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

[nparmalee]

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

[zhengzhenxian]

@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.

[nparmalee]

Thanks so much for your quick reply.

Here are the contents of the run_clairs.log file:

[COMMAND] /gpfs/home/nparma/programs/ClairS/run_clairs --tumor_bam_fn /home/nparma/eee_bams_dsa/DSA_hifiasm_60x/ONT/COLO829-T_PS00361.all.sorted.bam --normal_bam_fn /home/nparma/eee_bams_dsa/DSA_hifiasm_60x/ONT/COLO829-BL_PS00342.all.sorted.bam --ref_fn /home/nparma/eee_bams_dsa/references/dsa60/COLO829-BL_60X_hifisam_merged_haplotypes.fasta --threads 4 --platform ont_r10_dorado_sup_5khz --output_dir /home/nparma/eee_bams_dsa/myanalysis/clairs/T/dsa/clairsout

[INFO] --include_all_ctgs not enabled, use chr{1..22,X,Y} and {1..22,X,Y} by default

On Apr 26, 2024, at 10:47 PM, zhenxian @.***> wrote:

@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 @.***, thanks.

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[nparmalee]

Thanks for pointing me to that log file, I had missed it. I updated the code and so far this is running. This bam file is aligned to a donor specific assembly and I’m not sure how the contains are named so this error makes some sense.

./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 \ --include_all_ctgs

On Apr 27, 2024, at 10:18 AM, Nancy Parmalee @.***> wrote:

Thanks so much for your quick reply.

Here are the contents of the run_clairs.log file:

[COMMAND] /gpfs/home/nparma/programs/ClairS/run_clairs --tumor_bam_fn /home/nparma/eee_bams_dsa/DSA_hifiasm_60x/ONT/COLO829-T_PS00361.all.sorted.bam --normal_bam_fn /home/nparma/eee_bams_dsa/DSA_hifiasm_60x/ONT/COLO829-BL_PS00342.all.sorted.bam --ref_fn /home/nparma/eee_bams_dsa/references/dsa60/COLO829-BL_60X_hifisam_merged_haplotypes.fasta --threads 4 --platform ont_r10_dorado_sup_5khz --output_dir /home/nparma/eee_bams_dsa/myanalysis/clairs/T/dsa/clairsout

[INFO] --include_all_ctgs not enabled, use chr{1..22,X,Y} and {1..22,X,Y} by default

On Apr 26, 2024, at 10:47 PM, zhenxian @.***> wrote:

@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 @.***, thanks.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

[nparmalee]

Hello, and thank you for your help earlier. Unfortunately the run finished without producing a vcf file. This is the code I ran. I am attaching the log file. I would really appreciate your help with this.

Thanks, Nancy

./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 \ --include_all_ctgs

On Apr 27, 2024, at 10:29 AM, Nancy Parmalee @.***> wrote:

Thanks for pointing me to that log file, I had missed it. I updated the code and so far this is running. This bam file is aligned to a donor specific assembly and I’m not sure how the contains are named so this error makes some sense.

./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 \ --include_all_ctgs

On Apr 27, 2024, at 10:18 AM, Nancy Parmalee @. @.>> wrote:

Thanks so much for your quick reply.

Here are the contents of the run_clairs.log file:

[COMMAND] /gpfs/home/nparma/programs/ClairS/run_clairs --tumor_bam_fn /home/nparma/eee_bams_dsa/DSA_hifiasm_60x/ONT/COLO829-T_PS00361.all.sorted.bam --normal_bam_fn /home/nparma/eee_bams_dsa/DSA_hifiasm_60x/ONT/COLO829-BL_PS00342.all.sorted.bam --ref_fn /home/nparma/eee_bams_dsa/references/dsa60/COLO829-BL_60X_hifisam_merged_haplotypes.fasta --threads 4 --platform ont_r10_dorado_sup_5khz --output_dir /home/nparma/eee_bams_dsa/myanalysis/clairs/T/dsa/clairsout

[INFO] --include_all_ctgs not enabled, use chr{1..22,X,Y} and {1..22,X,Y} by default

On Apr 26, 2024, at 10:47 PM, zhenxian @. @.>> wrote:

@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 @.***, thanks.

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[xianyu0623]

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!