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arzwa / wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.
http://wgd.readthedocs.io/en/latest/
GNU General Public License v3.0
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paranome is empty #41

Closed cintiaiha closed 3 years ago

cintiaiha commented 3 years ago

Hi

I am having problem to run wgd dmd to some of my samples. The diamond result in wgd_dmd directory returns empty. It is happening for only some genomes, but works well in others. I supposed that it could be because there was no paralogs but when I run direct diamond I found paralogues.

I would appreciated any help.

The verbosity debug log is attached.

Thank you. dmd_log.txt

arzwa commented 3 years ago

Hi, could your provide an example data set for me to look into? I can't see from the log what is causing this.

cintiaiha commented 3 years ago

Hi Arthur,

Thank you for your reply. Please, find attached an example dataset. cre.cds.fasta.zip

arzwa commented 3 years ago

Hmm, it works fine with me using the latest wgd version on the master branch (v1.2) and diamond version 0.9.34...

(venv) $ dmd cre.cds.fasta 
2020-09-23 08:40:11: WARNING    dir wgd_dmd exists!
2020-09-23 08:40:12: ERROR  Translation error (First codon 'GTT' is not a start codon) in seq Cre08.g386000.t1.1
2020-09-23 08:40:12: ERROR  Translation error (First codon 'GTT' is not a start codon) in seq Cre08.g386000.t2.1
2020-09-23 08:40:12: ERROR  Translation error (First codon 'GCC' is not a start codon) in seq Cre45.g760797.t1.1
[...]
2020-09-23 08:40:17: ERROR  Translation error (Final codon 'AAG' is not a stop codon) in seq Cre12.g524850.t3.1
2020-09-23 08:40:17: INFO   One CDS file: will compute paranome
$ sed -n 500,510p ./wgd_dmd/cre.cds.fasta.mcl
Cre17.g704750.t1.1  Cre01.g021550.t1.1  Cre17.g704400.t1.1  Cre17.g704700.t1.1  Cre17.g704450.t1.1
Cre17.g700750.t1.2  Cre17.g702900.t1.2  Cre17.g702950.t1.2  Cre17.g700650.t1.2  Cre17.g700450.t1.2
Cre17.g714450.t1.2  Cre17.g714200.t1.1  Cre17.g714150.t1.1  Cre04.g217350.t1.2  Cre04.g214657.t1.1
Cre17.g719900.t1.2  Cre02.g091750.t2.1  Cre02.g091750.t3.1  Cre02.g091750.t1.2  Cre10.g450500.t1.1
Cre05.g239550.t1.1  Cre05.g239650.t1.1  Cre05.g239700.t1.2  Cre05.g239600.t1.2  Cre05.g239600.t2.1
Cre05.g238500.t1.1  Cre02.g086550.t1.1  Cre02.g109250.t1.1  Cre01.g043000.t1.1  Cre01.g028450.t1.2
Cre12.g529450.t1.2  Cre12.g529450.t2.1  Cre12.g529450.t3.1  Cre12.g529450.t4.1  Cre10.g433050.t1.1
Cre05.g236450.t1.1  Cre05.g236450.t2.1  Cre05.g236300.t1.1  Cre05.g236600.t1.1  Cre04.g225800.t1.2
Cre13.g577600.t1.2  Cre13.g577600.t2.1  Cre13.g578700.t1.1  Cre03.g208609.t1.1  Cre03.g208497.t1.1
Cre13.g584600.t1.1  Cre13.g584551.t1.1  Cre13.g584619.t1.2  Cre02.g100600.t1.1  Cre02.g100700.t1.1
Cre13.g563500.t1.1  Cre01.g017600.t1.1  Cre01.g017900.t1.1  Cre03.g157751.t1.1  Cre01.g017600.t2.1
cintiaiha commented 3 years ago

Ok, I just tried with diamond 0.9.34 and it worked. I was using diamond v2.0.2.140... Thank you for your help!

arzwa commented 3 years ago

OK great, thanks for reporting, I'll have to update to make it work with newer diamond versions apparently!