I tried editing the nextflow config file to modify the docker runoptions, but i'm not sure if i am doing it right ?
runOptions = '-u $(id -u):$(id -g)'
Again i am really new to all of this do i do apologise if my error is something rather pathetic
thank you so much for your time :)
this is the full log
Checking fastq input.
[37/f78267] Submitted process > pipeline:prep_nextclade
[2f/3fd205] Submitted process > validate_sample_sheet
[f1/82936f] Submitted process > pipeline:lookup_medaka_variant_model (1)
[b5/f64be6] Submitted process > pipeline:getVersions
[f9/4b522a] Submitted process > pipeline:getParams
ERROR ~ Error executing process > 'pipeline:prep_nextclade'
Caused by:
Process pipeline:prep_nextclade terminated with an error exit status (1)
Command executed:
workflow-glue scheme_to_nextclade SARS-CoV-2.scheme.bed reference.fasta primers.csv
Command exit status:
1
Command output:
(empty)
Command error:
touch: cannot touch '.command.trace': Permission denied
Work dir:
/home/navin/epi2melabs/instances/wf-artic_66d7b69d-4680-45d8-89af-75a0289c8a07/work/37/f78267f6ac9699aec7f9c6187cec41
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
-- Check '/home/navin/epi2melabs/instances/wf-artic_66d7b69d-4680-45d8-89af-75a0289c8a07/nextflow.log' file for details
WARN: Input directory 'barcode64' was found, but sample sheet '/home/navin/epi2melabs/demo/epi2me-labs/wf-artic/v0.3.30/wf-artic-demo/sample_sheet.csv' has no such entry.
WARN: Killing running tasks (2)
Ask away!
Hiya, I'm very new to linux, sequence analysis, docker and epi2me
I have been trying to run the demo dataset on the wf-arctic pipeline using epi2me and i'm always getting this error,
Command error: touch: cannot touch '.command.trace': Permission denied
I tried editing the nextflow config file to modify the docker runoptions, but i'm not sure if i am doing it right ?
runOptions = '-u $(id -u):$(id -g)'
Again i am really new to all of this do i do apologise if my error is something rather pathetic
thank you so much for your time :)
this is the full log
Checking fastq input. [37/f78267] Submitted process > pipeline:prep_nextclade [2f/3fd205] Submitted process > validate_sample_sheet [f1/82936f] Submitted process > pipeline:lookup_medaka_variant_model (1) [b5/f64be6] Submitted process > pipeline:getVersions [f9/4b522a] Submitted process > pipeline:getParams ERROR ~ Error executing process > 'pipeline:prep_nextclade' Caused by: Process
pipeline:prep_nextclade
terminated with an error exit status (1) Command executed: workflow-glue scheme_to_nextclade SARS-CoV-2.scheme.bed reference.fasta primers.csv Command exit status: 1 Command output: (empty) Command error: touch: cannot touch '.command.trace': Permission denied Work dir: /home/navin/epi2melabs/instances/wf-artic_66d7b69d-4680-45d8-89af-75a0289c8a07/work/37/f78267f6ac9699aec7f9c6187cec41 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named.command.sh
-- Check '/home/navin/epi2melabs/instances/wf-artic_66d7b69d-4680-45d8-89af-75a0289c8a07/nextflow.log' file for details WARN: Input directory 'barcode64' was found, but sample sheet '/home/navin/epi2melabs/demo/epi2me-labs/wf-artic/v0.3.30/wf-artic-demo/sample_sheet.csv' has no such entry. WARN: Killing running tasks (2)