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nf-core / nanoseq

Nanopore demultiplexing, QC and alignment pipeline
https://nf-co.re/nanoseq
MIT License
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Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT #141

Open wdiao-zju opened 2 years ago

wdiao-zju commented 2 years ago 
  It runs well in the non-basecalling, non-demultiplexing, non-alignment pipeline. However, it not runs well in the non-basecalling, non-demultiplexing pipeline. The test dataset is from nf-core/test-datasets. The version of nanoseq is v2.01. Code is as follows:

nextflow run nf-core/nanoseq \ --input samplesheet_nobc_nodx.csv \ --protocol cDNA \ --skip_basecalling \ --skip_demultiplexing \ --max_cpus 40 \ --max_memory 100.GB \ -profile docker

Error information is as follows (Note: the subsequent process such as alignment is okay, and I found only html file not png file in work/"hash dir"/fastq/MCF7_R1): " Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT (MCF7_R1)'

Caused by: Missing output file(s) fastq/MCF7_R1/*.png expected by process NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT (MCF7_R1) "

trum994 commented 2 years ago

I'm seeing a similar issue with other nanoplot processes:

Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCBASECALL_PYCOQC_NANOPLOT:NANOPLOT (sample1)'

Caused by: Missing output file(s) summary/*.png expected by process NFCORE_NANOSEQ:NANOSEQ:QCBASECALL_PYCOQC_NANOPLOT:NANOPLOT (sample1)

trum994 commented 2 years ago

@wdiao-zju if you go into that summary directory and open the *log file what's the error message that you see? I created an issue at Nanoplot here.