Segmentation fault

[Jakob Nissen]

During my most recent run:

/bin/bash: line 1: 31787 Segmentation fault: 11  kma -ipe tmp/trim/XXXXXX/fw.fq tmp/trim/XXXXX/rv.fq -o tmp/aln/XXXXX/initial -t_db /Users/jakobnissen/code/SSIRegistry/refdir/refout/refs -t 2 -mrs 0.3 -ConClave 2 -nc -nf 2> tmp/log/aln/XXXX.initial.log

I’m not entirely sure how to track this down. If it helps, the log file is:

# Running KMA.
# Reading inputfile:    tmp/trim/XXXXXX/fw.fq tmp/trim/XXXX/rv.fq
# Phred scale:  33
#
# Total time used for DB loading: 0.01 s.
#
# Finding k-mer ankers
#
# Query converted
#
# Query ankered
#
# KMA mapping done
#
# Sort, output and select KMA alignments.
# Total time for sorting and outputting KMA alignment   1.76 s.
#
# Doing local assemblies of found templates, and output results

Can you use that report for anything? If not, how can I figure out what causes the segfault?

[ptlcc]

Hi Jakob

I think I know what it is. Can you try to use the version on the “nano” branch, and see if that makes the same error.

Best,
Philip

[Jakob Nissen]

It works on commit f33577d on the nano branch! Great! Leaving this issue open until the fix is in a release, but from my point of view, the problem is gone. Thanks again!

[ptlcc]

It has been updated on the main branch now too.