finally worked?

[Liangliang Gao]

lgao@llgao-Studio-1458:~/spada_soft/spada$ sudo cpanm BioPerl
! Finding BioPerl on cpanmetadb failed.
--> Working on BioPerl
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz ... OK
Configuring BioPerl-1.006901 ... OK
Building and testing BioPerl-1.006901 ... OK
Successfully installed BioPerl-1.006901
1 distribution installed
llgao@llgao-Studio-1458:~/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
MSP /home/llgao/spada_soft/spada_data/tmp/aln_score2_223.fa was not created

[Peng Zhou]

er, wait a minute, there seems to an error at the end. Just to double check - did you update to the latest version:

cd spada

svn update

Peng,

[Liangliang Gao]

What error? Yes I used the updated version. There seems to be no error in output files.


Liang

[Peng Zhou]

It seems the program died and threw this error:

MSP /home/llgao/spada_soft/spada_data/tmp/aln_score2_223.fa was not created

There are still a number of steps in the pipeline after this.

Peng, 

[Liangliang Gao]

Could these be problems

 You chose to install Clone and it installed fine
Checking prerequisites...
  recommends:
    *  You chose to install Ace but it failed to install
    *  You chose to install GraphViz but it failed to install
    *  You chose to install XML::Twig but it failed to install
Checking features:
  Network...................enabled
  BioDBSeqFeature_mysql.....disabled
    - DBD::mysql is not installed
    - DBI is not installed
  BioDBGFF..................disabled
    - DBI is not installed
  BioDBSeqFeature_BDB.......enabled
  BioDBSeqFeature_SQLite....disabled
    - DBD::SQLite is not installed
    - DBI is not installed
  BioDBSeqFeature_Pg........disabled
    - DBD::Pg is not installed
    - DBI is not installed