Can't skip preprocessing

xapple commented 11 years ago

So I got MetaPathways installed and working. There were some minor hurdles such as a statically linked prodigal binary to a version of glibc not available and relative path reference to the blastDB directory. Otherwise it went fine.

One of the first things I tried to do that failed was skip the fasta preprocessing, as our pipeline already includes a cleaning step which we are happy with. I added this to the param.txt file:

 metapaths_steps:PREPROCESS_FASTA   skip

I got this error when running the pipeline:

xapple@cluster metapathways $ ./MetaPathways.py -i sequences.fasta -o output/ -c config.txt -p param.txt -v -r overwrite
template_config.txt
config.txt
sequences.fasta
output//sequences
WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.

  **********************************************************
  **************** Running  MetaPathways *******************
  **********************************************************
              sequences.fasta
  **********************************************************

Issuing Command : /bubo/home/h3/lucass/proj38/nobackup/metapathways/libs/python_scripts/MetaPathways_filter_input.py  --min_length 180 --log_file output//sequences/run_statistics//sequences.nuc.stats  -i sequences.fasta -o  output//sequences/preprocessed//sequences.fasta -M output//sequences/preprocessed//sequences.mapping.txt

1. Running Quality Check ......... Skipping!

Issuing Command : /bubo/home/h3/lucass/proj38/nobackup/metapathways/executables/linux/bit64/prodigal  -m -p meta -f gff -i output//sequences/preprocessed//sequences.fasta -o output//sequences/orf_prediction/sequences.gff

2. Running Orf Prediction ......... Error!
Error! : -------------------------------------
PRODIGAL v2.50 [November, 2010]
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.
-------------------------------------

Error: can't open input file output//sequences/preprocessed//sequences.fasta.

nielshanson commented 11 years ago

You should be able to do this. I'll look into it.

hallamlab commented 7 years ago

Please use the newest version of MP on GitHub

hallamlab / MetaPathways

Can't skip preprocessing #30