[E::idx_find_and_load] Could not retrieve index file

[Xuelei-Dai]

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]

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]

Same issue for 2.4a, any suggestions?

[cassisnaro]

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

[cassisnaro]

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]

I also encountered the same bug. -_-

[ivargr]

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]

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