Running error of exit status 255

[aslangabriel99]

Description of the bug

I ran the pipeline with my own data the command line is "nextflow run nf-core/bacass -r 2.2.0 -profile docker --input ./minikrakendb/baccsamplesheet.tsv --kraken2db /home/aslangabriel/minikrakendb/k2_standard_08gb_20240112.tar.gz --max_cpus 12 --max_memory '125.GB' --outdir ./minikrakendb/results", my sample sheet looks like that

and the error message was as follows
"-[nf-core/bacass] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP (JSAHVC01)'

Caused by:
Process NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP (JSAHVC01) terminated with an error exit status (255)

Command executed:

[ ! -f JSAHVC01_1.fastq.gz ] && ln -sf JSAHVC01_S1_R1.fastq.gz JSAHVC01_1.fastq.gz
[ ! -f JSAHVC01_2.fastq.gz ] && ln -sf JSAHVC01_S1_R2.fastq.gz JSAHVC01_2.fastq.gz
fastp
--in1 JSAHVC01_1.fastq.gz
--in2 JSAHVC01_2.fastq.gz
--out1 JSAHVC01_1.fastp.fastq.gz
--out2 JSAHVC01_2.fastp.fastq.gz
--json JSAHVC01.fastp.json
--html JSAHVC01.fastp.html



--thread 8
--detect_adapter_for_pe

2> >(tee JSAHVC01.fastp.log >&2)

cat <<-END_VERSIONS > versions.yml
"NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP":
fastp: $(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS

Command exit status:
255

Command output:
(empty)

Command error:
ERROR: Failed to open file: JSAHVC01_1.fastq.gz

Work dir:
/home/aslangabriel/work/d0/6d8835e9fba25be3a34dcf33080fa2

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 have changed the file name per se the test example. please help me to fix it.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[Daniel-VM]

Hi @aslangabriel99 !,

Command error says that is something related to the file/filepath. Let's try to debug it.

• Double check filepath
• try gunzip -t /home/shpc_1100038APECrawread/JSAHVC01_S1_R1.fastq.gz to verify file integrity.
• Does the /home/aslangabriel/work/d0/6d8835e9fba25be3a34dcf33080fa2/.command.* files provide any clue?.