BBMap error

Question

[allifc]

BBMap is throwing this error, when it is called as part of the StrainR.R pipeline, can anybody help?

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: /Users/allison/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.

Answer 1

[GenoMax]

As the error suggests you need to add -XmxNNg ( e.g. do not more than 80% of actual RAM you have in place of NN, so if you have 8G of RAM in your machine then add -Xmx6g to the BBMap command line in the R script you are trying to use.