xxu1022 commented 2 years ago

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:

--our_dir: midnight
Ignore this warning: params.schema_ignore_params = "our_dir"

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:

The nf-core framework https://doi.org/10.1038/s41587-020-0439-x

Checking input directory structure.

Found barcode directories executor > local (3) executor > local (3) [ae/d15473] process > pipeline:getVersions [100%] 1 of 1, failed: 1 ✘ [be/7ad0fc] process > pipeline:getParams [100%] 1 of 1, cached: 1 ✔ [- ] process > pipeline:copySchemeDir - [24/9dd3be] process > pipeline:preArticQC (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > pipeline:runArtic - [- ] process > pipeline:allConsensus - [- ] process > pipeline:allVariants - [- ] process > pipeline:nextclade - [- ] process > pipeline:pangolin - [- ] process > pipeline:telemetry - [- ] process > pipeline:report - [- ] process > output - Error executing process > 'pipeline:preArticQC (1)'

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

bede commented 2 years ago

I think the the problem is that ‘—our_dir’ should be ‘—out_dir’

xxu1022 commented 2 years ago

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

bede commented 2 years ago

I'd try removing--scheme_name SARS-CoV-2

--scheme_version V1200 should be sufficient

xxu1022 commented 2 years ago

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!

mattdmem commented 2 years ago

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?

xxu1022 commented 2 years ago

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,

mattdmem commented 2 years ago

https://labs.epi2me.io/nextflow-on-windows/ <- check this out and see if it's of any use.

mattdmem commented 2 years ago

Hi @xxu1022 - any updates - have you got the workflow running now?

xxu1022 commented 2 years ago

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

sarahjeeeze commented 2 years ago

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.

mattdmem commented 2 years ago

@xxu1022 did you manage to get it working? If so I'll close this issue!

xxu1022 commented 2 years ago

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:

Output nextflow params object to JSON

  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:

Output nextflow params object to JSON

  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.

mattdmem commented 1 year ago

@xxu1022 this issue is very old now... if you are still having problems then please post a new issue with the details!

Thanks

Matt

epi2me-labs / wf-artic

Process `pipeline:preArticQC (1)` terminated with an error exit status (127) #32

!! Only displaying parameters that differ from the pipeline defaults !!

Output nextflow params object to JSON

Output nextflow params object to JSON