User: yp19

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yp1920
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Posts by yp19

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Eggnog emapper.py error
... SLURM, and I just requested a node with more memory ...
written 19 days ago by yp1920
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Answer: A: Eggnog emapper.py error
... In case this happens to anyone else, it turned out it was just a memory issue! Just ran it with more memory and it now runs fine. Thanks for your input everyone. ...
written 19 days ago by yp1920
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Comment: C: Eggnog emapper.py error
... Tried installing eggnog-mapper directly from git repo, it ran for ~30mins then the same kind of error: Building reference index... Traceback (most recent call last): File "emapper.py", line 1210, in main(args) File "emapper.py", line 226, in main dump_diamond_matche ...
written 19 days ago by yp1920
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Comment: C: Eggnog emapper.py error
... I will try that and report back. Thank you for the help! ...
written 20 days ago by yp1920
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Comment: C: Eggnog emapper.py error
... Thank you. Just tried this, no luck unfortunately ...
written 20 days ago by yp1920
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Comment: C: Eggnog emapper.py error
... Thanks for your help, I tried running it directly, got this > Error: Syntax: diamond COMMAND [OPTIONS]. To print help message: > diamond help which diamond results in /usr/bin/which: no diamond in (/cvmfs/home/etc..etc) ...
written 20 days ago by yp1920
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Comment: C: Eggnog emapper.py error
... I installed eggnog by downloading this file (1.03.tar.gz) found here: https://github.com/jhcepas/eggnog-mapper/releases and then running `download_eggnog_data.py` (to get the databases, took a long time) That is all I did, I did not install diamond separately as I thought it came with the package a ...
written 20 days ago by yp1920
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Eggnog emapper.py error
... Hi guys, I'm trying to run eggnog to annotate some proteins. I followed the exact instructions found on [their wiki page for downloading and basic usage](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2). It runs for a few minutes then I get an error. $ python emapper.py -i prot ...
emapper annotation protein eggnog written 20 days ago by yp1920
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Comment: C: custom database in HH-suite
... Thanks for the suggestion! I will try to format headers and report back. ...
written 23 days ago by yp1920
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Comment: C: custom database in HH-suite
... Thanks! Yeah, I was just worried about losing the orthogroup information, if i create the database using all proteins. I would just use 'cat' to join all the fasta files from each orthogroup and then use that file to make the database. Also the MSA step in making the database would be done overall ...
written 25 days ago by yp1920

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