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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Hello! I'm not shure this is the right place to ask for help but I'm having problems when running MaltExtract, I get this error: Error in image.default(x = 1:ncol(red.res), y = 1:nrow(red.res), z = t(red.res), : increasing 'x' and 'y' values expected Calls: image -> image.default #991

Closed crisamor closed 1 year ago

crisamor commented 1 year ago

Check Documentation

I have checked the following places for your error:

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line: nextflow run ...
  2. See error: Please provide your error message

Expected behaviour

Log files

Have you provided the following extra information/files:

System

Nextflow Installation

Container engine

Additional context

crisamor commented 1 year ago

Error executing process > 'maltextract (1)'

Caused by: Process maltextract (1) terminated with an error exit status (1)

Command executed:

MaltExtract -Xmx100g -t taxa_interes.txt -i sample.unmapped.rma6 -o results/ -r Resources -p 8 -f def_anc -a 0.01 --minPI 85.0 --destackingOff

postprocessing.AMPS.r -r results/ -m def_anc -t 8 -n taxa_interes.txt -j

Command exit status: 1

Command output: (empty)

Command error: jun 01, 2023 5:43:07 PM utility.InputParameterProcessor process INFORMACIÓN: Using 8 threads jun 01, 2023 5:43:07 PM utility.InputParameterProcessor process INFORMACIÓN: Custom Behaviour set to: def_anc jun 01, 2023 5:43:07 PM utility.InputParameterProcessor process INFORMACIÓN: Top Percent value set to: 0.01 jun 01, 2023 5:43:07 PM utility.InputParameterProcessor process INFORMACIÓN: Minimum pIdent set to 85.0 jun 01, 2023 5:43:07 PM utility.InputParameterProcessor GetParameters INFORMACIÓN: MaltExtract Version 1.7 jun 01, 2023 5:43:07 PM RMAExtractor.RMAExtractor main INFORMACIÓN: MaltExtract 1.7 --input sample.unmapped.rma --taxa PlasmodiuPlasmodium vivaPlasmodium falciparuPlasmodium malariaPlasmodium inui San Antonio Plasmodium knowlesi strain Toxoplasma gondiEimeria mitiToxoplasma gondii ME4ToxoplasmEmiliania huxleyi CCMP151Aureococcus anophagefferenStaphylococcus phage AndhrEimeria tenellEimeriEimeriorin --output results/ --filter def_anc --top 0.01 --maxLength 0 --minPI 85.0 --resources Resources --threads 8 --destackingOff

jun 01, 2023 5:43:07 PM RMAExtractor.RMAExtractor main INFORMACIÓN: Setting up Taxon Name and Taxon ID maps jun 01, 2023 5:43:17 PM RMAExtractor.RMAExtractor main INFORMACIÓN: Setting up Phylogenetic Tree jun 01, 2023 5:43:17 PM RMAExtractor.RMAExtractor main INFORMACIÓN: Using 8cores jun 01, 2023 5:43:17 PM RMAExtractor.RMAExtractor main INFORMACIÓN: Finished Processing RMA6 files jun 01, 2023 5:43:17 PM RMA6Processor.RMA6Processor process INFORMACIÓN: Reading File: TSFI6_SE.unmapped.rma6 jun 01, 2023 5:43:23 PM RMA6TaxonProcessor.NodeProcessor process ADVERTENCIA: For Toxoplasma_gondii_ME49 in file TSFI6_SE.unmapped.rma6 downsampling was turned on jun 01, 2023 5:43:27 PM RMA6Processor.RMA6Processor process INFORMACIÓN: Finished File: TSFI6_SE.unmapped.rma6 jun 01, 2023 5:43:27 PM RMAExtractor.RMAExtractor main INFORMACIÓN: Writing Summary File jun 01, 2023 5:43:27 PM RMAExtractor.RMAExtractor main INFORMACIÓN: Runtime: 0 Minutes jun 01, 2023 5:43:27 PM RMAExtractor.RMAExtractor main INFORMACIÓN: Peak memory: 3,3 of 88,9G jun 01, 2023 5:43:27 PM RMAExtractor.RMAExtractor main INFORMACIÓN: Shutdown Read 16 items Error in image.default(x = 1:ncol(red.res), y = 1:nrow(red.res), z = t(red.res), : increasing 'x' and 'y' values expected Calls: image -> image.default Ejecución interrumpida

jfy133 commented 1 year ago

Hi @crisamor !

The error is already known, you can see the issue on the AMPs repository here.

Maybe you can report you have the same issue there :) as this isn't a problem with nf-core/eager itself