Error while opening BGZF compressed FASTA reference file

[dennishendriksen]

Running clair3 without --longphase_for_phasing results in an error when using a bgzipped reference indexed with samtools:

apptainer exec clair3-v0.1-r12.sif \
/opt/bin/run_clair3.sh \
--bam_fn=test.cram \
--ref_fn=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
--platform="ilmn" \
--model_path="/opt/models/ilmn" \
--output="./output"

Error:

[INFO] 3/7 Phase VCF file using Whatshap
This is WhatsHap 1.4 running under Python 3.9.0
ERROR: whatshap error: Error while opening FASTA reference file: Compressed FASTA is only supported in BGZF format. Use the samtools bgzip utility (instead of gzip) to compress your FASTA.

Note that the reference is actually bgzipped with the bgzip utility even though the error states that the format is not bgzip.

Possibly related issues:

• Error reading bgzipped reference whatshap/whatshap#151
  • Create or load htslib .fai and .gzi index files when using BGZF files mdshw5/pyfaidx#126

Currently we are working around the issue by using an uncompressed reference.

[zhengzhenxian]

Hi,

We confirmed it was a bug from WhatsHap. Sadly, we could not do more before WhatsHap fixed it. We suggest you use LongPhase, which performed comparably to WhatsHap with ≥20x long-reads.

[aquaskyline]

Scheduled to integrate a newer WhatsHap version that fixed the problem.