nf-validation-1.1.3: Operation not supported #272
Comments
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oddly enough testing on my laptop there is a different error: nextflow run nf-core/fetchngs -profile test,singularity -revision 1.11.0 --outdir ./test
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/nf-core/fetchngs` [hopeful_perlman] DSL2 - revision: 04ee5031a4 [1.11.0]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
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`._,._,'
nf-core/fetchngs v1.11.0-g04ee503
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Core Nextflow options
revision : 1.11.0
runName : hopeful_perlman
containerEngine : singularity
launchDir : /home/adomingues/sandbox
workDir : /home/adomingues/sandbox/work
projectDir : /home/adomingues/.nextflow/assets/nf-core/fetchngs
userName : adomingues
profile : test,singularity
configFiles :
Input/output options
input : ${projectDir}/tests/sra_ids_test.csv
outdir : ./test
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 6.h
!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/fetchngs for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.5070524
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
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ERROR ~ ERROR: Validation of pipeline parameters failed!
-- Check '.nextflow.log' file for details
The following invalid input values have been detected:
* --input: the file or directory '${projectDir}/tests/sra_ids_test.csv' does not exist.
-- Check script '/home/adomingues/.nextflow/assets/nf-core/fetchngs/./subworkflows/local/nf_core_fetchngs_utils/../../nf-core/nfvalidation_plugin_utils/main.nf' at line: 55 or see '.nextflow.log' file for more detailsOS: Ubuntu 22.04.3 LTS x86_64 |
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Can you try the dev branch? |
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Sorry, I forgot to mention that I also tested it had the the error remains (this one the server which is ultimately where I want to test pipelines): |
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FYI I did another test, this time on an ec2 instance without any prior nextflow install - go / singlularity / nextflow were are all installed for the first time - and the error remains: |
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This looks like a Java version error, which version of Java are you using? Currently we require 11 - 21, we recommend using SDKMan: https://www.nextflow.io/docs/latest/getstarted.html#requirements |
My bad. Without It can't find the input file so I will point directly to the file in the repo and this time the pipeline runs! This tells me that the issue is not related to |
The version seems correct but openjdk: For reference, this is the version in the ec2 ubuntu instance in which the pipeline runs successfully: |
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Can you try this one?
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The |
The nf-validation error is still there :(
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But I can confirm on the clean nextflow install that |
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It looks like Nextflow is trying to make a symbolic link to or from the plugin directory but is failing. Here is the code that throws the error: https://github.com/nextflow-io/nextflow/blob/5e2ce9ed82ccbc70ec24a83e04f24b8d45855a78/modules/nf-commons/src/main/nextflow/plugin/LocalPluginManager.groovy#L115 Do you have permissions to write to |
In my system it's changed to a mount point, but I have write permissions (just tested with
P.S.: I did change many of the default NFX paths in this system due to limited space in |
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Hmmm this is confusing! |
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OK consulted with Nextflow team, does your filesystem support symbolic links? Can you run the following to symlink the nf-validation directory to the working directory? |
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Here you go - it fails: adomingues@vm-ad-genome:sandbox$ ls $NXF_HOME/plugins/nf-validation-1.1.3
classes lib META-INF
adomingues@vm-ad-genome:sandbox$ ls .nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3
ls: cannot access '.nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3': No such file or directory
adomingues@vm-ad-genome:sandbox$ ln -s $NXF_HOME/plugins/nf-validation-1.1.3 .nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3
ln: failed to create symbolic link '.nextflow/plr/d5f4a7bd-accd-4d3c-8033-0add9ef29a00/nf-validation-1.1.3': No such file or directory
adomingues@vm-ad-genome:sandbox$ ll .nextflow/plr/
total 0
drwxr-xr-x 2 root root 0 Feb 13 15:38 ./
drwxr-xr-x 2 root root 0 Feb 13 15:38 ../
drwxr-xr-x 2 root root 0 Mai 16 2022 empty/ |
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OK that seems to be the problem, your filesystem doesn't support symbolic links. What filesystem are you using? |
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@adamrtalbot it's a cifs mount on linux. I am in touch our sys admin to get it sorted, cheers! |
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@adamrtalbot I can confirm that after the changes to the file system everything is working as expected. Thanks! |
Description of the bug
(possibly related to #254 ?)
I ran into this error while testing the pipeline on a small server (VM):
Log file below. I initially though this was an issue with my
.nextflow/pluginsbeing too old so I removed it, but the error remains.Command used and terminal output
nextflow run nf-core/fetchngs -profile test,singularity -revision 1.11.0 --outdir ./testRelevant files
nextflow.log
System information
nextflow version 23.10.1.5891
local computer (VM on a server):
OS: Ubuntu 20.04.6 LTS x86_64
Host: KVM RHEL 7.0.0 PC (i440FX + PIIX, 1996)
Kernel: 5.4.0-170-generic
Shell: bash 5.0.17
CPU: Intel Xeon (Skylake, IBRS) (32) @ 2.294GHz
GPU: 00:02.0 Red Hat, Inc. QXL paravirtual graphic card
Memory: 663MiB / 64302MiB
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