IGS: 'autofs' change file paths

[Matthew-A-epi]

I tried to retest the pipeline today and now am getting errors involving the automounter (autofs). I made no adjust for the automounter last week, but it seems to be an issue now.

Even when I attempt to use the /autofs/ paths, the pipeline/server still finds a a way to use /local/ paths and when I try to use /local/ paths, the pipeline/server still figures out a way to use /autofs/ paths. I'm hoping you have a sly trick that will solve this.

I tried modifying environmental variables to the autofs paths instead of local such as:

Link the automounter path for the ref directory:

mkdir -p ref
ln -s /autofs/projects-t2/CVD/Takala-Harrison/Cambodia_Bing/ref/* ref/

export WORK_DIR="/autofs/projects-t2/CVD/TEMPWORK/temp_madams/malawi/snp_call_nf/work"

Command to run pipeline:

nextflow run /autofs/projects-t2/CVD/TEMPWORK/temp_madams/malawi/snp_call_nf/main.nf -profile slurm -work-dir $WORK_DIR

But bowtie2 keeps giving these same errors (and there will likely be more further in the pipeline):

Nov-04 18:02:00.449 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 289134; id: 2; name: BOWTIE2_ALIGN_TO_HOST (Sample02~r1); status: COMPLETED; exit: 0; error: -; workDir: /autofs/projects-t2/CVD/TEMPWORK/temp_madams/malawi/snp_call_nf/work/7b/228c7ef8265cdb7cc12adaae8f6c44 started: 1730761260501; exited: 2024-11-04T23:01:55.246117Z; ]
Nov-04 18:02:00.547 [Actor Thread 64] DEBUG nextflow.util.CacheHelper - Unable to get file attributes file: /autofs/projects-t2/CVD/TEMPWORK/temp_madams/malawi/snp_call_nf/ref/host/hg38 -- Cause: java.nio.file.NoSuchFileException: /autofs/projects-t2/CVD/TEMPWORK/temp_madams/malawi/snp_call_nf/ref/host/hg38

Thanks!

[bguo068]

Hi @Matthew-A-epi , Have you tried to replace '/autofs' with '/local'?