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Problems during running PSI-CD-HIT:Name "main::bl_dir" used only once: possible typo at ./psi-cd-hit.pl line 103.
After entering the command according to the user's guide,psi-cd-hit produce output files,but there is no clustering.
./psi-cd-hit.pl -i /root/yzm/dataset/db_60.fasta -o /root/yzm/dataset/db_25 -c 0.25 -ce 1e-5 -g 1
Output:
Name "main::bl_dir" used only once: possible typo at ./psi-cd-hit.pl line 103. BLAST version: blastp: 2.12.0+ Package: blast 2.12.0, build Jul 13 2021 09:03:00 /root/yzm/dataset/seq.fasta.7527-bl.sh: 8: .//root/yzm/dataset/seq.fasta.7527-bl.pl: not found /root/yzm/dataset/seq.fasta.7527-bl.sh: 8: .//root/yzm/dataset/seq.fasta.7527-bl.pl: not found /root/yzm/dataset/seq.fasta.7527-bl.sh: 8: .//root/yzm/dataset/seq.fasta.7527-bl.pl: not found /root/yzm/dataset/seq.fasta.7527-bl.sh: 8: .//root/yzm/dataset/seq.fasta.7527-bl.pl: not found /root/yzm/dataset/seq.fasta.7527-bl.sh: 8: .//root/yzm/dataset/seq.fasta.7527-bl.pl: not found /root/yzm/dataset/seq.fasta.7527-bl.sh: 8: .//root/yzm/dataset/seq.fasta.7527-bl.pl: not found
After running the commend, I open the output file and find that the number of clustrs is the same as that of the input file. I dont know how to fix this problem, im new in the bioinformatics world so i have no idea whats wrong and how to recompile this program. Any help would be appreciated.
I have exactly the same error . How did you solve the problem?
I have exactly the same error . How did you solve the problem?
I downloaded a new installation package from other bloggers and deleted the variable 'bl_dir' from the file. It can be used normally.
Hey @AL-Yan can you share what the new file should look like? Also what new installation package did you install?
The following edits to psi-cd-hit-local.pl got it to work for me:. This is neither elegant nor a full solution.
### lines 140-141 correct the blast_exe and makeblastdb commands
$blast_exe = "/home/path/to/ncbi-blast-2.13.0+/bin/blastp";
$formatdb = "/home/path/to/ncbi-blast-2.13.0+/bin/makeblastdb -dbtype prot";
my $bl_ver = `$blast_exe -version`;
if ($bl_ver =~ /blast/) {
print "BLAST version:\n$bl_ver\n\n";
}
else {
die "BLAST program not found: $blast_exe\n";
}
## adds the outfmt to the blast_exe, can't be added before the version call
$blast_exe = "/home/path/to/ncbi-blast-2.13.0+/bin/blastp -outfmt 6";