nf-core
Command error: ln: Sample_Name.fastq.gz: File exists
I'm running methylseq v2.6.0 on some RRBS data, but am having some trouble. I've been getting the error:
ERROR ~ Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE (MBioS_BACD)'
Caused by:
Process NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE (MBioS_BACD) terminated with an error exit status (1)
Command executed:
[ ! -f MBioS_BACD.fastq.gz ] && ln -s L10767_EKDL240033743-1A_22FYT3LT4_L2_1.fq.gz L10767_EKDL240033743-1A_22FYT3LT4_L2_2.fq.gz MBioS_BACD.fastq.gz
trim_galore
--fastqc --rrbs
--cores 8
--gzip
MBioS_BACD.fastq.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE":
trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.version //; s/Last.$//')
cutadapt: $(cutadapt --version)
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
ln: MBioS_BACD.fastq.gz: File exists
Work dir:
/gpfs01/home/sbzoh/F3_Liver/work/c4/02282c9975862e1425406903f4193c
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
I'm not sure why the file existing would give an error, as this should surely stop the symbolic link to the 2 input files being formed and trim galore should continue with the merged MBioS_BACD.fastq.gz file?
