Problems during running PSI-CD-HIT:Name "main::bl_dir" used only once: possible typo at ./psi-cd-hit.pl line 103.

[AL-Yan]

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.

[alyzart22]

I have exactly the same error . How did you solve the problem?

[AL-Yan]

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.

[kthurimella]

Hey @AL-Yan can you share what the new file should look like? Also what new installation package did you install?

[frodoCombs]

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"; 

[wcfgit]

Hello @frodoCombs and @AL-Yan ,

I know it has been a while but any chance you could share how your psi-cd-hit-local.pl and psi-cd-hit.pl scripts are looking like after the modifications?
I tried to follow what you mentioned here but no success.

Thank you in advance!