[Bug]: Error executing process > 'handleSingleFile
Rohit-Satyam opened this issue · 8 comments
Rohit-Satyam commented
What happened?
Workflow unable to take fastq or fastq.gz file as an input
Operating System
ubuntu 20.04
Workflow Execution
Command line
Workflow Execution - EPI2ME Labs Versions
No response
Workflow Execution - Execution Profile
Docker
Workflow Version
v0.3.18
Relevant log output
nextflow run epi2me-labs/wf-artic --fastq ~/Documents/COVID_Project/longread/dataset2/results/01_read_filtering/0055219_barcode49.fastq --scheme_version ARTIC/V4.1 --out_dir dataset2_output
N E X T F L O W ~ version 21.10.6
Launching `epi2me-labs/wf-artic` [awesome_poitras] - revision: a60a1e1e73 [master]
WARN: Found unexpected parameters:
* --scheme_dir: primer_schemes
- Ignore this warning: params.schema_ignore_params = "scheme_dir"
Core Nextflow options
revision : master
runName : awesome_poitras
containerEngine: docker
launchDir : /home/subudhak/Documents/COVID_Project/longread/dataset2/results
workDir : /home/subudhak/Documents/COVID_Project/longread/dataset2/results/work
projectDir : /home/subudhak/.nextflow/assets/epi2me-labs/wf-artic
userName : subudhak
profile : standard
configFiles : /home/subudhak/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config
Basic Input/Output Options
out_dir : dataset2_output
fastq : /home/subudhak/Documents/COVID_Project/longread/dataset2/results/01_read_filtering/0055219_barcode49.fastq
Primer Scheme Selection
scheme_version : ARTIC/V4.1
Advanced options
normalise : 200
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use epi2me-labs/wf-artic for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
------------------------------------
Available Primer Schemes:
------------------------------------
Name Version
spike-seq ONT/V1
spike-seq ONT/V4.1
SARS-CoV-2 NEB-VarSkip/v2b
SARS-CoV-2 NEB-VarSkip/v2
SARS-CoV-2 NEB-VarSkip/v1a-long
SARS-CoV-2 NEB-VarSkip/v1a
SARS-CoV-2 Midnight-IDT/V1
SARS-CoV-2 ARTIC/V2
SARS-CoV-2 ARTIC/V1
SARS-CoV-2 ARTIC/V4
SARS-CoV-2 ARTIC/V4.1
SARS-CoV-2 ARTIC/V3
SARS-CoV-2 Midnight-ONT/V2
SARS-CoV-2 Midnight-ONT/V1
SARS-CoV-2 Midnight-ONT/V3
------------------------------------
Checking fastq input.
Single file input detected.
executor > local (5)
[c3/60f565] process > handleSingleFile (1) [100%] 1 of 1, failed: 1 ✘
[3d/0aeed3] process > pipeline:getVersions [ 0%] 0 of 1
[65/94cee2] process > pipeline:getParams [ 0%] 0 of 1
[26/9faa6b] process > pipeline:copySchemeDir [ 0%] 0 of 1
[- ] process > pipeline:preArticQC -
[- ] process > pipeline:runArtic -
[- ] process > pipeline:combineDepth -
[- ] process > pipeline:allConsensus -
[- ] process > pipeline:allVariants [ 0%] 0 of 1
[45/37c873] process > pipeline:prep_nextclade [ 0%] 0 of 1
[- ] process > pipeline:nextclade -
[- ] process > pipeline:pangolin -
[- ] process > pipeline:telemetry -
[- ] process > pipeline:report -
[- ] process > output -
WARN: Input tuple does not match input set cardinality declared by process `pipeline:telemetry` -- offending value: [[]]
WARN: Input tuple does not match input set cardinality declared by process `pipeline:allVariants` -- offending value: [[]]
Error executing process > 'handleSingleFile (1)'
Caused by:
Process `handleSingleFile (1)` terminated with an error exit status (127)
Command executed:
mkdir 0055219_barcode49
mv 0055219_barcode49.fastq 0055219_barcode49
Command exit status:
127
Command output:
(empty)
Command error:
.command.run: line 279: docker: command not found
Work dir:
/home/subudhak/Documents/COVID_Project/longread/dataset2/results/work/c3/60f565cf743de304ec4990011ed328
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
WARN: Killing pending tasks (2)cjw85 commented
The log above states:
.command.run: line 279: docker: command not foundIt appears that you are running with the default docker option, but do not have docker installed on your system. Please refer to our installation instructions: https://labs.epi2me.io/wfindex/#installation
Rohit-Satyam commented
I ran the pipeline with -profile conda and this time it ran few steps successfully but here comes the new error
(wfartic) subudhak@KW61216:~/Documents/test$ nextflow run epi2me-labs/wf-artic -profile conda --fastq ~/Documents/COVID_Project/longread/dataset2/results/01_read_filtering/0055219_barcode49.fastq --out_dir testing --scheme_version ARTIC/V4.1
N E X T F L O W ~ version 22.04.5
Launching `https://github.com/epi2me-labs/wf-artic` [dreamy_wescoff] DSL2 - revision: a60a1e1e73 [master]
WARN: Found unexpected parameters:
* --scheme_dir: primer_schemes
- Ignore this warning: params.schema_ignore_params = "scheme_dir"
Core Nextflow options
revision : master
runName : dreamy_wescoff
launchDir : /home/subudhak/Documents/test
workDir : /home/subudhak/Documents/test/work
projectDir : /home/subudhak/.nextflow/assets/epi2me-labs/wf-artic
userName : subudhak
profile : conda
configFiles : /home/subudhak/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config
Basic Input/Output Options
out_dir : testing
fastq : /home/subudhak/Documents/COVID_Project/longread/dataset2/results/01_read_filtering/0055219_barcode49.fastq
Primer Scheme Selection
scheme_version: ARTIC/V4.1
Advanced options
normalise : 200
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use epi2me-labs/wf-artic for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
------------------------------------
Available Primer Schemes:
------------------------------------
Name Version
spike-seq ONT/V1
spike-seq ONT/V4.1
SARS-CoV-2 NEB-VarSkip/v2b
SARS-CoV-2 NEB-VarSkip/v2
SARS-CoV-2 NEB-VarSkip/v1a-long
SARS-CoV-2 NEB-VarSkip/v1a
SARS-CoV-2 Midnight-IDT/V1
SARS-CoV-2 ARTIC/V2
SARS-CoV-2 ARTIC/V1
SARS-CoV-2 ARTIC/V4
SARS-CoV-2 ARTIC/V4.1
SARS-CoV-2 ARTIC/V3
SARS-CoV-2 Midnight-ONT/V2
SARS-CoV-2 Midnight-ONT/V1
SARS-CoV-2 Midnight-ONT/V3
------------------------------------
Checking fastq input.
Single file input detected.
[- ] process > handleSingleFile -
executor > local (6)
[8f/00286e] process > handleSingleFile (1) [100%] 1 of 1 ✔
[fd/300385] process > pipeline:getVersions [ 0%] 0 of 1
[78/1c8cb4] process > pipeline:getParams [100%] 1 of 1 ✔
[09/027dc7] process > pipeline:copySchemeDir [ 0%] 0 of 1
[17/715685] process > pipeline:preArticQC (1) [ 0%] 0 of 1
[- ] process > pipeline:runArtic -
[- ] process > pipeline:combineDepth -
[- ] process > pipeline:allConsensus -
[- ] process > pipeline:allVariants -
[80/260e62] process > pipeline:prep_nextclade [100%] 1 of 1 ✔
[- ] process > pipeline:nextclade -
[- ] process > pipeline:pangolin -
executor > local (6)
[8f/00286e] process > handleSingleFile (1) [100%] 1 of 1 ✔
[fd/300385] process > pipeline:getVersions [100%] 1 of 1, failed: 1 ✘
[78/1c8cb4] process > pipeline:getParams [100%] 1 of 1 ✔
[- ] process > pipeline:copySchemeDir -
[- ] process > pipeline:preArticQC (1) -
[- ] process > pipeline:runArtic -
[- ] process > pipeline:combineDepth -
[- ] process > pipeline:allConsensus -
[- ] process > pipeline:allVariants -
[80/260e62] process > pipeline:prep_nextclade [100%] 1 of 1 ✔
[- ] process > pipeline:nextclade -
[- ] process > pipeline:pangolin -
[- ] process > pipeline:telemetry -
[- ] process > pipeline:report -
[- ] process > output -
Error executing process > 'pipeline:getVersions'
Caused by:
Process `pipeline:getVersions` terminated with an error exit status (1)
Command executed:
medaka --version | sed 's/ /,/' >> versions.txt
minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
bcftools --version | head -n 1 | sed 's/ /,/' >> versions.txt
samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
artic --version | sed 's/ /,/' >> versions.txt
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/home/subudhak/Documents/test/work/conda/epi2melabs-nf-artic-69fb201e5af3477012a411f0f53f1cd9/bin/medaka", line 7, in <module>
from medaka.medaka import main
File "/home/subudhak/Documents/test/work/conda/epi2melabs-nf-artic-69fb201e5af3477012a411f0f53f1cd9/lib/python3.8/site-packages/medaka/medaka.py", line 11, in <module>
import medaka.models
File "/home/subudhak/Documents/test/work/conda/epi2melabs-nf-artic-69fb201e5af3477012a411f0f53f1cd9/lib/python3.8/site-packages/medaka/models.py", line 7, in <module>
import requests
File "/home/subudhak/.local/lib/python3.8/site-packages/requests/__init__.py", line 44, in <module>
import chardet
ModuleNotFoundError: No module named 'chardet'
Work dir:
/home/subudhak/Documents/test/work/fd/300385ca6639e88faa7e197c752f92
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`I tried installing chardet using mamba install -c conda-forge chardet but the workflow is unable to detect it.
Rohit-Satyam commented
Update: I tried installing docker and running the command again. The docker version works. But I wish to run this pipeline on cluster using conda where we don't have docker.
nextflow run epi2me-labs/wf-artic --fastq ~/Documents/COVID_Project/longread/dataset2/results/01_read_filtering/0055219_barcode49.fastq --out_dir testing --scheme_version ARTIC/V4.1
cjw85 commented
Do you have any other container runtime available on your cluster, such as singularity?
Unfortunately we've had various problems using conda with our workflows, and intend to deprecate it's use in favour of containers.
Rohit-Satyam commented
Yes, we have Singularity.
Rohit-Satyam commented
I was able to run the pipeline using singularity on cluster. One last query: I have multiple fastq.gz files. When I give entire directory containing multiple fastq files, I get a single BAM file. How can I get separate BAM and VCF files and consensus FASTA file. Using --fastq data/*.gz didn't work.
cjw85 commented
The workflow assumes a directory structure as would be output by the MinKNOW sequencing device software. So something like:
- fastq_pass
- barcode01
- *.fastq.gz
- barcode02
- *.fastq.gz
- barcode03
- *.fastq.gz
If you want to analysis fastq files independently you will need to place them in subfolders to the directory provided as the input to the workflow. In the above example passing --fastq fastq_pass would result in the three barcodeXX directories being analysed independently.
Rohit-Satyam commented
Thanks. My issue is resolved so I am closing this.