BBMap error with no output

Question

[h.l.wong]

Hi all,

I am using bbmap to map reads but it came up with this error

java -Djava.library.path=/share/apps/bbmap/35.82/bin/jni/ -ea -Xmx56124m -cp /share/apps/bbmap/35.82/bin/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=contig.fa Picked up _JAVA_OPTIONS: -Xmx80g Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=contig.fa]

BBMap version 35.82 Retaining first best site only for ambiguous mappings. No output file. Writing reference. Executing dna.FastaToChromArrays2 [contig.fa, 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 Writing chunk 2 Set genome to 1

Loaded Reference: 0.541 seconds. Loading index for chunk 1-2, build 1 No index available; generating from reference genome: /srv/scratch/z3336178/Metagenomics/SD3/Min20Max124/ref/index/1/chr1-2_index_k13_c2_b1.block Indexing threads started for block 0-2 Indexing threads finished for block 0-2 Generated Index: 51.420 seconds. Finished Writing: 0.136 seconds. No reads to process; quitting.

Total time: 58.617 seconds.

I am currently using a 126Gb ram cluster and I have tried different parameters but it still didn't work. Any help will be much appreciated. Cheers and many thanks Alan

Answer 1

[Brian Bushnell]

Ah! You didn't specify an input file or output file. So, all it did was index the reference. You need to do something like this:

bbmap.sh ref=contig.fa in=reads.fq out=mapped.sam

[h.l.wong]

Thank you Brian, for forward and reverse reads do I just replace in=reads.fq with in1=read1.fq in2=read2fq?

[Brian Bushnell]

Yes, if you have paired reads in twin files, use "in1=read1.fq in2=read2.fq".