This is a great tool however I'm running into a hurdle on the final step - regarding the multiQC reporting step. It appears to not be finding the multiqc config file?
jovyan@rlmt278-scdownstream-0:~/osteomics/projects/scdownstream$ nextflow run /home/jovyan/osteomics/projects/scdownstream/scdownstream/ --input /home/jovyan/osteomics/projects/scdownstream/scdownstream/sample_sheet.csv --outdir ./results -c /cache-juicefs/nextflow-workspace/test/work/marcus_config.config --preprocess_only TRUE --ambient_removal soupx -resume
N E X T F L O W ~ version 24.04.4
Launching `/home/jovyan/osteomics/projects/scdownstream/scdownstream/main.nf` [happy_lichterman] DSL2 - revision: 456139e594
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nf-core/scdownstream 0.0.1dev
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Input/output options
input : /home/jovyan/osteomics/projects/scdownstream/scdownstream/sample_sheet.csv
outdir : ./results
Pipeline options
preprocess_only: true
ambient_removal: soupx
Core Nextflow options
runName : happy_lichterman
containerEngine: docker
launchDir : /home/jovyan/osteomics/projects/scdownstream
workDir : /cache-juicefs/nextflow-workspace/work
projectDir : /home/jovyan/osteomics/projects/scdownstream/scdownstream
userName : jovyan
profile : standard
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/scdownstream/blob/master/CITATIONS.md
WARN: The following invalid input values have been detected:
* --max_memory: 1200.GB
* --max_cpus: 14
* --max_time: 7.d
executor > k8s (4)
[- ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:SCANPY_READH5 -
[94/e0d742] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_READRDS (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[- ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_READCSV -
[a5/e012e5] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_UNIFY (SAMN14430801) [100%] 4 of 4, cached: 4 ✔
[2a/142145] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_UNFILTERED_SIZE (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[- ] NFC…SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND -
[- ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:EMPTY_DROPLET_REMOVAL:ADATA_BARCODES -
[d4/39273a] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_FILTERED_SIZE (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[56/8db6a1] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:QC_RAW (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[32/6c1937] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:AMBIENT_RNA_REMOVAL:SOUPX (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[a8/a6515b] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:SCANPY_FILTER (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[0b/799ebf] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_THRESHOLDED_SIZE (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[8b/3178ae] NFC…_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:DOUBLET_DETECTION:SCANPY_SCRUBLET (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[fb/954257] NFC…_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:DOUBLET_DETECTION:DOUBLET_REMOVAL (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[ca/ef2870] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_DEDOUBLETED_SIZE (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[3c/3b9bac] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:QC_FILTERED (SAMN14430799) [100%] 2 of 2, cached: 2 ✔
[69/40a1d5] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:COLLECT_SIZES (sizes) [100%] 1 of 1, cached: 1 ✔
[04/152249] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC [ 75%] 3 of 4, failed: 3, retries: 3
[79/eb0e4e] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (1)
[ea/158996] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (2)
[77/661a8e] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (3)
ERROR ~ Error executing process > 'NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC'
Caused by:
Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2)
Command executed:
multiqc \
--force \
\
--config multiqc_config.yml \
\
executor > k8s (4)
[- ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:SCANPY_READH5 -
[94/e0d742] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_READRDS (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[- ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_READCSV -
[a5/e012e5] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_UNIFY (SAMN14430801) [100%] 4 of 4, cached: 4 ✔
[2a/142145] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_UNFILTERED_SIZE (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[- ] NFC…SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND -
[- ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:EMPTY_DROPLET_REMOVAL:ADATA_BARCODES -
[d4/39273a] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_FILTERED_SIZE (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[56/8db6a1] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:QC_RAW (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[32/6c1937] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:AMBIENT_RNA_REMOVAL:SOUPX (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[a8/a6515b] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:SCANPY_FILTER (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[0b/799ebf] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_THRESHOLDED_SIZE (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[8b/3178ae] NFC…_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:DOUBLET_DETECTION:SCANPY_SCRUBLET (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[fb/954257] NFC…_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:DOUBLET_DETECTION:DOUBLET_REMOVAL (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[ca/ef2870] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_DEDOUBLETED_SIZE (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[3c/3b9bac] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:QC_FILTERED (SAMN14430799) [100%] 2 of 2, cached: 2 ✔
[69/40a1d5] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:COLLECT_SIZES (sizes) [100%] 1 of 1, cached: 1 ✔
[04/152249] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC [100%] 4 of 4, failed: 4, retries: 3 ✘
[79/eb0e4e] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (1)
[ea/158996] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (2)
[77/661a8e] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (3)
ERROR ~ Error executing process > 'NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC'
Caused by:
Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2)
Command executed:
multiqc \
--force \
\
--config multiqc_config.yml \
\
\
\
\
\
.
cat <<-END_VERSIONS > versions.yml
"NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC":
multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
Command exit status:
2
Command output:
(empty)
Command error:
/// MultiQC 🔍 v1.25.1
Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY]
This is MultiQC v1.25.1
For more help, run 'multiqc --help' or visit http://multiqc.info
╭─ Error ──────────────────────────────────────────────────────────────────────╮
│ Invalid value for '-c' / '--config': Path 'multiqc_config.yml' does not │
│ exist. │
╰──────────────────────────────────────────────────────────────────────────────╯
Work dir:
/cache-juicefs/nextflow-workspace/work/04/152249a7d6ba23010d2d6e46c9d33a
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
-[nf-core/scdownstream] Pipeline completed with errors-
Description of the bug
Hi,
This is a great tool however I'm running into a hurdle on the final step - regarding the multiQC reporting step. It appears to not be finding the multiqc config file?
Command used and terminal output
No response
Relevant files
No response
System information
No response