fetchngs
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Published
20 hours ago •
nf-core
nf-core
Test run for fetchngs failed
Description of the bug
Test run on the minimal dataset failed
Command used and terminal output
Command
nextflow run nf-core/fetchngs -profile test docker
Output
Core Nextflow options
revision : master
runName : nauseous_yalow
launchDir : /home/dalin/nf_core
workDir : /home/dalin/nf_core/work
projectDir : /home/dalin/.nextflow/assets/nf-core/fetchngs
userName : dalin
profile : test
configFiles : /home/dalin/.nextflow/assets/nf-core/fetchngs/nextflow.config
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6 GB
max_time : 6h
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/fetchngs for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.5070524
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
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executor > local (28)
[91/de6dcf] process > NFCORE_FETCHNGS:SRA:SRA_IDS... [ 70%] 7 of 10
[38/346b04] process > NFCORE_FETCHNGS:SRA:SRA_RUN... [100%] 7 of 7
[1b/9ccda1] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [ 0%] 0 of 4
[6b/3f1324] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [ 62%] 5 of 8, failed: 5..
[- ] process > NFCORE_FETCHNGS:SRA:SRA_FAS... -
[- ] process > NFCORE_FETCHNGS:SRA:SRA_TO_... -
[- ] process > NFCORE_FETCHNGS:SRA:SRA_MER... -
[- ] process > NFCORE_FETCHNGS:SRA:MULTIQC... -
[- ] process > NFCORE_FETCHNGS:SRA:CUSTOM_... -
executor > local (30)
[91/de6dcf] process > NFCORE_FETCHNGS:SRA:SRA_IDS... [ 70%] 7 of 10
[38/346b04] process > NFCORE_FETCHNGS:SRA:SRA_RUN... [100%] 7 of 7
[1b/9ccda1] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [ 0%] 0 of 4
[bd/9bd173] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [ 66%] 6 of 9, failed: 6..
[- ] process > NFCORE_FETCHNGS:SRA:SRA_FAS... -
[- ] process > NFCORE_FETCHNGS:SRA:SRA_TO_... -
[- ] process > NFCORE_FETCHNGS:SRA:SRA_MER... -
[- ] process > NFCORE_FETCHNGS:SRA:MULTIQC... -
[- ] process > NFCORE_FETCHNGS:SRA:CUSTOM_... -
[68/a3b0c4] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (1)
[2d/b2d3a5] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (1)
[9a/02508e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (1)
[29/3ce30d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (2)
[c1/c5b350] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (2)
[b3/0c2b7d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (2)
Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)'
Caused by:
Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1)
Command executed:
eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
if [[ ! -f "${NCBI_SETTINGS}" ]]; then
mkdir -p "$(dirname "${NCBI_SETTINGS}")"
printf '/LIBS/GUID = "b6aa337c-d642-4239-a4ab-552792ae78b2"\n/libs/cloud/report_instance_identity = "true"\n' > "${NCBI_SETTINGS}"
fi
retry_with_backoff.sh prefetch \
\
--progress \
SRR14709033
vdb-validate SRR14709033
cat <<-END_VERSIONS > versions.yml
"NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH":
sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
.command.sh: line 2: vdb-config: command not found
.command.sh: line 3: NCBI_SETTINGS: unbound variable
executor > local (30)
[e7/f6dad9] process > NFCORE_FETCHNGS:SRA:SRA_IDS... [100%] 7 of 7
[38/346b04] process > NFCORE_FETCHNGS:SRA:SRA_RUN... [100%] 7 of 7
[- ] process > NFCORE_FETCHNGS:SRA:SRA_FAS... -
[bd/9bd173] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [100%] 9 of 9, failed: 9..
[- ] process > NFCORE_FETCHNGS:SRA:SRA_FAS... -
[- ] process > NFCORE_FETCHNGS:SRA:SRA_TO_... -
[- ] process > NFCORE_FETCHNGS:SRA:SRA_MER... -
[- ] process > NFCORE_FETCHNGS:SRA:MULTIQC... -
[- ] process > NFCORE_FETCHNGS:SRA:CUSTOM_... -
[68/a3b0c4] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (1)
[2d/b2d3a5] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (1)
[9a/02508e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (1)
[29/3ce30d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (2)
[c1/c5b350] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (2)
[b3/0c2b7d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (2)
Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)'
Caused by:
Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1)
Command executed:
eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
if [[ ! -f "${NCBI_SETTINGS}" ]]; then
mkdir -p "$(dirname "${NCBI_SETTINGS}")"
printf '/LIBS/GUID = "b6aa337c-d642-4239-a4ab-552792ae78b2"\n/libs/cloud/report_instance_identity = "true"\n' > "${NCBI_SETTINGS}"
fi
retry_with_backoff.sh prefetch \
\
--progress \
SRR14709033
vdb-validate SRR14709033
cat <<-END_VERSIONS > versions.yml
"NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH":
sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
.command.sh: line 2: vdb-config: command not found
.command.sh: line 3: NCBI_SETTINGS: unbound variable
Work dir:
/home/dalin/nf_core/work/6b/3f1324636644f4b5afbc809ce41f5f
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Relevant files
No response
System information
nextflow: v22.04 Hardware: Desktop Container: Docker OS: Ubuntu 22.04 nf-core/fetch ngs: v1.5
You need to separate profiles by comma without any spaces:
nextflow run nf-core/fetchngs -profile test,docker
Assuming the fix above resolved the issue. In the future it may be easier to join the #fetchngs channel on nf-core Slack to get real-time help. You can join via the link below: https://nf-co.re/join
