Problem running the pipeline on MacOS
imerelli opened this issue · 1 comments
imerelli commented
Operating System
macOS
Other Linux
No response
Workflow Version
v1.3.0
Workflow Execution
EPI2ME Desktop (Local)
Other workflow execution
Other workflows work nicely
EPI2ME Version
v5.1.14
CLI command run
No response
Workflow Execution - CLI Execution Profile
None
What happened?
The test is not working, I also tried with my own data.
Other Epi2Me workflows work nicely
Relevant log output
N E X T F L O W ~ version 23.04.2
Launching `/Users/imerelli/epi2melabs/workflows/epi2me-labs/wf-basecalling/main.nf` [eloquent_mirzakhani] DSL2 - revision: 13c8f247e4
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
|||||||||| | ____| _ \_ _|___ \| \/ | ____| | | __ _| |__ ___
||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-basecalling v1.3.0
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Core Nextflow options
runName : eloquent_mirzakhani
containerEngine: docker
launchDir : /Users/imerelli/epi2melabs/instances/wf-basecalling_01J2XMCRBFH4QKS09YESE31E92
workDir : /Users/imerelli/epi2melabs/instances/wf-basecalling_01J2XMCRBFH4QKS09YESE31E92/work
projectDir : /Users/imerelli/epi2melabs/workflows/epi2me-labs/wf-basecalling
userName : imerelli
profile : standard
configFiles : /Users/imerelli/epi2melabs/workflows/epi2me-labs/wf-basecalling/nextflow.config, /Users/imerelli/epi2melabs/instances/wf-basecalling_01J2XMCRBFH4QKS09YESE31E92/demo.config
Input Options
input : /Users/imerelli/epi2melabs/demo/epi2me-labs/wf-basecalling/1.3.0/wf-basecalling-demo/input
ref : /Users/imerelli/epi2melabs/demo/epi2me-labs/wf-basecalling/1.3.0/wf-basecalling-demo/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
Output Options
out_dir : /Users/imerelli/epi2melabs/instances/wf-basecalling_01J2XMCRBFH4QKS09YESE31E92/output
Basecalling options
basecaller_cfg : dna_r10.4.1_e8.2_400bps_hac@v4.1.0
remora_cfg : dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-basecalling for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-basecalling v1.3.0.
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[e6/29697f] Submitted process > wf_dorado:make_mmi
[6e/d60e3f] Submitted process > cram_cache
[f9/c6c403] Submitted process > getParams
[96/5bb109] Submitted process > getVersions
ERROR ~ Error executing process > 'getVersions'
Caused by:
Process `getVersions` terminated with an error exit status (127)
Command executed:
dorado --version 2>&1 | head -n1 | sed 's/^/dorado,/' >> versions.txt
minimap2 --version | head -n 1 | sed 's/^/minimap2,/' >> versions.txt
Command exit status:
127
Command output:
(empty)
Command error:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Work dir:
/Users/imerelli/epi2melabs/instances/wf-basecalling_01J2XMCRBFH4QKS09YESE31E92/work/96/5bb109aa097231ca729bc317c738b8
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '/Users/imerelli/epi2melabs/instances/wf-basecalling_01J2XMCRBFH4QKS09YESE31E92/nextflow.log' file for details
WARN: Killing running tasks (3)Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
No
Other demo data information
No response
cjw85 commented
Note that the compute requirements section of the README states that ARM processors are not supported.
And further down in the pipeline overview section macOS is specifically mentioned as not being supported.