Hello, I'm having trouble running this pipeline with a Docker profile. Although I receive no errors when running the provided test, errors occur when I use my own reads (sequenced sputum) with the Docker profile.
This issue is the same as #2 and may be due to a faulty creation of the Conda environment. I'm opening a new issue on this error since the previous one was not responded to.
This is the error message I get:
Error executing process > 'QC (1)'
Caused by:
Process `QC (1)` terminated with an error exit status (255)
Command executed:
barcode=$(basename $(dirname /Volumes/NanoporeM1C/Nanopore_sequencer_data/Cobalt/sediment_16S/20220613_1441_MC-112933_FAS49702_5a81a876/fastq_pass/barcode09/consolidated09.fastq))
fastp -i /Volumes/NanoporeM1C/Nanopore_sequencer_data/Cobalt/sediment_16S/20220613_1441_MC-112933_FAS49702_5a81a876/fastq_pass/barcode09/consolidated09.fastq -q 8 -l 1400 --length_limit 1700 -o $barcode\_qced_reads.fastq --json $barcode\_qc_report.txt
head -n30 $barcode\_qc_report.txt | sed '30s/,/\n}/' > $barcode\_qc_report.json
echo "}" >> $barcode\_qc_report.json
Command exit status:
255
Command output:
(empty)
Command error:
ERROR: Failed to open file: /home/brijvers/data/volume_2/subsets/bc09_10/bc09_10.fastq
I triple checked the path to the input reads and other tools can open the file and use it. Nextflow is installed (and works) in the Conda environment I'm working in, Docker is also properly installed.
In the work directory, the '.command.begin', '.command.out', '.command.trace' and '.exitcode' files are empty.
If anyone could provide me with some guidance on how to resolve this issue or suggest a starting point for fixing it, I would be grateful!
Hello, I'm having trouble running this pipeline with a Docker profile. Although I receive no errors when running the provided test, errors occur when I use my own reads (sequenced sputum) with the Docker profile.
This issue is the same as #2 and may be due to a faulty creation of the Conda environment. I'm opening a new issue on this error since the previous one was not responded to.
This is the error message I get:
I triple checked the path to the input reads and other tools can open the file and use it. Nextflow is installed (and works) in the Conda environment I'm working in, Docker is also properly installed.
In the work directory, the '.command.begin', '.command.out', '.command.trace' and '.exitcode' files are empty.
If anyone could provide me with some guidance on how to resolve this issue or suggest a starting point for fixing it, I would be grateful!