Skipping [NO INPUT]!

[sunitj]

I was testing my install of metapathways2 and trying to compare the results with the older version. The job is still running but, here are a few things I'm noticing:

• While MetaPathways 1 runs Step 3. Creating the Amino Acid file successfully (I checked the output), MP2 simply skips over this and the following steps. Upon checking the output folder, I can't find any of the relevant files.
• I also can't find what command was tried, metapathways_run_log.txt is empty.
• I've checked the template_params.txt file and made sure nothing was being skipped.
• template_config.txt point to similar paths as well
• I've found the same issue with the GUI version of MP2.

Has anyone else come across anything similar? My best guess is that the python script can't find prodigal, but I don't see an error message regarding this directly.

Please let me know if there is anything else that I can post here that would help.

Here are the STDOUT from both the runs.

MetaPathways 1 - STDOUT

[sunitj@vondamm MP1Test]$ MetaPathways.py -i INPUT/ -o OUTPUT/ -c template_config.txt -p template_param.txt -r overwrite
template_config.txt
template_config.txt
INPUT//test.fasta
OUTPUT//test

  ********************************************************** 
  **************** Running  MetaPathways ******************* 
  ********************************************************** 
              INPUT//test.fasta                       
  ********************************************************** 

1. Running Quality Check ......... Success!

2. Running Orf Prediction ......... Success!

3. Creating the Amino Acid sequences ......... Success!

4. Creating the filtered fasta sequences ......... Success!

5. Computing refscores for the ORFs ......... Success!

6. Blasting  ORFs against reference database - metacyc-v5-2011-10-21 ......... Success!

                                               COG_2013-02-05 ....

MetaPathways 2 (2.4.5) - STDOUT

[sunitj@cayman MP2Test]$ python /scratch/sunitj/MP2/MetaPathways.py -i INPUT/ -o OUTPUT_cmd/ -c /scratch/sunitj/MP2/config/template_config.txt -p /scratch/sunitj/MP2/config/template_param.txt -r overwrite -s test --runid cmd1
COMMAND : /scratch/sunitj/MP2/MetaPathways.py -i INPUT/ -o OUTPUT_cmd/ -c /scratch/sunitj/MP2/config/template_config.txt -p /scratch/sunitj/MP2/config/template_param.txt -r overwrite -s test --runid cmd1
['test']
['INPUT//test.fasta']
FIX ME: diagnoze
##################################

PROCESSING INPUT INPUT//test.fasta
PREPROCESSING THE INPUT                                     ..... Success!
ORF PREDICTION                                              ..... Success!
CREATING AMINO ACID SEQS FROM GFF FILE                      ..... Skipping [NO INPUT]!
FILTER AMINO ACID SEQS                                      ..... Skipping [NO INPUT]!
COMPUTING REFSCORES FOR BITSCORE                            ..... Skipping [NO INPUT]!
BLASTING AMINO SEQS AGAINST COG_2013-12-27                  ..... Skipping [NO INPUT]!
PARSING BLAST OUTPUT FOR COG_2013-12-27                     ..... Skipping [NO INPUT]!
SCANNING FOR rRNA USING DB LSURef_115_tax_silva_2013-12-12  ..... Success!
SCANNING FOR tRNA USING tRNA-Scan                           ..... Success!
ANNOTATE ORFS                                               ..... Skipping [NO INPUT]!
PATHOLOGIC INPUT                                            ..... Skipping [NO INPUT]!
GENBANK FILE                                                ..... Skipping [NO INPUT]!
CREATING REPORT FILE FOR ORF ANNOTATION                     ..... Skipping [NO INPUT]!
RUNNING MLTREEMAP                                           
Run BLAST

[nielshanson]

Hi there,

Sorry for the late reply, were you able to get this resolved? We've been continuously developing this software and I've spend the last day or two testing the current version for a release of v2.5. I can't seem to replicate your error.

Would you mind taking a pull of the latest code to see if this is still a problem? It also helps to run MetaPathways in verbose mode with -v which prints out the python commands to standard out.

Generally, [NO INPUT] problems are generally caused by not having all the files in MetaPathways_DBs, but it could also the code is changing quite rapidly.

Let me know how it goes.

Thanks, Niels

[nielshanson]

Found the gbk, rRNA, and RPKM [No Input] problems. See commit 81100ea9b2