[jmwhitha]

Okay, so what can I do now? My gcc was already newest version.

[GenoMax]

Okay, so what can I do now? My gcc was already newest version.

This kind of debugging may have to be done sitting in front of the computer. Do you have access to a local expert who can help?

I am surprised that you have run into so many problems with this.

[jaredroach]

I suspect the problem is in the read simulator, not bwa

We have had the same problem, getting the same results with bwa when using simulated reads. I suspect the problem you are having is with your read simulator, not bwa. Something in your simulated fastq files is not in the format that bwa expects.

Good morning,

I am trying to map simulated reads generated from GemSIM to an index generated from a multi-fasta of the CLJU (bacteria) coding sequence from NCBI. I used these two commands and discovered there were no alignment lines in the SAM file, only header lines. Commands head and tail only returned lines starting with @, and grep -vnm1 '^@' returned nothing.

bwa-0.7.3a/bwa index -a is -p CLJU ./CLJUcoding.fasta

bwa-0.7.3a/bwa mem CLJU CLJUsimreadsCodeTrial.single.fastq > CLJUsimreadsCodeTrial.single.sam

Any suggestions?

Thanks and God bless,
Jason