/bin/bash: .command.sh: No such file or directory

[Lcornet]

Bug report

When I activate the singularity container, nextflow crash and tells me that .command.sh don't exist
This appears after an update to singularity 3.6.0

Expected behavior and actual behavior

nextflow ORPER.nf --refgroup=Nostocales --outgroup=Gloeobacterales --ribodb=/data1/ORPER/ribo/ --companion=ORPER/ORPER-companion.py --SSU=Nostocales-silva.fasta --cdhit=no

This commands and pipeline work well. but is I activate the container with :

process.container = '/data1/ORPER/ORPER.sif'
singularity.enabled = true

it crash

Steps to reproduce the problem

but when I activate the container with :

process.container = '/data1/ORPER/ORPER.sif'
singularity.enabled = true

it crash

Program output

ommand exit status:
1

Command output:
(empty)

Command error:
/bin/bash: line 0: cd: /data1/ORPER/work/17/5e87858643dcc828837406eecff1b8: No such file or directory
/bin/bash: .command.sh: No such file or directory

Work dir:
/data1/ORPER/work/17/5e87858643dcc828837406eecff1b8

Environment

• Nextflow version: 20.07
• Java version: openjdk 11.0.8 2020-07-14
• Operating system: Linux 18
• Bash version: GNU bash, version 4.4.20(1)-release (x86_64-pc-linux-gnu)

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[sckinta]

Is this issue solved? I used most updated nextflow (version 21.10.6.5660), but still have the same error. my singularity version is 3.7.0

[Lcornet]

I finally found a solution for our cluster. The config file (nextflow.config) should look like this:

process.container = 'PATH to your container'
singularity.enabled = true
singularity.cacheDir = "$PWD"
singularity.autoMounts = false
singularity.runOptions = '-B -B '

the two links can be identified with pwd and readlink -f .

Hope it helps

[james-guevara]

When using a singularity container, I have to specify a bind path in the nextflow.config like so:

singularity {
    enabled = true
    runOptions = "--bind $PWD"
}

where $PWD is the folder with my main.nf file, nextflow.config file, and work folder.