I'm running cutadapt using singularity on WSL2. I'm using the biocontainers container version 3.5 (also tested on 3.2).
When running:
singularity exec docker://quay.io/biocontainers/cutadapt:3.5--py36hc5360cc_0 cutadapt --cores=0 -a GTGYCAGCMGCCGCGGTAA -A GGACTACNVGGGTWTCTAAT -o out_R1.fastq.gz -p out_R2.fastq.gz 1a_S103_L001_R1_001.fastq.gz 1a_S103_L001_R2_001.fastq.gz
I get:
This is cutadapt 3.5 with Python 3.6.13 Command line parameters: --cores=0 -a GTGYCAGCMGCCGCGGTAA -A GGACTACNVGGGTWTCTAAT -o out_R1.fastq.gz -p out_R2.fastq.gz 1a_S103_L001_R1_001.fastq.gz 1a_S103_L001_R2_001.fastq.gz Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation. cutadapt: error: [Errno 2] No such file or directory
It works with --cores=1 and it also works on an ubuntu machine (with multiple cores) using singularity.
The input files were downloaded from nf-core ampliseq test files, they are valid.
I'm running cutadapt using singularity on WSL2. I'm using the biocontainers container version 3.5 (also tested on 3.2).
When running:
singularity exec docker://quay.io/biocontainers/cutadapt:3.5--py36hc5360cc_0 cutadapt --cores=0 -a GTGYCAGCMGCCGCGGTAA -A GGACTACNVGGGTWTCTAAT -o out_R1.fastq.gz -p out_R2.fastq.gz 1a_S103_L001_R1_001.fastq.gz 1a_S103_L001_R2_001.fastq.gzI get:
This is cutadapt 3.5 with Python 3.6.13 Command line parameters: --cores=0 -a GTGYCAGCMGCCGCGGTAA -A GGACTACNVGGGTWTCTAAT -o out_R1.fastq.gz -p out_R2.fastq.gz 1a_S103_L001_R1_001.fastq.gz 1a_S103_L001_R2_001.fastq.gz Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation. cutadapt: error: [Errno 2] No such file or directoryIt works with
--cores=1and it also works on an ubuntu machine (with multiple cores) using singularity.The input files were downloaded from nf-core ampliseq test files, they are valid.