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MissingOutputException error in rnaVariantCalling #640

@helenine

Description

@helenine

Hello, I'm using rnaVariantCalling module in my own dataset (6 samples, each has 2 replicas). But I got the following error:

Finished job 28.
1 of 20 steps (5%) done
Waiting at most 60 seconds for missing files.
MissingOutputException in rule bqsr in file /home/arda/rnaseq/DROP_project/config/Scripts/rnaVariantCalling/pipeline/Snakefile, line 446:
Job 19 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/mnt/active2/rnaseq/drop_family1/processed_data/rnaVariantCalling/out/bqsr/3620-B_recal.table
Waiting at most 60 seconds for missing files.
MissingOutputException in rule bqsr in file /home/arda/rnaseq/DROP_project/config/Scripts/rnaVariantCalling/pipeline/Snakefile, line 446:
Job 27 completed successfully, but some output files are missing. Missing files after 60 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/mnt/active2/rnaseq/drop_family1/processed_data/rnaVariantCalling/out/bqsr/3620-A_recal.table
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-09-22T123226.419881.snakemake.log

What is the reason of this, and how can I fix it?

I also added config.yaml and full log file;

config.yaml
2025-09-22T123226.419881.snakemake.log

Thank you!

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