Error at fastqc when we use multibyte characters.

EFEXP commented 3 years ago

Description of the bug

Process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RbohA_KO) terminated with an error exit status (1)

Without usefull traces and logs.

Steps to reproduce

Set the current directory to folder with multibyte characters. (ex:./ゼニゴケ) nextflow run nf-core/rnaseq --input ./samplesheet.csv --fasta ./MpTak_v6.1.genome.fasta --gff ./MpTak_v6.1r1.gff -profile docker --max_memory 32GB
and it throws LinkageError occurred while loading main class uk.ac.babraham.FastQC.FastQCApplication.

Renaming the folder name into marchantia works for me.

Expected behaviour

Before run it,make sure the working folder is not child of folder with multibyte characters. And should warn in log file.

Log files

6月-07 16:37:04.709 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RbohA_KO)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RbohA_KO)` terminated with an error exit status (1)

Command executed:

  [ ! -f  RbohA_KO.fastq.gz ] && ln -s IonXpressRNA_015.R_2019_11_01_14_59_29_user_Proton-184-Marpoly_RNA_Seq.fastq.gz RbohA_KO.fastq.gz
  fastqc --quiet --threads 6 RbohA_KO.fastq.gz
  fastqc --version | sed -e "s/FastQC v//g" > fastqc.version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error: LinkageError occurred while loading main class uk.ac.babraham.FastQC.FastQCApplication
    java.lang.ExceptionInInitializerError: null

Work dir:
  /ゼニゴケ/work/91/69696258ea67457b6eae16feb588e4

System

Hardware:Macbook Pro 2019,2.4GHz 8 core i9,32GB memory
OS: macOS
Version:11.4

Nextflow Installation

Version:21.04.0

Container engine

Engine: Docker
version: 3.3.3
Image tag: nfcore/rnaseq:3.1

EFEXP commented 3 years ago

This looks like the same issue seen in #335. But it uses no multibyte characters. So not only multibyte characters but some symbols may lead to this error.

drpatelh commented 3 years ago

Did you ever manage to figure this one out @EFEXP ?

EFEXP commented 3 years ago

This issue is still reproducible. I renamed the directory into ゼニゴケ and this issue occurred again. I confirmed multibyte character makes the FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE process crashed. Next, I renamed it into marchantia-rnaseq_data like #335 and no error occured. So, symbols bring #335 are not identified.

nf-core / rnaseq