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hallamlab / MetaPathways

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information
http://hallam.microbiology.ubc.ca/MetaPathways
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Seems to do quality check step every time... #10

Closed hallamlab closed 11 years ago

hallamlab commented 11 years ago

Code does not seem to recogniz already computed results for quality check

  ********************************************************** 
  ********************   Running  metapaths ******************* 
  ********************************************************** 
              input/Fosmid_Ends_WL_Jan17//LTSP_ends.fasta                       
  ********************************************************** 

Issuing Command : /Users/ariahahn/Desktop/MetaPathways/libs/perl_scripts/filter_input_fasta.pl  --min_length 180 --log_file output//LTSP_ends/run_statistics//LTSP_ends.nuc.stats  -i input/Fosmid_Ends_WL_Jan17//LTSP_ends.fasta -o  output//LTSP_ends/preprocessed//LTSP_ends.fasta -m output//LTSP_ends/preprocessed//LTSP_ends.mapping.txt

1. Running Quality Check ......... Success!
nielshanson commented 11 years ago

Fixed the issue of using doing the quality check stage on every run (Issue #10). The code seemed to be using shouldRunStep1() instead of shouldRunStep() which was not correctly finding previously computed results. See metapathways.py lines ~830