issue while running nf core

[Varda06]

Description of the bug

ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (ctrl1)'

Caused by:
Process NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (ctrl1) terminated with an error exit status (1)

Command executed:

fq lint
--disable-validator P001
ctrl1_1.merged.fastq.gz ctrl1_2.merged.fastq.gz > ctrl1.fq_lint.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT":
fq: $(echo $(fq lint --version | sed 's/fq-lint //g'))
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
ctrl1_2.merged.fastq.gz:50027986:114: [S002] AlphabetValidator: invalid sequence character: 'I'

Work dir:
/wynton/group/ahituv/bin/pipelines/nf-core-rnaseq/work/work/68/45178fc0bb9f79f0f7cdc7b7c65a99

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

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

Command used and terminal output

Relevant files

No response

System information

No response

[tdanhorn]

The key message is ctrl1_2.merged.fastq.gz:50027986:114: [S002] AlphabetValidator: invalid sequence character: 'I'. This means that you apparently have an "I" in the nucleotide sequence of your FASTQ (could be for "inosine", or just a corrupted file), which is not standard and therefore not allowed by the tools. Make sure your file is not corrupted. If it is not and the base is actually supposed to be inosine or something, you can replace it with an N.