How to Suppress Warning Messages

[biozzq]

Dear all,

Describe the issue:
I encountered frequent warning messages when running the following command

Setup

• Operating system:
• DeepVariant version: 1.8.0

Steps to reproduce:

• Command:
• singularity exec ~/01.software/install/deepvariant_latest.sif run_deepvariant
  --model_type=WGS
  --ref=${ref}
  --reads=/work/home/acu6cshe3p/data/03.mapping/${pre}.dup.sort.fix.bam
  --output_vcf=/work/home/acu6cshe3p/data/01.reference/04.VCF/${pre}.vcf.gz
  --output_gvcf=/work/home/acu6cshe3p/data/01.reference/03.mapping/${pre}.gvcf.gz
  --num_shards=12
  --regions="/work/home/acu6cshe3p/data/01.reference/chr.bed"
  --vcf_stats_report=true
  --disable_small_model=false
  --logging_dir=/work/home/acu6cshe3p/data/tmp/${pre}.logs
  --haploid_contigs="X,Y"
  --par_regions_bed="/work/home/acu6cshe3p/data/01.reference/GRCh38.PAR.bed"
  --dry_run=false
  --intermediate_results_dir /work/home/acu6cshe3p/data/tmp/${pre}

warning message
W0312 23:18:06.734651 47884493201408 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.747291 47428323979264 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.750297 47450901491712 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.754469 47668816019456 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.762939 47907004751872 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.775703 47884493201408 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.773818 47509988696064 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.779358 47081304915968 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.788240 47155342680064 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.803741 47355960147968 ranges.py:500] BED file does not have a tabix index. Reading full bed file.
W0312 23:18:06.807463 47450901491712 ranges.py:500] BED file does not have a tabix index. Reading full bed file.

Best wishes,
Zheng zhuqing

[kishwarshafin]

Hi @biozzq currently there isn't a way to suppress this log from command line. We would look into it to remove this line from the logs in the next release. However, you can index your bed file using:

tabix -p bed <name.bed>

And have the index file be present locally so this warning goes away.

[biozzq]

Dear @kishwarshafin,

Thank you for your prompt reply. I would like to clarify whether DeepVariant can recognize a compressed BED file as input. Specifically, since tabix requires BED files to be position-sorted and compressed using bgzip, I wanted to confirm if DeepVariant supports this format.

Best regards

[kishwarshafin]

I can confirm that it can read from gzipped files.

[biozzq]

I know that tabix can only recognize BGZF files. Can DeepVariant read from BGZF files?

Another question is about the BED file format, is it one or zero based for the start coordinate?

Thank you very much.