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lauguma / GWideCodeML

A Python package for testing evolutionary hypotheses in genome-wide approaches.
https://github.com/lauguma/GWideCodeML/wiki
GNU General Public License v3.0
31 stars 11 forks source link

there is an error when i try to run GWideCodeML #3

Open yananzh opened 3 years ago

yananzh commented 3 years ago

Traceback (most recent call last): File "/home/zhangyanan/miniconda3/envs/gwcodeml/bin/gwidecodeml", line 33, in sys.exit(load_entry_point('gwidecodeml==1.1', 'console_scripts', 'gwidecodeml')()) File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/main.py", line 82, in main File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/pkg_utils/utils.py", line 55, in dup_tags File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/biopython-1.78-py3.6-linux-x86_64.egg/Bio/SeqIO/init.py", line 607, in parse return iterator_generator(handle) File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/biopython-1.78-py3.6-linux-x86_64.egg/Bio/SeqIO/FastaIO.py", line 183, in init super().init(source, mode="t", fmt="Fasta") File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/biopython-1.78-py3.6-linux-x86_64.egg/Bio/SeqIO/Interfaces.py", line 47, in init self.stream = open(source, "r" + mode)

Sher-Ojala commented 3 years ago

I am getting that same error. Any ideas? Thanks!

lijunyuan commented 2 years ago

Also confronting the same error while testing the example data, please help!

Sher-Ojala commented 2 years ago

Hello,

I have to tell you, we never got this program to work for us. I have notes that it could not find a program it needed to run (ete), and then both I am my student abandoned it once we got it working, because it would run for a few seconds, and then stop:

"That is exactly what I found with the GWideCodeML. I tried several different ways to keep it running, including continuously hitting the return key in the terminal, but it would run a job only a few minutes and they never finished. She might have used a version of ETE that was having that issue. The author of ETE fixed that, but maybe she did not update the ete installed."

So sorry I can not help more! Good luck to you! Sher

Sher Hendrickson, PhD @.***

Associate Professor of Biology, Shepherd University, Shepherdstown, WV Research Associate, Smithsonian National Zoo and Conservation Biology Institute, Center for Conservation Genomics,Washington, DC

From: lijunyuan @.> Sent: Monday, August 1, 2022 9:57 AM To: lauguma/GWideCodeML @.> Cc: Sher Hendrickson-Lambert @.>; Comment @.> Subject: Re: [lauguma/GWideCodeML] there is an error when i try to run GWideCodeML (#3)

Also confronting the same error while testing the example data, please help!

— Reply to this email directly, view it on GitHubhttps://github.com/lauguma/GWideCodeML/issues/3#issuecomment-1201241325, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQNLUUF4URTIZPETQ6YEPZ3VW7JS7ANCNFSM42BIZ5OQ. You are receiving this because you commented.Message ID: @.***>

lijunyuan commented 2 years ago

Thanks for your promptly reply, Sher. Since GWideCodeML does not work by far, have you discovered other tools available online instead and do you mind recommending some user-friendly?

With respects, Junyuan Post doc, IOCAS, China

Sher-Ojala commented 2 years ago

Hello Junyuan!

I never did find a user-friendly method, but went back to using PAML following this paper: Genome-wide signatures of complex introgression and adaptive evolution in the big cats

By Henrique V. Figueiró,et al. 2018

I used ETE3 directly on a set of genes we were interested in.

This fall, I am adapting it to use gene predictions, but I have been distracted with aligning some new genomes. Good luck! Sher

From: lijunyuan @.> Sent: Thursday, August 4, 2022 9:28 PM To: lauguma/GWideCodeML @.> Cc: Sher Hendrickson-Lambert @.>; Comment @.> Subject: Re: [lauguma/GWideCodeML] there is an error when i try to run GWideCodeML (#3)

Thanks for your promptly reply, Sher. Since GWideCodeML does not work by far, have you discovered other tools available online instead and do you mind recommending some user-friendly?

With respects, Junyuan Post doc, IOCAS, China

— Reply to this email directly, view it on GitHubhttps://github.com/lauguma/GWideCodeML/issues/3#issuecomment-1205940815, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQNLUUDHNFGA5AZEJI57KILVXRU5DANCNFSM42BIZ5OQ. You are receiving this because you commented.Message ID: @.***>