HKU-BAL/ClairS

ClairS quits with exit code 0 but no output, no error logged

nparmalee opened this issue · 5 comments

I'm using ClairS on three samples right now. Two have been running since last night, no issue yet. The third quits within seconds of launching the job with exit code 0 but no output is written. The directory structure is created in the output file. No errors are written in the log. This job is using a custom reference but I get the same behavior with these files if I substitute hg38 as the reference. Is there a debug flag or something I can use to tell me what is going wrong? This is the code I'm running. Any help would be greatly appreciated.

./run_clairs
-T /home/nparma/eee_bams_dsa/DSA_hifiasm_60x/ONT/COLO829-T_PS00361.all.sorted.bam
-N /home/nparma/eee_bams_dsa/DSA_hifiasm_60x/ONT/COLO829-BL_PS00342.all.sorted.bam
-R /home/nparma/eee_bams_dsa/references/dsa60/COLO829-BL_60X_hifisam_merged_haplotypes.fasta
-t 4
-p ont_r10_dorado_sup_5khz
-o /home/nparma/eee_bams_dsa/myanalysis/clairs/T/dsa/clairsout

@nparmalee

Could you share logs directory and run_clairs.log log file in your output dir /home/nparma/eee_bams_dsa/myanalysis/clairs/T/dsa/clairsout for us to pinpoint the issue?

My email address is zxzheng@cs.hku.hk, thanks.

Hello, nparmalee

I encountered a similar issue and wanted to share a potential solution. Please ensure that a .bai file exists in the same path as your bam file. ClairS relies on the 'samtools mpileup' command for candidate selection, which requires a .bai file. Without it, ClairS will not produce results or log errors, as it does not check stderr.

I hope this helps!