Open areebapatel opened 1 month ago
Hi, @areebapatel,
We have found another error message[ERROR] Failed to load reference sequence from file (/b06x-isilon/b06x-m/mnp_nanopore/software/hg38/hg38.fa).
from your running log. Along with the error message pos 0 missing GT value
, we believed that the program is not running normally, which could occur issues while reading and writing files. We suggest that you rerun ClairS-TO separately to see if the same issue still exists. If you have done so and still got the error, could you kindly provide your latest running log of run_clairs_to.log
file and some VCF files stored in /b06x-isilon/b06x-m/mnp_nanopore/analysis/ONT_R00200/snv/ClairsTo/tmp/phasing_output/vcf/
like chr1.vcf
? And we will check the issue for you further.
Lei
Hi, @areebapatel,
We suggest that you run ClairS-TO again with the same command to see if the issue still exists. If you have done so and still got the error, we will check the issue for you further.
Lei
Hi,
Firstly, many thanks for this incredibly useful tool.
I am running ClairS-TO with the singularity container on a ONT WGS run. The library was basecalled and aligned using dorado 0.6.2.
Command used to run
All the previous steps run fine and then it runs into this error at the phasing step:
The full log file is here- run_clairs_to.log
Could you please help me with this?
Many thanks, Areeba.