search

B-UMMI / chewBBACA

BSR-Based Allele Calling Algorithm
GNU General Public License v3.0
133 stars 27 forks source link

Issues with chewBBACA in Windows #74

Open erikalmecdc opened 3 years ago

erikalmecdc commented 3 years ago

chewBBACA seems to have some incompatibilities with Windows 10/Windows server.

  1. The check for blastp fails, it works if --b flag is specified and 'blastp' is changed to 'blastp.exe' in the code. The makeblastdb commands does not use the --b path, so blast must also be on the path. This is a bit of an inconsistency with the --b flag in general.

  2. Blast db creation fails. This is a bug in BLAST that is mitigated with setting BLASTDB_LMDB_MAP_SIZE=1000000 in the Windows env, but could also be set in chewBBACA.

  3. Piping of sequences to BLAST fails in windows because windows echo does not work like linux echo. Can be mitigated with temporary files or by creating the stream to pipe without using system echo.

  4. When performing an A/B-test with Mirko Rossi, we got quite different results using the same schema and genome (Linux vs Windows), especially the number of paralogue loci. I can provide more details if needed. I have currently no explanation for this, probably some more incompatibility with windows that does not cause a direct crash but rather incorrect results.

ramirma commented 3 years ago

@erikalmecdc to tell the truth we had not tested chewBBACA in Windows so thank you for the report. @rfm-targa will look into this and we will certainly put working on a Windows compatible version in the roadmap. For now could you provide more information on each of the points:

  1. Could you provide more specific information on what you changed in the code for it to work?

  2. Same here.

  3. Do you have a traceback of the errors so that we could look in more detail at what could be happening?

  4. Having more information on this would be great. If you prefer to share the information through email you can use the address imm-bioinfo(at)medicina.ulisboa.pt

Thank you.