Bug with RPSBLAST.sh

[campy1113]

$RPSBLAST.sh -f final_contigs_gt1000_c10K.faa -p -c 4 -r 1 [rpsblast] ERROR: Arguments must start with '-' (the offending argument #2 was: '6 qseqid sseqid evalue pident score qstart qend sstart send length slen') [rpsblast] ERROR: Arguments must start with '-' (the offending argument #2 was: '6 qseqid sseqid evalue pident score qstart qend sstart send length slen') [rpsblast] ERROR: Arguments must start with '-' (the offending argument #2 was: '6 qseqid sseqid evalue pident score qstart qend sstart send length slen') [rpsblast] ERROR: Arguments must start with '-' (the offending argument #2 was: '6 qseqid sseqid evalue pident score qstart qend sstart send length slen') [rpsblast] ERROR: Arguments must start with '-' (the offending argument #2 was: '6 qseqid sseqid evalue pident score qstart qend sstart send length slen') [rpsblast] ERROR: Arguments must start with '-' (the offending argument #2 was: '6 qseqid sseqid evalue pident score qstart qend sstart send length slen') rpsblast using GNU parallel took 1 seconds to generate final_contigs_gt1000_c10K.out from final_contigs_gt1000_c10K.faa

[campy1113]

fixed, need to change rpsblast to rpsblast+ in the script

[alneberg]

Hello @campy1113,

great that you fixed the issue and fantastic that you let us know. However, if you're aiming to use rpsblast in order to estimate completeness and contamination levels of you're bins, I would highly recommend the CHECKM software for that instead of our SCG scripts.

Best Wishes, Johannes