Error in cap3
Assembly runs fine, but cap3 throws an error. Any idea what is the cause of this?
bash: line 5: 20 Segmentation fault (core dumped) cap3 $NAME.cat.fa -p 98 -o 100
Error in job cap3 while creating output file Assembly/mg.assembly.merged.fa.
RuleException:
CalledProcessError in line 18 of /home/imp/code/rules/Assembly/common/merge-assembly.rules:
Command '
NAME=Assembly/mg.assembly
cat Assembly/mg.megahit_preprocessed.1.fa Assembly/mg.megahit_unmapped.2.fa > $NAME.cat.fa
# Run cap3
cap3 $NAME.cat.fa -p 98 -o 100
# Concatenate assembled contigs, singletons and rename the contigs
cat $NAME.cat.fa.cap.contigs $NAME.cat.fa.cap.singlets | awk '/^>/{print ">contig_" ++i; next}{print}' > $NAME.merged.fa
' returned non-zero exit status 139
File "/usr/lib/python3.4/concurrent/futures/thread.py", line 54, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message