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vib-singlecell-nf / vsn-pipelines

A repository of pipelines for single-cell data in Nextflow DSL2
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FATAL: container creation failed: mount #373

Open gianfilippo opened 2 years ago

gianfilippo commented 2 years ago

Hi,

I am trying to run the harmony_scenic pipeline on my data

I am setting nextflow to 21.04.3 (to avoid the include error. I already reported)

I first generate the config file. There, I edit the dataPATH and then run as described in the tutorial NXF_VER=21.04.3 nextflow -C $runDIR/harmony_scenic.config run vib-singlecell-nf/vsn-pipelines -entry harmony_scenic

I end-up with the following error FATAL: container creation failed: mount

The logfile (the relevant part of it) shows Process harmony_scenic:SCENIC_APPEND:scenic:ARBORETO_WITH_MULTIPROCESSING (1) terminated with an error exit status (255) Command error: FATAL: container creation failed: mount /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources->/ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources error: while mounting /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources: mount source /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources doesn't exist Process harmony_scenic:SCENIC_APPEND:scenic:ARBORETO_WITH_MULTIPROCESSING (1) terminated with an error exit status (255) Command error: FATAL: container creation failed: mount /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources->/ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources error: while mounting /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources: mount source /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources doesn't exist

Can you please help ?

Thanks

Jay-Leung commented 2 years ago

Hello,

I am facing this issue as well when running the 10k PBMC multirun SCENIC..(https://vsn-pipelines-examples.readthedocs.io/en/latest/PBMC10k_multiruns.html)

Regards, Jay

GreyRockIQ commented 2 years ago

Hi @gianfilippo @Jay-Leung I am facing same issue..

Command error: WARNING: skipping mount of /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources: stat /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources: no such file or directory FATAL: container creation failed: mount /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources->/ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources error: while mounting /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources: mount source /ddn1/vol1/staging/leuven/stg_00002/lcb/cflerin/resources doesn't exist

could you able to get it solved? Thanks GreyRock