Open jacopoM28 opened 1 year ago
Hi @jacopoM28,
Thanks for reporting this issue. On first glance, it appears that the SV VCF generated by Sniffles hassle format issues. Could you send the gzipped Sniffles VCF file and the full standard output to hanshunhua0829@gmail.com so I can take a look?
Also, could you share the conda package list you installed under TELR env using the following commands? This should be helpful in assessing whether the issue is caused by Sniffles/NGMLR/bcftools versions.
conda activate TELR
conda list
Thanks, Shunhua
Hi Shunhua,
thank you very much, I just sent you all the files!
Best Jacopo
@jacopoM28 Thanks for sending over the files and sorry for the late response (end of the year push).
I noticed two issues in the standard error log file. The first issue seems to be caused by Sniffles producing non-standard VCF format, which doesn't seem to affect the results (expect for having those format related warning messages), but I will keep it in my backlog.
The second issue is an actual error. Basically TELR will repeatmask the reference genome for reference TE insertions and use this annotation in the non-reference TE identification process. Currently, the reference TE BED file (Cgig_Ref.PacBio_genome.fa.te.bed
) is not properly sorted. I have now added a patch in TELR to fix the TE.bed out of sort error (see https://github.com/bergmanlab/TELR/pull/27). Please activate TELR conda env, pull the new patch in the GitHub repo, install the new TELR package locally using pip, and test on your failed sample jobs. Let me know if you can get normal TELR output files, or are stilling having issues. Thanks!
conda activate TELR
cd TELR # this is the TELR git folder
git pull # necessary to use this patched update
pip install . # necessary to use this patched update
Best, Shunhua
Hello,
I am having some issues using TELR and I think the problem arise after calling the SVs with SNIFFLE. Here the complete log file:
Any suggestion on what is going on?
Thanks in advanced! Jacopo