My sarek run seems to be unfinished but I cannot tell why. There is no error anywhere and the .nextlow.log looks like it just stopped.
I run haplotypecaller and snpeff and I can see they have run for one 5 of my samples. ( The same 5 run for both).
Without error how can I see what caused it to stop?
2024-08-07 12:49:51 - festering_kare - The last jobs to be submitted seem to have completed successfully, but not all that were in the queue were submitted before it stopped working.
Hi @Dimitrios_Pediotidis! Welcome to the community forum 
Can you share your .nextflow.log? Also, where are you running your pipeline? Laptop running macOS? HPC with Slurm? AWS? Windows Desktop? Give us as much detail as possible.
Hi @mribeirodantas, thank you.
I have since then resubmitted the workflow as I identified missing files from continuous reruns using -resume that sarek identified as completed. This explains why some files are completed ( partially at least).
That does not explain the stop. I am using HPC with slurm. Here are the last part of the log:
Aug-08 10:49:14.927 [Task submitter] INFO nextflow.Session - [d4/b6c1f7] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (9)
Aug-08 10:49:17.748 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor slurm > tasks in the submission queue: 174 – tasks to be submitted are shown below
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Aug-08 10:59:13.187 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (9) > jobId: 42759101; workDir: /faststorage/project/Daan/work/0c/1678eeda17ccda68423d8fc38a0e4f
Aug-08 10:59:13.224 [Task submitter] INFO nextflow.Session - [0c/1678ee] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (9)
And this is the last entry. There is no error which has led me to believe that something caused the screen session I used to launch to end.
If you also think this is the most plausible cause we can delete this.