After running this command I receive an error about unsorted indexes and it occurs on at least 3 sets of samples whether they are quality filtered or not.
```
[16:28:41 - Annotate] Getting chrom coordinates
Traceback (most recent call last):
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/bin/medaka", line 8, in
sys.exit(main())
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/medaka.py", line 724, in main
args.func(args)
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/vcf.py", line 1201, in annotate_vcf_n_reads
variants = list(vcf.fetch())
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/vcf.py", line 664, in fetch
self.index()
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/vcf.py", line 615, in index
for variant in self._parse():
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/vcf.py", line 596, in _parse
raise IOError(
OSError: .vcf is unsorted at index #88102.
Failed to annotate variants.
```
Environment (if you do not have a GPU, write No GPU):
cjw85
commented
10 months ago
Describe the bug
After running this command I receive an error about unsorted indexes and it occurs on at least 3 sets of samples whether they are quality filtered or not.
medaka_haploid_variant -i duplex_combined.fastq.gz -r reference.fa -o medaka_haploid_variant -m r1041_e82_260bps_sup_variant_g632This produces these files that all seem to be populated:
calls_to_ref.bam calls_to_ref.bam.bai consensus_probs.hdf medaka.vcf
Logging
``` [16:28:41 - Annotate] Getting chrom coordinates Traceback (most recent call last): File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/bin/medaka", line 8, in
sys.exit(main())
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/medaka.py", line 724, in main
args.func(args)
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/vcf.py", line 1201, in annotate_vcf_n_reads
variants = list(vcf.fetch())
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/vcf.py", line 664, in fetch
self.index()
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/vcf.py", line 615, in index
for variant in self._parse():
File "/bioinformatics/mambaforge-pypy3/envs/ont-variants/lib/python3.9/site-packages/medaka/vcf.py", line 596, in _parse
raise IOError(
OSError: .vcf is unsorted at index #88102.
Failed to annotate variants.
```
Environment (if you do not have a GPU, write No GPU):
Additional context
This was previously mentioned here: https://github.com/nanoporetech/medaka/issues/417#issue-1583437752