Closed xxu1022 closed 1 year ago
I think the the problem is that ‘—our_dir’ should be ‘—out_dir’
Thanks for the reminder of the mistake. Now I change to '--out_dir' but the error still appear and the error still is command error '/bin/bash: .command.run: No such file or directory'.
Checking input directory structure. WARN: Killing pending tasks (2) executor > local (4) [05/43b6ac] process > pipeline:getVersions [ 0%] 0 of 1 executor > local (4) [- ] process > pipeline:getVersions - [b4/50d933] process > pipeline:getParams [100%] 1 of 1 ✔ [5d/bbe943] process > pipeline:copySchemeDir [100%] 1 of 1, failed: 1 ✘ [- ] process > pipeline:preArticQC (1) - [- ] process > pipeline:runArtic - [- ] process > pipeline:allConsensus - [- ] process > pipeline:allVariants [ 0%] 0 of 1 [- ] process > pipeline:nextclade - [- ] process > pipeline:pangolin - [- ] process > pipeline:telemetry [ 0%] 0 of 1 [- ] process > pipeline:report - [- ] process > output - Error executing process > 'pipeline:copySchemeDir'
Caused by:
Process pipeline:copySchemeDir
terminated with an error exit status (127)
Command executed:
cp -RL primer_schemes scheme_dir
Command exit status: 127
Command output: (empty)
Command error: /bin/bash: .command.run: No such file or directory
Work dir: /home/grid/data/wf_artic/work/5d/bbe9434be6ed8f3ea58e054eaa8726
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
I'd try removing--scheme_name SARS-CoV-2
--scheme_version V1200
should be sufficient
Thanks for your suggestion on this. I have tried removing '--scheme_name SARS-CoV-2'. But it still not work and still is the same error info 'terminated with an error exit status (127)' and '/bin/bash: .command.run: No such file or directory'. Any further suggestion on this? Thanks!
Can you please provide a little more information on how you're running this? What's the operating system? Or are you running on a GridION?
Hi, Thanks for your comments on this. For your information, I am trying to run 'epi2me-labs/wf-artic' on subsystem (Ubuntu 20.04 focal) of Win10. I have installed docker on Win10 and on Ubuntu subsystem as well. Miniconda and nextflow have been installed on Ubuntu subsystem as well. The command 'nextflow run epi2me-labs/wf-artic --help' works well for me. Feel free to let me know if any more information is needed. Best,
https://labs.epi2me.io/nextflow-on-windows/ <- check this out and see if it's of any use.
Hi @xxu1022 - any updates - have you got the workflow running now?
Hi @mattdmem Thanks for your considering this. I am still struggling with the same issue. I assume that it is the docker issue in Ubuntu subsystem, since I use the subsystem Ubuntu focal on Win10. 1) The docker is installed on both in Ubuntu subsystem and win10 system as well. 2) I have successfully run epi2me-labs in Win10 and use the docker app in win10 system as well.
Is uninstall-install the docker in ubuntu subsystem works for this issue? And how to uninstall docker in subsystem ubuntu focal?
Thanks
Hi @xxu1022, I would suggest trying nextflow pull epi2me-labs/wf-artic
and running the cmd again. Also whilst the workflow is running could you check the container is running with docker ps -a
you would need to do that in another terminal or you can check docker desktop.
@xxu1022 did you manage to get it working? If so I'll close this issue!
Hi sarahjeeeze and mattdmem, Thanks for your comments and sorry for the late reply. I have tried ' nextflow pull epi2me-labs/wf-artic' first. The output is 'Checking epi2me-labs/wf-artic': Fast-forward - revision: eeb43e96f7 [master]'. While when I tried the 'nextflow run epi2me-labs/wf-artic --fastq sars-cov-2' with the other parameter as default, it stopped with the following error information very quickly. The output of 'docker ps -a' in another terminal is 'Cannot connect to the Docker daemon at unix://var/run/docker.sock. Is the docker daemon running?'.
Error information: Error executing process > 'pipeline:getParams'
Caused by:
Process pipeline:getParams
terminated with an error exit status (125)
Command executed:
echo '{
"help": false,
"out_dir": "output",
"fastq": "sars_cov_2_reads/",
"sanitize_fastq": false,
"sample": null,
"sample_sheet": null,
"normalise": 200,
"report_depth": 100,
"medaka_model": "r941_prom_variant_g360",
"scheme_name": "SARS-CoV-2",
"scheme_version": "V3",
"genotype_variants": null,
"report_clade": true,
"report_lineage": true,
"report_coverage": true,
"report_variant_summary": true,
executor > local (5) [- ] process > pipeline:getVersions - [fc/ddd833] process > pipeline:getParams [100%] 1 of 1, failed: 1 ✘ [- ] process > pipeline:copySchemeDir - [80/ae3fb8] process > pipeline:preArticQC (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > pipeline:runArtic - [- ] process > pipeline:allConsensus - [- ] process > pipeline:allVariants - [92/37dc6f] process > pipeline:prep_nextclade [100%] 1 of 1, failed: 1 ✘ [- ] process > pipeline:nextclade - [- ] process > pipeline:pangolin - [- ] process > pipeline:telemetry - [- ] process > pipeline:report - [- ] process > output - Error executing process > 'pipeline:getParams'
Caused by:
Process pipeline:getParams
terminated with an error exit status (125)
Command executed:
echo '{
"help": false,
"out_dir": "output",
"fastq": "sars_cov_2_reads/",
"sanitize_fastq": false,
"sample": null,
"sample_sheet": null,
"normalise": 200,
"report_depth": 100,
"medaka_model": "r941_prom_variant_g360",
"scheme_name": "SARS-CoV-2",
"scheme_version": "V3",
"genotype_variants": null,
"report_clade": true,
"report_lineage": true,
"report_coverage": true,
"report_variant_summary": true,
"report_detailed": false,
"wfversion": "v0.3.11",
"pangolin_version": "3.1.20",
"nextclade_version": "1.10.2",
"nextclade_data_tag": null,
"update_data": false,
"aws_image_prefix": null,
"aws_queue": null,
"lab_id": null,
"testkit": null,
"report_name": "report",
"monochrome_logs": false,
"validate_params": true,
"show_hidden_params": false,
"schema_ignore_params": "show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,pangolin_version,nextclade_version,wfversion",
"_min_len": 400,
"_max_len": 700,
"_max_softclip_length": 0,
"full_scheme_name": "SARS-CoV-2/V3"
}' > params.json
Command exit status: 125
Command output: (empty)
Command error: docker: Cannot connect to the Docker daemon at unix://var/run/docker.sock. Is the docker daemon running?. See 'docker run --help'.
Work dir: /home/grid/data/wf_artic/work/fc/ddd833be3f7203c493532bb10f64e5
Tip: when you have fixed the problem you can continue the execution adding the option -resume
to the run command line.
@xxu1022 this issue is very old now... if you are still having problems then please post a new issue with the details!
Thanks
Matt
Hi, Is any one can help me on the error (127)? Detail information is as follows. Thanks!
$ /home/grid/program/nextflow run epi2me-labs/wf-artic --scheme_name SARS-CoV-2 --scheme_version V1200 --min_len 200 --max_len 1100 --our_dir midnight --fastq sars_cov_2_reads/ -resume N E X T F L O W ~ version 21.10.6 Launching
epi2me-labs/wf-artic
[drunk_mercator] - revision: 8d13aab29f [master]WARN: Found unexpected parameters:
Core Nextflow options revision : master runName : drunk_mercator containerEngine: docker launchDir : /home/grid/data/wf_artic workDir : /home/grid/data/wf_artic/work projectDir : /home/grid/.nextflow/assets/epi2me-labs/wf-artic userName : grid profile : standard configFiles : /home/grid/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config
Basic Input/Output Options fastq : sars_cov_2_reads/
Primer Scheme Selection scheme_version : V1200
Advanced options min_len : 200 max_len : 1100
!! Only displaying parameters that differ from the pipeline defaults !!
If you use wf-artic for your analysis please cite:
Checking input directory structure.
Caused by: Process
pipeline:preArticQC (1)
terminated with an error exit status (127)Command executed:
fastcat -s barcode01 -r barcode01.stats -x barcode01 > /dev/null
Command exit status: 127
Command output: (empty)
Command error: /bin/bash: .command.run: No such file or directory
Work dir: /home/grid/data/wf_artic/work/24/9dd3be42bf36ee9ba8124473a00c7e
Tip: when you have fixed the problem you can continue the execution adding the option
-resume
to the run command line