search

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
81 stars 41 forks source link

running problem #23

Closed asher-616 closed 4 years ago

asher-616 commented 4 years ago

Hi, I trying to run a cDNA data and the mcl command doesn't create any file. I get a lot of warnings about codons that contain 'N' in them and about in-frame stop codons (can't do much about this, this is the data I got) and then: 100% (84303 of 84303) |#################################################################################################################| Elapsed Time: 0:00:07 Time: 0:00:07 2019-09-12 10:25:43: WARNING There were 139382 warnings during translation 2019-09-12 10:25:43: INFO Writing blastdb sequences to db.fasta. 2019-09-12 10:25:43: INFO Writing query sequences to query.fasta. 2019-09-12 10:25:44: INFO Performing all-vs.-all Blastp (this might take a while) 2019-09-12 10:25:44: INFO Making Blastdb makeblastdb: symbol lookup error: /powerapps/share/mpi/openmpi-1.10.4.c7/lib/libmpi_cxx.so.1: undefined symbol: ompi_mpi_char 2019-09-12 10:25:44: INFO Running Blastp 2019-09-12 10:25:44: INFO blastp -db wgd_blast/37b75c7448cc96.db.fasta -query wgd_blast/37b75c7464ccc4.query.fasta -evalue 1e-10 -outfmt 6 -num_threads 4 -out wgd_blast/ESTs_Cisavi_2018.fasta.blast.tsv 2019-09-12 10:25:44: INFO All versus all Blastp done rm: cannot remove ‘wgd_blast/37b75c7448cc96.db.fasta.phr’: No such file or directory rm: cannot remove ‘wgd_blast/37b75c7448cc96.db.fasta.pin’: No such file or directory rm: cannot remove ‘wgd_blast/37b75c7448cc96.db.fasta.psq’: No such file or directory then some more info about trying to perform mcl clustering but I think the problem is upstream from that

could you let me know what I'm doing wrong?

arzwa commented 4 years ago

Hmm, this is probably related to your sequences not being proper CDSs. wgd assumes your sequences can be translated, so they should really be sequences of codon triplets. It doesn't make sense to try to translate, make codon alignments, and estimate evolutionary distances at the codon level if you don't have proper codon sequences... If you have the latest version of wgd installed you can try to use the wgd pre <your_sequences.fasta> command to check your sequences.

asher-616 commented 4 years ago

Thank you for the quick reply. I'll try updating my version (and apparently get new data)

Thanks! Asher

On Thu, Sep 12, 2019 at 10:45 AM Arthur Zwaenepoel notifications@github.com wrote:

Hmm, this is probably related to your sequences not being proper CDSs. wgd assumes your sequences can be translated, so they should really be sequences of codon triplets. It doesn't make sense to try to translate, make codon alignments, and estimate evolutionary distances at the codon level if you don't have proper codon sequences... If you have the latest version of wgd installed you can try to use the wgd pre

command to check your sequences. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or mute the thread .

-- Asher Moshe Pupko lab, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel