Could not read base quality scores

Describe the issue: The prints that read base quality scores cannot be read, as result, no variants are reported. However, I can visualize these values in the reads in IGV. How is that these values cannot be read? This is the line with the error, which repeats one after.

2021-03-26 19:12:43.550815: W third_party/nucleus/io/sam_reader.cc:534] Could not read base quality scores m64036_210113_122249/147655225/ccs: Not found: Could not read base quality scores

Setup

• Operative system: Ubuntu 20.04
• DeepVariant version: 1.1.0 (latest)
• Installation method: docker
• Type of data: PacBio HiFi. BAM files aligned to the reference with minimap2 -ax map-pb.

Steps to reproduce:

• Command:

  docker run \
    -v /home/user/working_directory:/input \
    -v /home/user/working_directory:/output \
    google/deepvariant:1.1.0 \
    /opt/deepvariant/bin/run_deepvariant \
    --model_type=PACBIO \
    --ref=/input/reference.fa \
    --reads=/input/file.bam \
    --output_vcf=/output/file.vcf \
    --call_variants_extra_args="use_openvino=true" \
    --num_shards=4 \
    --logging_dir=/output/logs

Does the quick start test work on your system? Yes. The test works without problem.

[elcortegano]

I see! I am very grateful for the support. Not only the problem is solved, it is everything much more clear now, and I have learned a lot from your feedback. Thank you.

[AndrewCarroll]

Hi @elcortegano

Billy has provided some excellent, detailed answers. I’ll just add a little bit of context to your question

“Our understanding deepvariant is designed for read alignments (and not assembly-to-reference alignments as achieved with minimap2 -ax asm”

This is correct, DeepVariant is for read alignments not assembly-to-reference alignment. Because minimap2 has original written when most PacBio data was CLR, the choice of the word map-pb was chosen for this present. When CCS became more common, a new recommendation was made by minimap2 authors to use the parameters for assembly with an sequence divergence tuned to HiFi data (this is the 20 part of --asm20). If you search for the string ``ccs``` in the minimap2 github, this should pull up the line.

So in short, DeepVariant is for read alignments, and the parameter for read mapping HiFi reads happens to manifest in minimap2 as minimap2 -ax asm20.