gmap fail to align assembly to a reference

[pguarnizob]

Hi,
I have an issue in the gmap aligning step while using a reference genome. I attach some useful .logs.

rnaQUAST.log
gmap.transabyss_cdhit.err.log
gmap_build.err.log

The weird thing is that I could run rnaQUAST properly on other assemblies such as trinity or spades but not the "transabyss-final.fa" (from transabyss) nor the "transabyss-cdhit.fasta" (from transabyss+cdhit pipeline).

Hope some help, thank you in advance,

Best

[andrewprzh]

Dear @pguarnizob

Seems like something is wrong with GMAP, the error log states:

Signal received: SIGSEGV
Calling Access_emergency_cleanup
Problem sequence: R7827508 (117 bp)

I see your current gmap version is 2021-08-25, probably due to rnaQUAST requirements. However, it seems like rnaQUAST works with the newest version as well.
Unfortunately, I cannot say what causes the error, but probably upgrading gmap might fix it. If not, I'd suggest to report the issue to gmap developers.

All the best
Andrey