Blank QV plots?

[bibionid]

Hello,

Thanks for making this awesome tool! I'm recently installed it and am trying to use the sampleqc tool. I am running with the below call:

longQC.py sampleqc -p 16 -m 2 -d -x pb-hifi -s <sample_name> -o <out_dir> <sample_name.bam>

The tools appears to have run without any errors, but some of the output is not as I expected?

The fig_longQC_sampleqc_average_qv_<sample_name>.png and fig_longQC_sampleqc_olp_qv_<sample_name>.png files appear as below:

Is this expected for a given error, or do I need to review my installation? No error messages were created.

Many thanks in advance!

[yfukasawa]

Hello @bibionid ,

Sorry for heavy delay due to my personal situation, but thank you for asking.
You're absolutely right, and I'm aware of this issue, which happens when HiFi input format is bam.

This can be resolved relatively easily by tweaking codes for pysam, but it gets quite slower. The tentative workaround is using fastq format, and I hope this answer helps you.

Y.

[bibionid]

Hi @yfukasawa

Thank you very much for you time in responding here, this is even more valuable given the strain on your time.

Thank you fo suggesting the workaround - I have since tried using fastq and did successfully generate the plots.

Best wishes!