These are chat archives for nextflow-io/nextflow

31st
Dec 2018
Max Hargreaves
@DiDeoxy
Dec 31 2018 15:09
I am having an issue where nextflow is able to create the temp file in the workDir but then I get this error message /bin/bash: line 0: cd: /scratch/maxh/RNAseq/temp/a2/925b5b228449d8654531763ef71640: No such file or directory
i can navigate to the indicated folder and run bash .command.run and get the same error
Max Hargreaves
@DiDeoxy
Dec 31 2018 15:15
i am using this with singularity on a CentOS HPC which I am just a regular user on
does it have something to do with accessing the data in the container?
set autoMounts to true and it is working now!
Max Hargreaves
@DiDeoxy
Dec 31 2018 15:37
my HPC uses the SLURM scheduler, i can view the allocations I've recently used with sacct but I don't see those created by nextflow, how come? Am I missing something and nextflow isn't using allocations but running on my login node or interactive session?
Max Hargreaves
@DiDeoxy
Dec 31 2018 16:24
lol, had a spelling error, its executor not executer