DetermineGermlineContigPloidy error: line 137

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Carlos García Peral

• May 14, 2022 01:04

Hi, my names is Carlos, im using CNV in gatk  (version 4.2.2.0) for the first time, specifically im working with the genome of Mesocricetus auratus (version 1.0) which has hundreds of contigs and provide no sexual chromosomes yet. The fact is that when i use the function DetermineGermlineContigPloidy an error arises in the line 137 of the temporal python script  cohort_determine_ploidy_and_depth.py. Similar errors have been post in this link

https://github.com/broadinstitute/gatk/issues/7444 , but all of them apparently were using an out-of-date GATK python environment. As im using GATK 4.2.2.0 and i updated my python packages in the enviroment using the command

conda update --all

i suspect the problem is not the same but, im not sure. Furthermore all the epochs of the running command finish correctly (i think), but the error arises when the first files start to be written. Just before the error...

INFO gcnvkernel.io.io_ploidy - Writing psi_j_log__...
INFO gcnvkernel.io.io_ploidy - Writing mean_bias_j_lowerbound__...

and after that the entire program log (extract):

Traceback (most recent call last):
  File "/tmp/cohort_determine_ploidy_and_depth.15221897200612208395.py", line 137, in <module>
    args.output_calls_path)()
TypeError: __init__() takes 6 positional arguments but 7 were given
23:58:35.924 DEBUG ScriptExecutor - Result: 1
23:58:35.925 INFO  DetermineGermlineContigPloidy - Shutting down engine
[May 13, 2022 at 11:58:35 PM CEST] org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy done. Elapsed time: 38.57 minutes.
Runtime.totalMemory()=209715200
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: 
python exited with 1

I also provided my gcnvkernel version (0.7) , my python version in the enviroment (3.6.10), emphasize my gatk version (4.2.2.0)

The command i used is the next:

./gatk DetermineGermlineContigPloidy -L /mnt/d/Doctorado/gatk_CNV/GASH_control.cohort.gc.filtered.interval_list --interval-merging-rule OVERLAPPING_ONLY -I /mnt/d/Doctorado/gatk_CNV/HAMSTER_1_S16.hdf5 -I /mnt/d/Doctorado/gatk_CNV/HAMSTER_2_S17.hdf5 -I /mnt/d/Doctorado/gatk_CNV/HAMSTER_3_S18.hdf5 -I /mnt/d/Doctorado/gatk_CNV/HAMSTER_4_S19.hdf5 -I /mnt/d/Doctorado/gatk_CNV/HAMSTER_5_S20.hdf5 --contig-ploidy-priors /mnt/d/Doctorado/contig_ploidy_priors.tsv --output . --output-prefix ploidy --verbosity DEBUG

I hope you can help me, sorry for my english, and thanks in advance.

Regards, Carlos

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  Genevieve Brandt (she/her)

  • May 16, 2022 21:46

  Hi Carlos García Peral,

  Thank you for writing into the forum! Could you remove and recreate the GATK conda environment to confirm that there is not some underlying issue with the conda environment?

  Please follow these instructions: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-for-GATK4

  Let me know if that works.

  Best,

  Genevieve

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  Carlos García Peral

  • May 16, 2022 22:20

  Sorry for bothering you Genevieve, the problem was solved. It was a matter of the gcnvkernel version used. I was working with the 0.7 one install from https://anaconda.org/bioconda/gcnvkernel , but suddenly i decide to clone  the gatk official repository from github and use the command python3 setup_gcnvkernel.py install. The 0.8 was installed and everything worked fine. I think it could be useful to mention in the web how you can install the latest version of the python module gcnvkernel. It is only a suggestion :).

  Thanks for your time Genieve, and one more time apologize for bothering with that comment.

  Carlos

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  Genevieve Brandt (she/her)

  • May 16, 2022 22:21

  No problem, thanks for your suggestion! Glad you have solved the issue.

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