Why I am getting a Command Trace Error
navyn007 opened this issue · 4 comments
Operating System
Other Linux (please specify below)
Other Linux
Linux Mint 21.1 Cinnamon
Workflow Version
N E X T F L O W ~ version 23.04.1
Workflow Execution
EPI2ME Desktop application
EPI2ME Version
EPI2ME V5.1.0
CLI command run
No response
Workflow Execution - CLI Execution Profile
None
What happened?
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
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 :)
Relevant log output
N E X T F L O W ~ version 23.04.1
Launching `/home/navin/epi2melabs/workflows/epi2me-labs/wf-artic/main.nf` [hungry_visvesvaraya] DSL2 - revision: 966ee35cc0
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-artic v0.3.30
--------------------------------------------------------------------------------
Core Nextflow options
runName : hungry_visvesvaraya
containerEngine: docker
launchDir : /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371
workDir : /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/work
projectDir : /home/navin/epi2melabs/workflows/epi2me-labs/wf-artic
userName : navin
profile : standard
configFiles : /home/navin/epi2melabs/workflows/epi2me-labs/wf-artic/nextflow.config, /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/demo.config
Input Options
fastq : /home/navin/epi2melabs/demo/epi2me-labs/wf-artic/v0.3.30/wf-artic-demo/fastq
Primer Scheme Selection
scheme_version : Midnight-ONT/V3
Sample Options
sample_sheet : /home/navin/epi2melabs/demo/epi2me-labs/wf-artic/v0.3.30/wf-artic-demo/sample_sheet.csv
Output Options
out_dir : /home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/output
!! 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
--------------------------------------------------------------------------------
This is epi2me-labs/wf-artic v0.3.30.
--------------------------------------------------------------------------------
WARN: Nextflow version 23.04.1 does not match workflow required version: >=23.04.2 -- Execution will continue, but things may break!
------------------------------------
Available Primer Schemes:
------------------------------------
Name Version
SARS-CoV-2 Midnight-IDT/V2
SARS-CoV-2 Midnight-IDT/V1
SARS-CoV-2 Midnight-ONT/V3
SARS-CoV-2 Midnight-ONT/V2
SARS-CoV-2 Midnight-ONT/V1
SARS-CoV-2 NEB-VarSkip/v2
SARS-CoV-2 NEB-VarSkip/v1a
SARS-CoV-2 NEB-VarSkip/v1a-long
SARS-CoV-2 NEB-VarSkip/v2b
SARS-CoV-2 ARTIC/V3
SARS-CoV-2 ARTIC/V2
SARS-CoV-2 ARTIC/V4
SARS-CoV-2 ARTIC/V5.3.2
SARS-CoV-2 ARTIC/V4.1
SARS-CoV-2 ARTIC/V1
------------------------------------
Checking fastq input.
[12/02922a] Submitted process > pipeline:prep_nextclade
[a1/975cbc] Submitted process > pipeline:getVersions
[73/82bf7e] Submitted process > validate_sample_sheet
[df/92bb7a] Submitted process > pipeline:lookup_medaka_variant_model (1)
[5e/6159d6] Submitted process > pipeline:getParams
ERROR ~ Error executing process > 'pipeline:lookup_medaka_variant_model (1)'
Caused by:
Process `pipeline:lookup_medaka_variant_model (1)` terminated with an error exit status (1)
Command executed:
medaka_model=$(workflow-glue resolve_medaka_model lookup_table 'dna_r9.4.1_450bps_hac' "medaka_variant")
echo -n $medaka_model
Command exit status:
1
Command output:
(empty)
Command error:
touch: cannot touch '.command.trace': Permission denied
Work dir:
/home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/work/df/92bb7a914a77424b58759f53aeae27
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_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/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: Input tuple does not match input set cardinality declared by process `pipeline:allVariants` -- offending value: []
ERROR ~ Unexpected error [NullPointerException]
-- Check '/home/navin/epi2melabs/instances/wf-artic_cfc7af0a-f7b8-46ae-be0a-948f6d0b1371/nextflow.log' file for details
WARN: Killing running tasks (4)Application activity log entry
Nothing is listed in RedHi @navyn007 - Are you still having issues? My immediate thought is you're running with sudo or within a dir where you don't have permissions. Let me know if you still need assistance!
The error here appears reminiscent of other reports that we have with the use of Docker Desktop. (e.g. here).
Have you installed Docker Desktop? If so can I recommend that you follow the instructions here to install the docker.io package on your system:
https://labs.epi2me.io/installation/#installing-docker-on-linux-without-docker-desktop
As an aside I noticed you commented:
I'm very new to linux, sequence analysis, docker and epi2me
Have you considered using EPI2ME Desktop on Windows?
Closing due to lack of response.