Jin Khoo
04/10/2025, 4:01 PMRun nextflow run ${GITHUB_WORKSPACE} -profile test,docker docker --outdir ./results
N E X T F L O W ~ version 25.02.3-edge
Launching `/home/runner/work/methylong/methylong/main.nf` [disturbed_khorana] DSL2 - revision: cccd09db65
Downloading plugin nf-schema@2.1.1
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`._,._,'
nf-core/methylong 1.0.0
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Input/output options
input : <https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/methylong/test_data/test_samplesheet.csv>
outdir : ./results
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Core Nextflow options
runName : disturbed_khorana
containerEngine : docker
launchDir : /home/runner/work/methylong/methylong
workDir : /home/runner/work/methylong/methylong/work
projectDir : /home/runner/work/methylong/methylong
userName : runner
profile : test,docker
configFiles :
!! Only displaying parameters that differ from the pipeline defaults !!
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* The nf-core framework
<https://doi.org/10.1038/s41587-020-0439-x>
* Software dependencies
<https://github.com/nf-core/methylong/blob/master/CITATIONS.md>
WARN: nf-core pipelines do not accept positional arguments. The positional argument `docker` has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
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.
]
[da/36deee] Submitted process > NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP (Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz)
[a3/f441fe] Submitted process > NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP (Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz)
ERROR ~ Error executing process > 'NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP (Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz)'
Caused by:
Process `NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP (Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz)` terminated with an error exit status (126)
Command executed:
# Not calling gunzip itself because it creates files
# with the original group ownership rather than the
# default one for that user / the work directory
gzip \
-cd \
\
Col-CEN_v1.2.Chr1_5MB-7MB.fasta.gz \
> Col-CEN_v1.2.Chr1_5MB-7MB.fasta
cat <<-END_VERSIONS > versions.yml
"NFCORE_METHYLONG:METHYLONG:FASTQ_UNZIP:GUNZIP":
gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
END_VERSIONS
Command exit status:
126
Command output:
(empty)
Command error:
9f0d519e5362: Pulling fs layer
2fc3b27fe229: Pulling fs layer
4f4fb700ef54: Waiting
17dc7ea432cc: Waiting
92dc97a3ef36: Waiting
403f74b0f85e: Waiting
bb36d6c3110d: Waiting
10b8c00c10a5: Waiting
030a47592a0a: Waiting
0ea1a16bbe82: Waiting
9f0d519e5362: Waiting
2fc3b27fe229: Waiting
dec6b097362e: Verifying Checksum
dec6b097362e: Download complete
f88da01cff0b: Verifying Checksum
f88da01cff0b: Download complete
dafa2b0c44d2: Verifying Checksum
dafa2b0c44d2: Download complete
4f4fb700ef54: Download complete
92dc97a3ef36: Download complete
403f74b0f85e: Verifying Checksum
403f74b0f85e: Download complete
10b8c00c10a5: Verifying Checksum
10b8c00c10a5: Download complete
17dc7ea432cc: Download complete
bb36d6c3110d: Verifying Checksum
bb36d6c3110d: Download complete
0ea1a16bbe82: Verifying Checksum
0ea1a16bbe82: Download complete
dafa2b0c44d2: Pull complete
030a47592a0a: Download complete
9f0d519e5362: Verifying Checksum
9f0d519e5362: Download complete
2fc3b27fe229: Verifying Checksum
2fc3b27fe229: Download complete
dec6b097362e: Pull complete
f88da01cff0b: Pull complete
4f4fb700ef54: Pull complete
92dc97a3ef36: Pull complete
403f74b0f85e: Pull complete
10b8c00c10a5: Pull complete
17dc7ea432cc: Pull complete
bb36d6c3110d: Pull complete
0ea1a16bbe82: Pull complete
030a47592a0a: Pull complete
9f0d519e5362: Pull complete
2fc3b27fe229: Pull complete
Digest: sha256:63c2c6b22e83b2f656e88fbb1553e595da4e9e58794e3bfcb98b20b3837f328a
Status: Downloaded newer image for <http://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8|community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8>
/bin/bash: line 10: .command.run: Permission denied
Work dir:
/home/runner/work/methylong/methylong/work/a3/f441fe3ce24371e2940f1e402a266b
Container:
<http://community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8|community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8>
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
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>
-- Check '.nextflow.log' file for details
-[nf-core/methylong] Pipeline completed with errors-
Error: Process completed with exit code 1.