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HKU-BAL / ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling
BSD 3-Clause "New" or "Revised" License
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IndexError in STEP5 #6

Closed naziafrin closed 3 months ago

naziafrin commented 4 months ago

I am getting the following IndexError in STEP 5 while running ClairS_TO with the latest docker image and I am using PacBio Hifi data (haplotagged.bam file) as the input.

Traceback (most recent call last): File "/opt/bin/clairs_to.py", line 107, in main() File "/opt/bin/clairs_to.py", line 101, in main submodule.main() File "/opt/bin/src/postprocess_vcf.py", line 231, in main merge_vcf(args) File "/opt/bin/src/postprocess_vcf.py", line 99, in merge_vcf qual = float(columns[5]) IndexError: list index out of range

Even with the error, the final output file output.vcf.gz is generated but I am concerned about the output. Could you please help me with that?

JasonCLEI commented 4 months ago

Hi, @naziafrin,

Thanks a lot for your interest. It seems that the error was caused by the wrong file of /tmp/vcf_output/pileup_filtering.vcf in the vcf post-processing step. Could you please provide your running log of run_clairs_to.log file and /tmp/vcf_output/pileup_filtering.vcf file with me (if possible, send them to my email address lchen@cs.hku.hk), and I will check the issue for you.

Lei