samtools index: failed to open error

Question

samtools index: failed to open error

Closed this issue 6 months ago · 9 comments

Good day,
I am using ClairS-TO using the following command:

singularity exec /apps/chpc/bio/clairs_to/clairs-to_latest.sif run_clairs_to -T BC1.sorted.bam -R GCF_000001405.40_GRCh38.p14_genomic.fna -t 8 -p ont_r10_dorado_hac_4khz --include_all_ctgs --output_dir output-BC1

I however get the following error (I don't get a final .vcf file but I do get many vcf files in the tmp folder):

samtools index: failed to open "/mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/output-BC1/tmp/phasing_output/phased_bam_output/tumor_NT_187421.1.bam": No such file or directory
ERROR in STEP 11, THE FOLLOWING COMMAND FAILED: ( parallel --joblog /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/output-BC1/logs/phasing_log/parallel_3_haplotag_tumor.log -j 8 /opt/micromamba/envs/clairs-to/bin/longphase haplotag -o /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/output-BC1/tmp/phasing_output/phased_bam_output/tumor_{1}.bam --reference /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/GCF_000001405.40_GRCh38.p14_genomic.fna --region {1} -s /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/output-BC1/tmp/phasing_output/phased_vcf_output/tumor_phased_{1}.vcf.gz -b /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/BC1.sorted.bam :::: /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/output-BC1/tmp/CONTIGS ) 2>&1 | tee /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/output-BC1/logs/phasing_log/3_tumor_haplotag.log && parallel -j 8 samtools index -@8 /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/output-BC1/tmp/phasing_output/phased_bam_output/tumor_{1}.bam :::: /mnt/lustre/groups/CBBI1617/BreastCancer-fastq/SNV-analysis/input/output-BC1/tmp/CONTIGS

Could I please get some assistance on this.

Answer 1 · 2024-05-22T14:27:31.000Z

Hi, @DIPLOMICS-SA,

Thanks a lot for your interest on ClairS-TO. It seems that the issue was caused in the LongPhase haplotagging process, but we cannot be certain due to the lack of complete running log. Could you please provide your complete running log of run_clairs_to.log file, and we will check the issue for you further.

Lei

Answer 2 · 2024-05-23T07:38:37.000Z

Hi @JasonCLEI thank you for getting back to me. please find the attached log file
Uploading run_clairs_to.log…

Answer 3 · 2024-05-23T08:53:30.000Z

Hi, @DIPLOMICS-SA sorry for not seeing the attached log file. Could you please upload it again?

Answer 4 · 2024-05-23T09:33:56.000Z

run_clairs_to.log

Hopefully this works @JasonCLEI

Answer 5 · 2024-05-23T09:59:20.000Z

Hi, @DIPLOMICS-SA,

We have checked your complete running log and found that you are not using the latest image of ClairS-TO, which caused the issue above. You are suggested to re-pull the image and rerun the program with your own data with the latest release of ClairS-TO, and the issue may disappear. Let us know if there are any issues after that. Thanks a lot again for your interest on ClairS-TO.

Lei

Answer 6 · 2024-05-23T16:18:58.000Z

Hi @JasonCLEI so I tried to re install the tool and I still get the same error?

Answer 7 · 2024-05-24T04:37:57.000Z

Hi @DIPLOMICS-SA have you tried to delete the original clairs-to_latest.sif and then re-pull the latest image of ClairS-TO? If you have done so and still got the error, could you kindly provide your latest running log of run_clairs_to.log file?

Answer 8 · 2024-05-27T12:56:57.000Z

Hi @JasonCLEI yes I have tried deleting and reinstalling.

Answer 9 · 2024-05-28T04:09:32.000Z

Hi @DIPLOMICS-SA have you solved this problem at the moment? If you have done so and still got the error, could you kindly provide your latest running log of run_clairs_to.log file?