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nf-core / mcmicro

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
https://nf-co.re/mcmicro
MIT License
4 stars 12 forks source link

Issues running Exemplar001 #35

Open josenimo opened 1 month ago

josenimo commented 1 month ago

Description of the bug

I am running Exemplar001. I created a samplesheet (1 row per cycle) Running defaults

It gets stuck at ASHLAR creating a too large image.. is it just an ashlar bug? or something else going wrong? Will try to change some parameters and report back

Command used and terminal output

nextflow run nf-core/mcmicro -r dev 
--outdir /Users/jnimoca/Jose_BI/P12E19_nfcore_mcmicro/output/ 
--marker_sheet 
/Users/jnimoca/Jose_BI/P12E19_nfcore_mcmicro/markers.csv 
-profile 
docker 
--input_cycle 
/Users/jnimoca/Jose_BI/P12E19_nfcore_mcmicro/samplesheet.csv

Output:

N E X T F L O W  ~  version 23.10.1
Launching `https://github.com/nf-core/mcmicro` [silly_newton] DSL2 - revision: b8d46de48e [dev]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/mcmicro v2.0.0-gb8d46de
------------------------------------------------------
Core Nextflow options
  revision       : dev
  runName        : silly_newton
  containerEngine: docker
  launchDir      : /Users/jnimoca/Jose_BI/P12E19_nfcore_mcmicro
  workDir        : /Users/jnimoca/Jose_BI/P12E19_nfcore_mcmicro/work
  projectDir     : /Users/jnimoca/.nextflow/assets/nf-core/mcmicro
  userName       : jnimoca
  profile        : docker
  configFiles    :

Input/output options
  input_cycle    : /Users/jnimoca/Jose_BI/P12E19_nfcore_mcmicro/samplesheet.csv
  outdir         : /Users/jnimoca/Jose_BI/P12E19_nfcore_mcmicro/output/
  marker_sheet   : /Users/jnimoca/Jose_BI/P12E19_nfcore_mcmicro/markers.csv

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/mcmicro for your analysis please cite:

* The pipeline

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/mcmicro/blob/master/CITATIONS.md
------------------------------------------------------
WARN: Samplesheet warnings:
    The samplesheet contains following unchecked field(s): [Filter]
executor >  local (3)
[ca/23253c] process > NFCORE_MCMICRO:MCMICRO:INPUT_CHECK:SAMPLE_AND_MARKER_SHEET_CHECK (markers.csv) [100%] 1 of 1 ✔
[a3/b43fba] process > NFCORE_MCMICRO:MCMICRO:INPUT_CHECK:MARKER_SHEET_CHECK (markers.csv)            [100%] 1 of 1 ✔
executor >  local (3)
[ca/23253c] process > NFCORE_MCMICRO:MCMICRO:INPUT_CHECK:SAMPLE_AND_MARKER_SHEET_CHECK (markers.csv) [100%] 1 of 1 ✔
[a3/b43fba] process > NFCORE_MCMICRO:MCMICRO:INPUT_CHECK:MARKER_SHEET_CHECK (markers.csv)            [100%] 1 of 1 ✔
[62/73bd10] process > NFCORE_MCMICRO:MCMICRO:ASHLAR (Exemplar001)                                    [  0%] 0 of 1
[-        ] process > NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER                                         -
[-        ] process > NFCORE_MCMICRO:MCMICRO:MCQUANT                                                 -
[-        ] process > NFCORE_MCMICRO:MCMICRO:MULTIQC                                                 -

Relevant files

ASHLAR output from work folder: Screenshot 2024-05-13 at 13 02 57

WorkFolder.zip

System information

Nextflow: version 23.10.1 M2 Macbook pro executor: local Container engine: Docker OS: MacOS nf-core/mcmicro v2.0.0-gb8d46de