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tseemann / nullarbor

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prokka issue [Makefile:127: M008/contigs.gff] Error 2?? #250

Closed foamy1881 closed 4 years ago

foamy1881 commented 4 years ago

I started running nullarbor2 for 10 samples for test run. However it stop during tbl2asn? it returned with the following error

[07:35:32] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka' -Z \/tmp\/tmp.b0pDxC0wJ1\/prokka.err -i \/tmp\/tmp.b0pDxC0wJ1\/prokka.fsa 2> /dev/null [07:35:40] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka' -Z \/tmp\/tmp.b0pDxC0wJ1\/prokka.err -i \/tmp\/tmp.b0pDxC0wJ1\/prokka.fsa 2> /dev/null make: *** [Makefile:127: M008/contigs.gff] Error 2 make: Leaving directory '/home/yfong/Documents/software/nullarbor2/mtbtest10full'

I have attached the nullarbor log file. anyone can help? also how can we resume/continue nullarbor.log from it or I have to re-run the whole process again?

foamy1881 commented 4 years ago

case closed.. update prokka and tbl2asn via manually to conda env.. problem solved.