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mattb112885 / clusterDbAnalysis

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes
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Error (?) using setup_step1.sh #67

Closed qu4drupole closed 8 years ago

qu4drupole commented 9 years ago

As I understand it, setup_step1.sh should put all the paired BLAST results in "blastn_res" (I uploaded genomes I got from pubSEED). After running the setup script, I don't see anything in the results directory. I installed ITEP on a computer cluster at my university, so it's possible I screwed up installing one or more of the dependencies. I would really appreciate some help interpreting and using your software. The output running the script is quite long. I can't copy it all. Please let me know of anything I can do to help diagnosis this problem.

mattb112885 commented 9 years ago

First can you run a git update to make sure you have the latest version of ITEP? (many bugs have been fixed since publication) Do so with the following:

$ git pull origin master

Second, if that doesn't help I will need to see the output to diagnose the problem. Can you do the following:

  1. Run the setup script but redirect the output to a file: $ setup_step1.sh > output.txt 2> error.txt
  2. Email the output.txt and error.txt to mnb_0000 (at) hotmail.com

Thanks

mattb112885 commented 9 years ago

Can you also tell me if anything showed up in any of the other folders (raw/, db/, blastres/, etc.) and if so what is in there? That will also be useful to see where it failed...

Thanks