Cutadapt timeout

[priscilla-glenn]

Hi, I've tried running scATACpipe and while this time it started without issues, the cutadapt has timed out. I've included my nextflow.log for your convenience as I'm not sure why it was taking so long to run. I did notice one discrepancy where cutadapt said it was trying to use 32 cores (pasted below) even though in my config file I said the max should be 28 cores. So my one guess would be the computer is trying to use 32 cores when I didn't give it access to 32. Would there be a way to fix it so cutadapt is trying to use 32 cores?

Thanks!

Command output: This is cutadapt 3.4 with Python 3.9.1 Command line parameters: --cores=0 -a AGATCGGAAGAGC -A AGATCGGAAGAGC -o R1_Sample_S1_1.barcoded.trimmed.fastq.gz -p R2_Sample_S1_1.barcoded.trimmed.fastq.gz R1_Sample_S1_1.barcoded.fastq.gz R2_Sample_S1_1.barcoded.fastq.gz Processing reads on 32 cores in paired-end mode ... nextflow.log_May12.txt

Command wrapper: This is cutadapt 3.4 with Python 3.9.1 Command line parameters: --cores=0 -a AGATCGGAAGAGC -A AGATCGGAAGAGC -o R1_Sample_S1_1.barcoded.trimmed.fastq.gz -p R2_Sample_S1_1.barcoded.trimmed.fastq.gz R1_Sample_S1_1.barcoded.fastq.gz R2_Sample_S1_1.barcoded.fastq.gz Processing reads on 32 cores in paired-end mode ...