Illumina/paragraph

[E::idx_find_and_load] Could not retrieve index file

Xuelei-Dai opened this issue · 7 comments

Xuelei-Dai commented

Hello,
I used the test-data to run the multigrmpy.py

the command:

multigrmpy.py \
                          -i ./candidates.vcf \
                          -m ./samples.txt \
                          -r ./dummy.fa \
                          -o test

The error:

[E::idx_find_and_load] Could not retrieve index file for 'test/variants.vcf.gz'

finally, I can get the result file genotypes.vcf.gz, does the error have any effect, or how to solve it?

Best wishes~

jebrosen commented

I encountered the same issue, both with the precompiled binaries for 2.4a and built from source. The produced variants.vcf.gz file is also missing the last several columns of the reference output.

quanc1989 commented

Same issue for 2.4a, any suggestions?

cassisnaro commented

I have also the same error, is there a workaround?

cassisnaro commented

Is it possible that this bug appears only if executing in a folder where there was already a prior execution of the tool? I am testing this right now, will have the result in some hours, but from the looks of line [https://github.com/Illumina/paragraph/blob/e805e261336117a0c6901cdb3d61fd9d7d464611/src/python/bin/multigrmpy.py#L339], if the problematic file is present, it seems to take precedence over the input one, maybe explaining why I did not encounter the error before.

ColyFu commented

I also encountered the same bug. -_-

ivargr commented

I also encountered the same problem, both when using the test data and when using other data. I think adding this after line 58 in multigrmpy.py should fix the problem:

 pysam.tabix_index(vcf_with_event_ids_path, preset="vcf", force=True)
janawold1 commented

@ivargr This solution fixed it for me! Many thanks!

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