Bowtie2 refusing to parallelize job

[bfantinatti]

Hi guys, today I had a problem that I never heard of before.
I am aligning some transcriptome samples agains different references (mammals).
At first I tried to run these alignments in a Mac pro (2012), running Linux Mint 18.2 (kernel 4.10.0-33-generic), and bowtie2 (2.2.6) piping the output to samtools (1.5) for converting to bam on the fly.
I did the references normally (bowtie2-build etc etc...) for all the ten mammals downloaded from NCBI (https://www.ncbi.nlm.nih.gov/genome/browse/) using the same Linux machine.
I wrote the scripts in order to use all the cores available. At first, it was running correctly, using as many cores as I told to, but today it was using ony one... I did some tests and I realized that this only happens with a specific reference, not with others.
Thinking that perhaps it was a problem with the machine, I shared the data through NFS to a Centos 7 machine (kernel 3.10.0-514.16.1.el7.x86_64) and bowtie2 (2.2.9) piping the output to samtools (1.3.1) for converting to bam on the fly. Same problem here...

Now I am rebuilding the referenses using this second machine.

Basically bowtie is refusing to parallelize.

Any clue?

Thank you!

[bfantinatti]

Solved

Guys, problem solved when I rebuild the references. I do not know what caused this, but now is everything ok with both systems.