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Error running renee build for marmoset reference genome #161

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nmkuehn opened this issue Sep 30, 2024 · 0 comments
Open

Error running renee build for marmoset reference genome #161

nmkuehn opened this issue Sep 30, 2024 · 0 comments
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bug Something isn't working RENEE RepoName

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@nmkuehn
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nmkuehn commented Sep 30, 2024

I am attempting to build a marmoset reference genome from NCBI files using renee build.

qualimapinfo fails three times then shuts the job down.
The qualimap_error.log reads:

Traceback (most recent call last):
File "/data/$USER/MarmosetGenome/workflow/scripts/builder/generate_qualimap_ref.py", line 98, in
biotype = exons[0].attr["gene_type"]
KeyError: 'gene_type'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/data/$USER/MarmosetGenome/workflow/scripts/builder/generate_qualimap_ref.py", line 100, in
biotype = exons[0].attr["gene_biotype"]
KeyError: 'gene_biotype'

The fasta and .gtf files were downloaded from NCBI. The .gtf has "gene_biotype" attribute :
Example:

NC_071442.1 Gnomon gene 399914 559170 . - . gene_id "LOC118152095"; transcript_id ""; db_xref "GeneID:118152095"; description "glucose-6-phosphate 1-dehydrogenase-like"; gbkey "Gene"; gene "LOC118152095"; gene_biotype "transcribed_pseudogene"; pseudo "true";

@kopardev kopardev added the RENEE RepoName label Sep 30, 2024
@kelly-sovacool kelly-sovacool changed the title RENEE build from .gtf Error running renee build for marmoset reference genome Oct 25, 2024
@kelly-sovacool kelly-sovacool added the bug Something isn't working label Oct 25, 2024
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