test run have error

[YanyanLiuBio]

Description of the bug

running the test profile has this erorr:
ERROR ~ Error executing process > 'NFCORE_PHASEIMPUTE:CHRCHECK_INPUT:BAM_CHR_EXTRACT (NA12878)'

Caused by:
Process NFCORE_PHASEIMPUTE:CHRCHECK_INPUT:BAM_CHR_EXTRACT (NA12878) terminated with an error exit status (126)

Command executed:

samtools
head
NA12878.s.1x.bam|
grep '^@sq' | cut -d$' ' -f2 | sed -e 's/^SN://g'
> NA12878.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_PHASEIMPUTE:CHRCHECK_INPUT:BAM_CHR_EXTRACT":
samtools: $( samtools --version |& sed '1!d; s/^.*samtools //' )
grep: $( grep --version |& grep -o -E '[0-9]+.[0-9]+' )
END_VERSIONS

Command exit status:
126

Command output:
(empty)

Command error:
.command.run: line 300: .command.run: Permission denied

Work dir:
/home/ec2-user/temp_test/work/7e/ba614b2300480910dfd443c6a577d6

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

Command used and terminal output

Relevant files

No response

System information

No response

[LouisLeNezet]

Hi!
This error doesn’t seems to come from the pipeline itself, but from the execution permissions of your work directory /home/ec2-user/temp_test/work.

Exit code 126 means the command was found but could not be executed (Bash error codes reference). In your case, .command.run exists but isn’t allowed to run — this usually happens when the filesystem is mounted with the noexec option.

You can check with:

mount | grep temp_test

If you see noexec, please rerun with a different work directory, e.g.:

nextflow run nf-core/phaseimpute -profile test -work-dir $HOME/nf-work

[YanyanLiuBio]

Thanks! I asked in the slack channel, Phil Ewels replied. He said it is due to the incompatibility of the pipeline to the nextflow version, which is the same or higher than 25.04. He also mentioned most nf-core pipelines have fixed this issue. I used the nextflow version of 22, it works fine.

…

On Thu, Aug 28, 2025 at 3:05 AM Louis Le Nézet ***@***.***> wrote: *LouisLeNezet* left a comment (nf-core/phaseimpute#206) <#206 (comment)> Hi! This error doesn’t seems to come from the pipeline itself, but from the execution permissions of your work directory /home/ec2-user/temp_test/work . Exit code 126 means the command was found but could not be executed (Bash error codes reference <https://www.gnu.org/software/bash/manual/html_node/Exit-Status.html>). In your case, .command.run exists but isn’t allowed to run — this usually happens when the filesystem is mounted with the noexec option. You can check with: mount | grep temp_test If you see noexec, please rerun with a different work directory, e.g.: nextflow run nf-core/phaseimpute -profile test -work-dir $HOME/nf-work — Reply to this email directly, view it on GitHub <#206 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADKDLQINIUZPZBWWHMT5QMD3P2S5FAVCNFSM6AAAAACE4Q6HLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTEMZSGIYTENJYHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>