cannot locate fasta.pm

[Liangliang Gao]

gaoll@VM:~/spada_soft/spada$ perl spada.pl --cfg conf.txt --org test --fas test/01_refseq.fa --gff test/51_gene.gff
##########  working on test  ##########
  copying FASTA file to data directory...
  breaking genome sequence & translating in 6 frames ...
  copying GFF file to data directory...
  converting Gff to Gtb... (   441 RNA |   327 gene ) done
  converting Gtb to Gff... (   441 RNA |   327 gene ) done
  extracting sequence from Gtb...   441 out of 441 done
  running hmmsearch (might take long time) ...
  parsing HMM output...
  recovering to global coordinate for hmmsearchX...    79 out of 79 done
  tiling hits...
  collapsing neighboring hits...
  running hmmsearch (might take long time) ...
  parsing HMM output...
  recovering to global coordinate for hmmsearchP...   114 out of 114 done
  tiling hits...
  collapsing neighboring hits...
  collecting hits from multiple sources... 11 in total
  E-vlaue filer... 11 out of 11 passed filter
  sort hits into groups... 7 groups in total
  re-formatting hit info...
  removing multi hits... 1 out of 7 removed
  removing nearby hits... 1 out of 6 removed
  removing within-group hits...
  re-ordering htis...
  removing pseudogenes... 1 out of 5 removed
  computing MSA scores:     4/4 done...
  writing hit Gff file...
  preparing hit sequence...
  running Augustus:     4/4 done...
  collecting prediction results from /home/gaoll/spada_data/test/31_model_SPADA/12_augustus/02_raw
  changing to relative position...
  building 1/2 exon models...     4 out of 4 done
  writing output in Gtb format...
  collecting all prediction results...
  refining incomplete models...
  merging redundant models...  5 in total
  converting genomic positions to global coordinates...
  removing incompatible models...  1 deleted
  converting Gtb to Gff... (     4 RNA |     4 gene ) done
  computing MSA scores:     4/4 done...
Can't locate FASTA.pm in @INC (@INC contains: /home/gaoll/spdada_soft/signalp-4.0/lib /etc/perl /usr/local/lib/perl/5.12.4 /usr/local/share/perl/5.12.4 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.12 /usr/share/perl/5.12 /usr/local/lib/site_perl .) at /home/gaoll/spada_soft/signalp-4.0/signalp line 95.
BEGIN failed--compilation aborted at /home/gaoll/spada_soft/signalp-4.0/signalp line 95.
Can't locate FASTA.pm in @INC (@INC contains: /home/gaoll/spdada_soft/signalp-4.0/lib /etc/perl /usr/local/lib/perl/5.12.4 /usr/local/share/perl/5.12.4 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.12 /usr/share/perl/5.12 /usr/local/lib/site_perl .) at /home/gaoll/spada_soft/signalp-4.0/signalp line 95.
BEGIN failed--compilation aborted at /home/gaoll/spada_soft/signalp-4.0/signalp line 95.
Can't locate FASTA.pm in @INC (@INC contains: /home/gaoll/spdada_soft/signalp-4.0/lib /etc/perl /usr/local/lib/perl/5.12.4 /usr/local/share/perl/5.12.4 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.12 /usr/share/perl/5.12 /usr/local/lib/site_perl .) at /home/gaoll/spada_soft/signalp-4.0/signalp line 95.
BEGIN failed--compilation aborted at /home/gaoll/spada_soft/signalp-4.0/signalp line 95.
Can't locate FASTA.pm in @INC (@INC contains: /home/gaoll/spdada_soft/signalp-4.0/lib /etc/perl /usr/local/lib/perl/5.12.4 /usr/local/share/perl/5.12.4 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.12 /usr/share/perl/5.12 /usr/local/lib/site_perl .) at /home/gaoll/spada_soft/signalp-4.0/signalp line 95.
BEGIN failed--compilation aborted at /home/gaoll/spada_soft/signalp-4.0/signalp line 95.
  assessing SignalP scores:     4 /     4 done...
  assessing peptide scores:     4/4 done...
  merging statistics...
  picking best models...  0 picked

[Joseph Guhlin]

It's a SignalP error. In the signalp directory there is a .pl or .pm
file that needs to be edited to update the directory to the signalp
directory.

I don't have it in front of me but it should be easy to find.

--Joseph

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[Liangliang Gao]

Thanks!  I miss typed "spada" to "spdada". Now worked, ,?

gaoll@VM:~/spada_soft/spada$ perl spada.pl --cfg conf.txt --org test --fas test/01_refseq.fa --gff test/51_gene.gff
##########  working on test  ##########

  FASTA file already in data directory

  breaking genome sequence & translating in 6 frames ...

  GFF file already in data directory

  assessing SignalP scores:     4 /     4 done...
  assessing peptide scores:     4/4 done...
  merging statistics...

  picking best models...  3 picked
  converting Gtb to Gff... (     3 RNA |     3 gene ) done
  making sub-family alignments:     3 /     3 done...