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2.2 years ago
Kacper
▴
10
I'm very new to bioinformatics and currently struggling. I used SPAdes to assemble a bacterial genome and attempted to scaffold using SSPACE. My command was:
perl (path_to_SSPACE)/SSPACE_v2-0.pl -l libraries.txt -s contigs.fa -k 5 -a 0.7 -x 0 -b name_scaffolds_no_extension
On entering, it seemed like it started running, and shortly after Building Bowtie index for contigs I get an error message saying "Bowtie-build error; -1" and that the process failed.
Please advise.
check your bowtie version, SSPACE works with bowtie, not with bowtie2.
I downloaded bowtie using conda and then it ran perfectly. Thank you!