Centrifuge error : (ERR): mkfifo(/tmp/72.inpipe1) failed. #422
Description
Description of the bug
I downloaded the pre-built centrifuge database from https://benlangmead.github.io/aws-indexes/k2 (the full link is https://genome-idx.s3.amazonaws.com/centrifuge/nt_2018_3_3.tar.gz) to use with taxprofiler. It does not run as expected. I first brought this up in slack.
This is my database file (the listed kraken2 databases worked fine):
tool,db_name,db_params,db_path
kraken2,nt,,../data/k2_nt_20230502.tar.gz
kraken2,viral,,../data/k2_viral_20231009.tar.gz
centrifuge,nt_2018,,../data/nt_2018_3_3.tar.gz
This is the error message:
Workflow execution completed unsuccessfully
The exit status of the task that caused the workflow execution to fail was: 17
Error executing process > 'NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:CENTRIFUGE_CENTRIFUGE (nt_2018|B002f_pe)'
Caused by:
Process `NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:CENTRIFUGE_CENTRIFUGE (nt_2018|B002f_pe)` terminated with an error exit status (17)
Command executed:
## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
db_name=`find -L nt_2018_3_3 -name "*.1.cf" -not -name "._*" | sed 's/\.1.cf$//'`
centrifuge \
-x $db_name \
-p 12 \
-1 B002f_VH00770.unmapped_1.fastq.gz -2 B002f_VH00770.unmapped_2.fastq.gz \
--report-file B002f_pe_VH00770_nt_2018.centrifuge.report.txt \
-S B002f_pe_VH00770_nt_2018.centrifuge.results.txt \
\
\
cat <<-END_VERSIONS > versions.yml
"NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:CENTRIFUGE_CENTRIFUGE":
centrifuge: $( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
END_VERSIONS
Command exit status:
17
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
(ERR): mkfifo(/tmp/72.inpipe1) failed.
Exiting now ...
Work dir:
/Volumes/IDGenomics_NAS/Bioinformatics/eriny/mosquito/2023-12-01/work/11/33708dd319d5e790a7d5b44e106865
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Command used and terminal output
nextflow run nf-core/taxprofiler \
-profile singularity \
--input sample_sheet.csv \
--databases database.txt \
--outdir taxprofiler \
--run_kraken2 \
--run_centrifuge \
-with-tower \
-resume \
--hostremoval_reference reference.fasta \
--save_hostremoval_bam true \
--perform_shortread_hostremoval \
--save_hostremoval_unmapped true \
--perform_shortread_qc \
-c time.configN E X T F L O W ~ version 23.10.0
Launching `https://github.com/nf-core/taxprofiler` [desperate_cuvier] DSL2 - revision: 3d4eda2dbb [master]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/taxprofiler v1.1.2-g3d4eda2
------------------------------------------------------
Core Nextflow options
revision : master
runName : desperate_cuvier
containerEngine : singularity
launchDir : /Volumes/IDGenomics_NAS/Bioinformatics/eriny/mosquito/2023-12-01
workDir : /Volumes/IDGenomics_NAS/Bioinformatics/eriny/mosquito/2023-12-01/work
projectDir : /home/eriny/.nextflow/assets/nf-core/taxprofiler
userName : eriny
profile : singularity
configFiles :
Input/output options
input : sample_sheet.csv
databases : database_all.txt
outdir : taxprofiler
Preprocessing short-read QC options
perform_shortread_qc : true
Preprocessing host removal options
perform_shortread_hostremoval: true
hostremoval_reference : reference.fasta
save_hostremoval_bam : true
save_hostremoval_unmapped : true
Profiling options
run_centrifuge : true
run_kraken2 : true
ganon_report_rank : default
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/taxprofiler for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.7728364
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/taxprofiler/blob/master/CITATIONS.md
Monitor the execution with Nextflow Tower using this URL: https://tower.nf/user/erin-olde/watch/5y7UeijszzHmnN
executor > local (4)
[11/307bce] process > NFCORE_TAXPROFILER:TAXPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (sample_sheet.csv) [100%] 1 of 1, cached: 1 ✔
[8e/78ff0d] process > NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR (k2_nt_20230502.tar.gz) [100%] 3 of 3, cached: 3 ✔
[d7/b16a2d] process > NFCORE_TAXPROFILER:TAXPROFILER:FASTQC (B016g) [100%] 16 of 16, cached: 16 ✔
[- ] process > NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_PREPROCESSING:SHORTREAD_FASTP:FASTP_SINGLE -
[c8/a8b135] process > NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_PREPROCESSING:SHORTREAD_FASTP:FASTP_PAIRED (B013f) [100%] 16 of 16, cached: 16 ✔
[41/94fab5] process > NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_PREPROCESSING:FASTQC_PROCESSED (B013g) [100%] 16 of 16, cached: 16 ✔
[97/b9c3b6] process > NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_HOSTREMOVAL:BOWTIE2_BUILD (reference.fasta) [100%] 1 of 1, cached: 1 ✔
[47/54c4f2] process > NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_HOSTREMOVAL:BOWTIE2_ALIGN (B015g) [100%] 16 of 16, cached: 16 ✔
[6d/fc97f5] process > NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_HOSTREMOVAL:SAMTOOLS_INDEX (B016f) [100%] 16 of 16, cached: 16 ✔
[98/78ecba] process > NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_HOSTREMOVAL:SAMTOOLS_STATS (B021f) [ 93%] 15 of 16, cached: 15
[b0/29c8c0] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:KRAKEN2_KRAKEN2 (nt|kraken2|B023f_pe) [ 15%] 5 of 32, cached: 5
[60/1788d7] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:CENTRIFUGE_CENTRIFUGE (nt_2018|B013f_pe) [ 12%] 2 of 16, cached: 2
[- ] process > NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:CENTRIFUGE_KREPORT [ 0%] 0 of 2
[- ] process > NFCORE_TAXPROFILER:TAXPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_TAXPROFILER:TAXPROFILER:MULTIQC -
Relevant files
No response
System information
Nextflow version : 23.10.0 build 5889
Hardware : Local
Executor : local
Container engine: Singularity
OS : CentOS
Version of nf-core/taxprofiler : current