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thiesgehrmann / proteny

A tool to analyze synteny at the protein level.
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Error running the sample dataset #4

Closed Pombert-JF closed 7 years ago

Pombert-JF commented 7 years ago

I'm encountering issues running the sample dataset; I get the following error message below when I type the provided command line from the README. Looks like an issue with the fasta.py wrapper from ibidas. Any idea how to fix/circumvent this?

Thanks, Jean-Francois Pombert Illinois Tech, Chicago, IL

RUNNING PROTENY WARNING:root:Could not determine FASTA separator. Please specify through sep parameter WARNING:root:Could not determine FASTA separator. Please specify through sep parameter [5645, 5572] Running BLAST for Cglabrata v Zrouxii (a_chrid=bytes, a_start=int64, a_end=int64, a_strand=bytes, a_geneid=bytes, a_transcriptid=bytes, a_exonid=int64, a_sequence=protein) (b_chrid=bytes, b_start=int64, b_end=int64, b_strand=bytes, b_geneid=bytes, b_transcriptid=bytes, b_exonid=int64, b_sequence=protein) ... BLAST Database creation error: FASTA-Reader: No residues given ERROR: Failed in cmd: makeblastdb -in '/tmp/tmpgimE45' -out '/tmp/tmpgimE45.blastdb' -dbtype 'prot' ERROR: Failed in cmd: makeblastdb -in '/tmp/tmpHCFchE' -out '/tmp/tmpHCFchE.blastdb' -dbtype 'prot'

thiesgehrmann commented 7 years ago

Hello Jean-Francois,

Thanks for reporting this issue. Unfortunately this seems to be a common problem, which I can't find the solution to. It seems to be a problem with a version dependency of ibidas, numpy and ipython. I should make some time to investigate this. I am really sorry that I can't help you at this time.

Best, Thies

thiesgehrmann commented 7 years ago

Hello Jean-Francois,

I have re-implemented Proteny, removing a lot of dependencies, including ibidas. This makes the pipeline much more simple and portable. If you are still interested in trying proteny, you can find the re-implementation at: https://github.com/thiesgehrmann/pty

Thank you, -Thies