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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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Fix issues in Step_first_add_custom_phage_sequence.pl #7

Closed brymerr921 closed 7 years ago

brymerr921 commented 7 years ago

Line 222 says "my $cmd_blast="$path_to_blastp -queury $prot_file_to_cluster -db $db -out $out_blast -outfmt 6 -num_threads 10 -evalue 0.00001"; # On 10 cores to keep a few alive for the rest of the scripts" and it's causing BLAST to throw an error Error: Unknown argument: "queury". (Change queury to query)

Also, both of these lines should have (I assume) -dbtype prot added to them (shown in bold). line 212: my $cmd_format="$path_to_makeblastdb -in $prot_file_to_cluster -out $db -dbtype prot"; line 324: $out=$path_to_makeblastdb -in $final_pool_unclustered -out $final_blastable_unclustered **-dbtype prot**;

simroux commented 7 years ago

Good catch, this is now fixed (in the github version). Thanks for notifying us !

brymerr921 commented 7 years ago

I kept getting an error while trying to run VirSorter if I didn't add -dbtype prot at the specified locations. Is this just me or is it supposed to be in the code?

line 212: my $cmd_format="$path_to_makeblastdb -in $prot_file_to_cluster -out $db -dbtype prot"; line 324: $out=$path_to_makeblastdb -in $final_pool_unclustered -out $final_blastable_unclustered **-dbtype prot**;