Closed Bioloko closed 1 year ago
Hi @Bioloko,
To help me troubleshoot this problem - could you let me know if you're on a Mac with an "M" (ARM) processor?
Has the workflow run previously on the machine you're using, has something changed?
Thanks
Matt
i Matt,
Thank you for your response. No, its an intel Mac (3,2 GHz Intel Xeon W 16 nucleus).
Best
Thanks @Bioloko - and have you successfully run the workflow previously or was this your 1st attempt?
Sorry i forgot to answer the second question: Im using this worflow more than a year without problems. But since last week started with problems and i decided to update docker and pull the pipeline and got this message and the pipeline sotopped working :
epi2me-labs/wf-artic contains uncommitted changes -- cannot pull from repository
Ok let's get you a fresh repository and go from there. You should have the following directory:
~/.nextflow/assets/epi2me-labs/wf-artic
Delete it and try your nextflow command again. You could either run nextflow pull
or you could just execute your command above to run the workflow and nextflow will do a pull anyway.
Hi Matt,
Sorry but i cant find any directory as you tell me (~/.nextflow/assets/epi2me-labs/wf-artic), even i cant find any with the name of epi2me-labs. If i remember well when i installed this pipeline i did a conda environment called wf-artic where nextflow was installed and no more i did (docker was installed before for other pipelines i was using).
Hi @Bioloko,
May I suggest that we try running the workflow through the EPI2ME labs application?
https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/installers/EPI2ME-x86-5.1.2-x64.pkg
Download and install and lets see if we can get wf-artic
running in the app,
Matt
Hi Matt,
I run the workflow with one sample with EPI2ME as you mentioned and got the same error, now i can attach you the nextflow.log .
Best
Hi @Bioloko - this is an issue with sed - I'm working on a fix now, we'll release a new version ASAP.
@Bioloko v0.3.32 is just releasing now - should be here soon - let me know if this fixes your issue with sed.
Operating System
macOS
Other Linux
No response
Workflow Version
fails with more than one version
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-artic --fastq /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass --sample_sheet /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass/148_sec_pend.csv --scheme_name SARS-CoV-2 --scheme_version Midnight-IDT/V1 --out_dir /Users/agaliana/wf-ARTIC/CORONA_230928 --update_data --report_detailed true --medaka_variant_model r1041_e82_400bps_fast_g632
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
The pipeline fails when starts pipeline:runArtic steps.
Relevant log output
Application activity log entry
No response