ABySS 1.9.0 error at bwa index step

Question

[cmstouthamer]

I am having a persistent error in assembling my data. I have both Illumina short reads and PacBio assembled long reads combined in this command:

abyss-pe  k=51 np=28 j=28 v=-v n=1 in="cinaIT.end1.mcf.fq.gz cinaIT.end2.mcf.fq.gz" long="polished_assembly.fasta" name=ITpb_AB19

everything in the assembly goes fine until around step 8 where I get the following error:

Reading `ITpb_AB19-7.dot'...
Reading `ITpb_AB19-7.path'...
/bin/bash: bwa: command not found
make: *** [ITpb_AB19-8.fa.bwt] Error 127

Does BWA need to be installed for this command to function, or is the bwa command separate from the BWA program.

Additional information: I am running ABySS 1.9.0 that has been compiled for Open MPI.

Thank you so much in advance for your help!

[GenoMax]

bwa (BWA if you want to use all caps) is needed based on the error above. If you have bwa package installed on your system make sure to add the executable to your $PATH.

[cmstouthamer]

Thank you genomax2! I've added the bwa program to my path, and got another error. I posted about this in a different post, because it is slightly different than the problem that I was experiencing above: ABySS fails with -long reads at BWA step

Thank you so much for you help!

[lieven.sterck]

also note that we are at version 2.0.2 of ABySS in the meantime ;)