 0-1 Indexing threads finished for block 0-1 Generated Index: 8.385 seconds. No reads to process; quitting.

Total time: 9.455 seconds. Sat Nov 5 12:18:36 2022 PreProcessR complete`

BisanzLab commented 1 year ago

Interesting, can you tell me more about the system this is being run on and what your command was that invoked it?

allifc commented 1 year ago

Thank you for the reply. This is being run on a MBP with M1 chip, Monterey OS. The command to run PreProcessR.R was: Rscript PreProcessR.R --indir Assemblies --outdir TestPre --threads 1 --jobs 4 --kmersize 120