Probably pysam error

[poddarharsh15]

Hi @kcleal,

I hope you're doing well. I'm encountering some errors while using the latest version of Dysgu within a Conda environment. I have attached the log.txt file for your reference. Could you please take a look when you have a moment?

Thank you in advance for your help!

command used

dysgu run -x -p 16 --min-support 5 --mq 5 GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta $temp1 UD_AN001_F.sorted.uniq.bam --regions $exones_padded_50bp_sorted.bed | bgzip -c > dysgu_output.vcf.gz

log.txt
process_bams_dysgu_732982_1.txt

[kcleal]

Hi @poddarharsh15,

It looks like the posA and posB coordinates are the wrong way around. This should be straight forward to fix. Thanks for raising the issue

[poddarharsh15]

Thanks for the fast response :)

[poddarharsh15]

Hi @poddarharsh15,

It looks like the posA and posB coordinates are the wrong way around. This should be straight forward to fix. Thanks for raising the issue

Hi @kcleal,
I wanted to follow up and ask if the issue has been resolved, as I'm still a bit unclear on the current status. Could you please provide an update when you have a moment?
Thank you very much for your help.

[kcleal]

Hi @poddarharsh15,
Sorry the issue was closed automatically when I created the release. The new release should be available from conda, I will add it ti pypi at some point today

[poddarharsh15]

great thanks for clarifying I will run some test with newer version :)

[poddarharsh15]

Hi @kcleal,
Thank you again for the update. I wanted to share two scenarios I’ve tested with the same sample set. Please see the details below:

Using the --regions parameter to exclude certain regions in my WES data
I ran test samples using the --regions parameter to exclude specific exons, but unfortunately, I am still encountering the same errors. Please refer to the attached log files for detailed error descriptions. I am not 100% sure but I think there is some problem with .bed files I am using with my WES data and I think I can ignore the regions parameters.
with_region_param.txt

Without including the --regions parameter
When I omit the --regions parameter, the pipeline runs successfully and completes without any errors.
no_regions.txt

Conda installs a new version of dysgu, but shows version 1.6.6
Even though I installed the latest version of dysgu via Conda, it still reports version 1.6.6 when checked.

Please let me know if you have any suggestions or insights into these issues.

Many thanks again for your help.

[kcleal]

Oh that's unexpected. Sometimes if you install via pip, then install using conda, the pip version still gets used. Perhaps this is the reason? You might need to run pip uninstall dysgu a few times.

If the bed regions have the start and end coordinates in the wrong order, that may also cause problems

[poddarharsh15]

Hi @kcleal,
I’ve tried several times to uninstall (through pip) the old version of dysgu and reinstall it using Conda. Unfortunately, I still end up with version 1.6.6 after the installation.
However, I have decided not to use the --regions parameter anymore, as I do not have accurate BED files for the regions I intended to exclude.

Many thanks again for your help!

[kcleal]

Ok no problem. Sorry, I dont know why you are seeing v1.6.6, I seem to have no issues downloading 1.6.7