Renee build: qualimapinfo errors

[slsevilla]

I'm attempting to create a reference for T2T (HS1). Ran into two issues:

Problem 1

Running renee build and had the rule qualimapinfo fail. The .err. and .out log were unhelpful. The script produces an error file but this being passed to qualimap_error.log which is not saved.

Solution 1

The output should be to .err and not to a separate file

Problem 2

Running this process:

python3 \
        data/Boufraqech_group/analysis/renee_build_240125/hs1_t2t/workflow/scripts/builder/generate_qualimap_ref.py \
        -g /data/Boufraqech_group/analysis/renee_build_240125/hs1_t2t/genes.gtf \
        -f /data/Boufraqech_group/analysis/renee_build_240125/hs1_t2t/hs1.fa \
        -o qualimap_info.txt \
        --ignore-strange-chrom 2> qualimap_error.log

Getting this error:

...
  File "/usr/local/Anaconda/envs/py3.10/lib/python3.10/site-packages/HTSeq/features.py", line 140, in __iter__
    (attr, name) = self.parse_GFF_attribute_string(
  File "/usr/local/Anaconda/envs/py3.10/lib/python3.10/site-packages/HTSeq/features.py", line 194, in parse_GFF_attribute_string
    raise ValueError(
ValueError: The attribute string seems to contain mismatched quotes.

Solution 2

I figure out that this is because of single quotes in my GTF file

...addition of 3' A residues to the mRNA...

Still getting an error though - need to troubleshoot further.

[kopardev]

@slsevilla use pyGTF to rewrite the GTF without unwanted "keys" from the last column for eg. "Note"

[kelly-sovacool]

solution was to rewrite the GTF without single quotes