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Error running obiconvert - Printable Version

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+---- Thread: Error running obiconvert (/showthread.php?tid=106)



Error running obiconvert - laur34 - 10-20-2016

Hi,

I am also going through the tutorial for OBITools, and I run into an error when formatting the data using obiconvert:

command:
  • obiconvert --embl -t ./TAXO --ecopcrdb-output=embl_last ./EMBL/std/*.dat.gz
After a few minutes, it causes the error
Error on sequence : EU394480;
and
struct.error: cannot convert argument to integer

I tried downloading a new taxdump tarball, but I still get the same error.
I found on another forum that it is caused by a discrepancy with the taxid, but I'm still not sure how to overcome it and get the program to finish running.
Thank you to anyone who helps. Heart


RE: Error running obiconvert - laur34 - 10-26-2016

OK, I am going to reply to my own thread, just in case it helps anyone else having the same problem.
I just found the the --skip-on-error option for obiconvert. This causes the program to skip the writing of sequences for which it encounters errors, instead of crashing.


RE: Error running obiconvert - coissac - 11-01-2016

Yes some genbank or embl entries are not correctly parsed by obitools. Several reasons explain this. They are not really corresponding to a bug but rather to the none implementation of some EMBL/Genbank features like contig entries. The other reason is when you are parsing a file containing *taxids* absent for the used taxonomy. For all that reasons, the `--skip-on-error` option exists on most of the obitools


RE: Error running obiconvert - laur34 - 11-01-2016

(11-01-2016, 08:09 PM)coissac Wrote: Yes some genbank or embl entries are not correctly parsed by obitools. Several reasons explain this. They are not really corresponding to a bug but rather to the none implementation of some EMBL/Genbank features like contig entries. The other reason is when you are parsing a file containing *taxids* absent for the used taxonomy. For all that reasons, the `--skip-on-error` option exists on most of the obitools

Oh, I understand. Thank you for the reply.

Laur