Error during strainphlan

Megan Folkerts

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Dec 19, 2019, 3:39:27 PM12/19/19

to MetaPhlAn-users

Hello again,

I'm getting the following error when running strainphlan.py:

Traceback (most recent call last):

File "/scratch/mfolkerts/bin/metaphlan/strainphlan.py", line 1570, in <module>

strainphlan()

File "/scratch/mfolkerts/bin/metaphlan/strainphlan.py", line 1566, in strainphlan

strainer(args)

File "/scratch/mfolkerts/bin/metaphlan/strainphlan.py", line 1417, in strainer

kept_markers=kept_markers)

File "/scratch/mfolkerts/bin/metaphlan/strainphlan.py", line 1261, in load_all_samples

use_threads=args['use_threads'])

File "/scratch/mfolkerts/bin/metaphlan/strainphlan_src/ooSubprocess.py", line 258, in parallelize

results = pool.map(func, args)

File "/home/mfolkerts/miniconda3/envs/python2.7/lib/python2.7/multiprocessing/pool.py", line 253, in map

return self.map_async(func, iterable, chunksize).get()

File "/home/mfolkerts/miniconda3/envs/python2.7/lib/python2.7/multiprocessing/pool.py", line 572, in get

raise self._value

Exception: Traceback (most recent call last):

File "/scratch/mfolkerts/bin/metaphlan/strainphlan_src/ooSubprocess.py", line 244, in wrapper

return f(*args, **kwargs)

File "/scratch/mfolkerts/bin/metaphlan/strainphlan.py", line 1206, in load_sample

clade = db['markers'][marker]['taxon'].split('|')[-1]

KeyError: '227940__GeneID:1260616'

Here is the code I'm running:

strainphlan.py --ifn_samples samplemarkersout/*.markers --output_dir . --print_clades_only > clades.txt --nprocs_main 8 --mpa_pkl /scratch/mfolkerts/bin/metaphlan_databases/mpa_v295_CHOCOPhlAn_201901.pkl

I've downloaded metaphlan2 from the bitbucket repository to bypass the current bug that prevents strainphlan from running properly when it's installed through conda. Sample2markers.py seems to have worked as expected(after a lot of finagling), and I've checked the marker files themselves; they seem comparable in format to those in the tutorial. Do you have any idea what would cause this?

Thanks!

Megan

Aitor Blanco-Miguez

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Dec 20, 2019, 10:32:24 AM12/20/19

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Hi Megan,

It seems that there is a problem with some markers from viruses.

While we solve this issue, you can execute StrainPhlAn using the mpa_v294_CHOCOPhlAn_201901.pkl MetaPhlAn2.9 database.

It is the same database as the v295 but without the markers for the viruses.

I will contact with you again after when issue with the v295 database is solved.

Best,

Aitor

Megan Folkerts

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Dec 20, 2019, 11:41:35 AM12/20/19

to Aitor Blanco-Miguez, MetaPhlAn-users

Hi Aitor,

Thanks for getting back to me. Unfortunately, this seems to be database independent. I've tried multiple versions of chocophlan, as well as the old mpa_v20 database, and I get the same error every time (though the offending GeneID changes). I'll keep troubleshooting on my end; maybe sample2markers didn't run as it should have.

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Megan Folkerts, MS
Research Associate II
Center for Emerging Pathogens and Technologies
TGen North
Flagstaff, Arizona
928-226-6375

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Megan Folkerts

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Dec 20, 2019, 12:12:34 PM12/20/19

to Aitor Blanco-Miguez, MetaPhlAn-users

Nevermind on this. It seems the issue was that when I downloaded the repository from bitbucket, the version of strainphlan.py that downloaded was an older one. I updated versions and everything ran smoothly.

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