Missing file after bam sort (SAW 8.2)

[roanvanscheppingen]

This error happened twice at the same point with the same chip. Sequences align and bam sorting starts.
Other chips are getting past this point.

config.yaml

2025-10-18T031657.115351.snakemake.log

FP270009158_L01_13_1.Aligned.sortedByCoord.out.bam is 616GB
Then, for the next step, the snakemake pipeline seems to be looking for a file that did not generate.

Select jobs to execute...
Waiting at most 5 seconds for missing files.
MissingOutputException in rule map in file /exports/nieromics-hpc/roan/saw82/saw-8.2.0/config/base.smk, line 389:
Job 0 completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/exports/nierziekten-hpc/resultsRvS/Y01422L1/Y01422L1_A/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.Log.final.out
Removing output files of failed job map since they might be corrupted:
/exports/nierziekten-hpc/resultsRvS/Y01422L1/Y01422L1_A/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.cid_mapping_reads_counts.txt, /exports/nierziekten-hpc/resultsRvS/Y01422L1/Y01422L1_A/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.cid_mapping.stat, /exports/nierziekten-hpc/resultsRvS/Y01422L1/Y01422L1_A/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.rna_filter.stat
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /exports/nieromics-hpc/.snakemake_rhvanscheppingen/.snakemake/log/2025-10-18T031657.115351.snakemake.log

[Jinghao-Chen]

Hi, could you provide these files if they exist?

STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.run.log
STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.Log.out
STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.log
STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.Log.final.out
STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.cid_mapping.stat
STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/FP270009158_L01_13_1.rna_filter.stat

pipeline-logs/log
pipeline-logs/stereo_log

[roanvanscheppingen]

I've send the available logs to your email.

The 4th till 6th file are not available as the pipeline removes them when throwing this error.

[rhvanscheppingen@res-hpc-lo02 ALIGNMENT]$ ls
adt_fq1.list FP270009158_L01_13_1.Log.progress.out log_mask performance_mask Y01422L1_cid_pid_mid_reads.tsv Y01422L1_valid_cid_reads.tsv
adt_fq2.list FP270009158_L01_13_1.run.log log_proteinMap performance_proteinMap Y01422L1_map.stat
FP270009158_L01_13_1.log FP270009158_L01_13_1.SJ.out.tab performance_generate_cidcount Y01422L1.barcodeToPos.h5 Y01422L1.protein.raw.gef
FP270009158_L01_13_1.Log.out log_generate_cidcount performance_map_FP270009158_L01_13_1 Y01422L1.CIDCount Y01422L1.protein.raw.gem

[roanvanscheppingen]

Issue also happened with another chip (Y00913A3) and threw the same error.