Dear all

many thanks for putting together this great tool. I had the error pointed at this issue title. Here is what I have done:

1- Clone the repository git clone https://github.com/palmuc/TransPi.git

2- Move to the TransPi directory cd TransPi

3- Install bash precheck_TransPi.sh /media/david/90aba6e6-45be-4827-9400-ae7db2b6022c/

used the singularity option

4- Run the pipeline

nextflow run TransPi.nf --all --maxReadLen 150 --k 25,35,55,75,85 \ --reads '/media/david/90aba6e6-45be-4827-9400-ae7db2b6022c/fastqc_files/*_R[1,2].fastq.gz' --outdir out_Ccelo \ -profile singularity,TransPiContainer

Examples of the fastq files names: Ccelos_S1_L001_R1.fastq.gz ; Ccelos_S1_L001_R2.fastq.gz

ERROR:

Error executing process > 'fastp (Ccelos_S1_L001)'

Caused by: Process fastp (Ccelos_S1_L001) terminated with an error exit status (127)

Command executed:

fastp -i Ccelos_S1_L001_R1.fastq.gz -I Ccelos_S1_L001_R2.fastq.gz -o left-Ccelos_S1_L001.filter.fq -O right-Ccelos_S1_L001.filter.fq --detect_adapter_for_pe --average_qual null --overrepresentation_analysis --html Ccelos_S1_L001.fastp.html --json Ccelos_S1_L001.fastp.json --thread 1 --report_title Ccelos_S1_L001

v=$( fastp --version 2>&1 | awk '{print $2}' ) echo "fastp: $v" >fastp.version.txt

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 2: fastp: command not found

Work dir: /media/david/90aba6e6-45be-4827-9400-ae7db2b6022c/TransPi/work/51/626cb6ae865c314206ae95e7e67f70

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

Here is the equipment and software info: Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz ; Linux Linux version 5.4.0-73-generic (buildd@lcy01-amd64-019) (gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04))

Many thanks

Ricardo

PalMuc / TransPi

Process `fastp (Ccelos_S1_L001)` terminated with an error exit status (127) #42

used the singularity option