nf-core cannot run

[kaokaoshuangyu]

Description of the bug

ERROR ~ Error executing process > 'NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP (r-ERR044595)'

Caused by:
Process NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP (r-ERR044595) terminated with an error exit status (126)

Command executed:

[ ! -f r-ERR044595.fastq.gz ] && ln -sf r-ERR044595.fastq.gz

fastp
--in1 r-ERR044595.fastq.gz
--out1 r-ERR044595.fastp.fastq.gz
--thread 6
--json r-ERR044595.fastp.json
--html r-ERR044595.fastp.html



2> >(tee r-ERR044595.fastp.log >&2)

cat <<-END_VERSIONS > versions.yml
"NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP":
fastp: $(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS

Command exit status:
126

Command output:
(empty)

Command error:
.command.run: line 305: .command.run: Permission denied

Work dir:
/mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/work/e7/f74016d6d24a9bb47b3144d84f450f

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

I found that all the generated .command.sh files are non-executable. Why is that?
There is no problem with my file system, as it is /dev/sda on /mnt/00.Mount, type ext4 (rw,relatime,stripe=64).

-rw-rw-r-- 1 wangmei docker 11K Sep 30 12:28 /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/work/e7/f74016d6d24a9bb47b3144d84f450f/.command.run

Command used and terminal output

Relevant files

No response

System information

No response

[d4straub]

Hi there,
with so little information there is no way your problem can be solved. Could you please provide basic information as was requested already when you opened the issue:

• command that you used to start the pipeline
• pipeline version
• any config you might have used
• nextflow version

[kaokaoshuangyu]

Thank you for your reply. Here are the specific version details, error messages, and log information.

Version
nf-core/bacass 2.4.0

nextflow -v
nextflow version 25.04.7.5955

nextflow run bacass -profile docker --input samplesheet.tsv --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz" --skip_kmerfinder --outdir bacass_results

cat samplesheet.tsv
ID fastq_1 fastq_2
ERR064912 /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/bacass_test/ERR064912_1M_1.fastq.gz /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/bacass_test/ERR064912_1M_2.fastq.gz
r-ERR044595 /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/bacass_test/r-ERR044595_1M_1.fastq.gz /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/bacass_test/r-ERR044595_1M_2.fastq.gz

Error message

Input/output options
input : samplesheet.tsv
outdir : bacass_results

Contamination Screening
kraken2db : https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz

Assembly parameters
canu_mode : -nanopore

Annotation
dfast_config : /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/bacass/assets/test_config_dfast.py

Skipping Options
skip_kmerfinder: true

Core Nextflow options
runName : ecstatic_gautier
containerEngine: docker
launchDir : /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928
workDir : /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/work
projectDir : /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/bacass
userName : wangmei
profile : docker
configFiles :

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------* The pipeline
https://doi.org/10.5281/zenodo.2669428

• The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

• Software dependencies
  https://github.com/nf-core/bacass/blob/master/CITATIONS.md

WARN: Found the following unidentified headers in /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/samplesheet.tsv:
- fastq_1
- fastq_2
executor > local (8)
executor > local (8)
[- ] process > NFCORE_BACASS:BACASS:CAT_FASTQ -
[24/9ac007] process > NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (r-ERR044595) [ 0%] 0 of 2 ✘
[9e/70ada2] process > NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP (ERR064912) [ 0%] 0 of 2 ✘
[- ] process > NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM -
[7b/3ac091] process > NFCORE_BACASS:BACASS:NANOPLOT (r-ERR044595) [ 0%] 0 of 2 ✘
[4e/5de584] process > NFCORE_BACASS:BACASS:PYCOQC (1) [ 0%] 0 of 2 ✘
[- ] process > NFCORE_BACASS:BACASS:UNICYCLER -
[- ] process > NFCORE_BACASS:BACASS:KRAKEN2_DB_PREPARATION -
[- ] process > NFCORE_BACASS:BACASS:KRAKEN2 -
[- ] process > NFCORE_BACASS:BACASS:KRAKEN2_LONG -
[- ] process > NFCORE_BACASS:BACASS:QUAST -
[- ] process > NFCORE_BACASS:BACASS:GUNZIP -
[- ] process > NFCORE_BACASS:BACASS:PROKKA -
[- ] process > NFCORE_BACASS:BACASS:MULTIQC_CUSTOM -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/bacass] Pipeline completed with errors-
WARN: Directive process.shell cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
]
ERROR ~ Error executing process > 'NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (ERR064912)'

Caused by:
Process NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (ERR064912) terminated with an error exit status (126)

Command executed:

printf "%s %s\n" | while read old_name new_name; do
[ -f "${new_name}" ] || ln -s $old_name $new_name
done

fastqc
--quiet
--threads 6 \

cat <<-END_VERSIONS > versions.yml
"NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW":
fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
END_VERSIONS

Command exit status:
126

Command output:
(empty)

Command error:
/bin/bash: line 10: .command.run: Permission denied

Work dir:
/mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/work/e6/be01ec492083ece73a1bd9e991c474

Container:
quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- 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

in the .nextflow.log

Sep-30 14:21:48.132 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-30 14:21:48.135 [Task submitter] INFO nextflow.Session - [8e/3c7c25] Submitted process > NFCORE_BACASS:BACASS:PYCOQC (2)
Sep-30 14:21:48.153 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-30 14:21:48.154 [Task submitter] INFO nextflow.Session - [b2/410654] Submitted process > NFCORE_BACASS:BACASS:NANOPLOT (ERR064912)
Sep-30 14:21:48.167 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-30 14:21:48.168 [Task submitter] INFO nextflow.Session - [24/9ac007] Submitted process > NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (r-ERR044595)
Sep-30 14:21:48.177 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-30 14:21:48.178 [Task submitter] INFO nextflow.Session - [4e/5de584] Submitted process > NFCORE_BACASS:BACASS:PYCOQC (1)
Sep-30 14:21:48.188 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-30 14:21:48.188 [Task submitter] INFO nextflow.Session - [7b/3ac091] Submitted process > NFCORE_BACASS:BACASS:NANOPLOT (r-ERR044595)
Sep-30 14:21:48.196 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-30 14:21:48.197 [Task submitter] INFO nextflow.Session - [ff/5f1e4c] Submitted process > NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP (r-ERR044595)
Sep-30 14:21:48.204 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-30 14:21:48.205 [Task submitter] INFO nextflow.Session - [9e/70ada2] Submitted process > NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP (ERR064912)
Sep-30 14:21:48.211 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Sep-30 14:21:48.211 [Task submitter] INFO nextflow.Session - [e6/be01ec] Submitted process > NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (ERR064912)
Sep-30 14:21:48.690 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz to work dir: /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/work/stage-49c3426a-7a59-40e8-9c73-bf500497e906/fd/d32e66cfb3f5d69dd3e4a6394cdbba/k2_standard_8gb_20210517.tar.gz
Sep-30 14:21:48.884 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (ERR064912); status: COMPLETED; exit: 126; error: -; workDir: /mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/work/e6/be01ec492083ece73a1bd9e991c474]
Sep-30 14:21:48.885 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=384; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Sep-30 14:21:48.895 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (ERR064912); work-dir=/mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/work/e6/be01ec492083ece73a1bd9e991c474
error [nextflow.exception.ProcessFailedException]: Process NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (ERR064912) terminated with an error exit status (126)
Sep-30 14:21:48.911 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (ERR064912)'

Caused by:
Process NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (ERR064912) terminated with an error exit status (126)

Command executed:

printf "%s %s\n" | while read old_name new_name; do
[ -f "${new_name}" ] || ln -s $old_name $new_name
done

fastqc
--quiet
--threads 6 \

cat <<-END_VERSIONS > versions.yml
"NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW":
fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
END_VERSIONS

Command exit status:
126

Command output:
(empty)

Command error:
/bin/bash: line 10: .command.run: Permission denied

Work dir:
/mnt/00.Mount/001.wangmei/020.naopore_CompletionMap_20250928/work/e6/be01ec492083ece73a1bd9e991c474

Container:
quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

[d4straub]

Thanks for the info. Could you please check out the large red warning message shown at the top of https://nf-co.re/bacass/2.4.0? It leads you to https://nf-co.re/advisories/process-shell-configuration that elaborates that the nextflow version you use is not compatible with the pipeline version.
The easiest solution is to use a compaible nextflow version. To do so prepend NXF_VER=24.10.6 to your command, e.g. NXF_VER=24.10.6 nextflow run ....