Error executing QC

[vicho33]

Hi! I have this error that not recognize the files in .fastq

Execution cancelled -- Finishing pending tasks before exit -[nf-core/rtnanopipeline] Pipeline completed with errors- WARN: There's no process matching config selector: get_software_versions Error executing process > 'QC (5)'

Caused by: Process QC (5) terminated with an error exit status (255)

Command executed:

barcode=$(basename $(dirname /Users/vicentearriagada/centrigufe/porechop_tim/BC15.fastq)) fastp -i /Users/vicentearriagada/centrigufe/porechop_tim/BC15.fastq -q 8 -l 1000 --length_limit 2000 -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: /Users/vicentearriagada/centrigufe/porechop_tim/BC15.fastq

Work dir: /Users/vicentearriagada/nanotar/NanoRTax/work/20/b04195af89e9561ed0edcd321e4489

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

Using this pipeline:

nextflow run main.nf -profile docker --reads '/Users/vicentearriagada/centrigufe/porechop_tim/*.fastq' --outdir '/Users/vicentearriagada/centrigufe/results_seg_bar' --blast --centrifuge --kraken -name bar

Any idea what can be the problem?

[rjain1990]

Hey, could you resolve the issue. I am also returning similar issue. I am first running a trial command. Could you please help?

nextflow run main.nf -profile test, conda

Execution cancelled -- Finishing pending tasks before exit -[nf-core/rtnanopipeline] Pipeline completed with errors- WARN: There's no process matching config selector: get_software_versions Error executing process > 'QC (1)'

Caused by: Process QC (1) terminated with an error exit status (127)

Command executed:

barcode=$(basename $(dirname /zfs/omics/personal/rjain/NanoRTax/test_data/minimock.fastq)) fastp -i /zfs/omics/personal/rjain/NanoRTax/test_data/minimock.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: 127

Command output: (empty)

Command error: .command.sh: line 3: fastp: command not found

Work dir: /zfs/omics/personal/rjain/NanoRTax/work/02/8c17fa7aef2a323fec9689d2fa9715

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[vicho33]

I had solved this issue working with NanoCLUST on a server with linux centOS 7.7. I had this issue working on my MacBook Pro M1. So in the server just install fastp. conda install fastp

But then I tried the same on my MacBook and it was not possible to install. So I take contact with Hector (developer), and retrieve last time some others issues and he is trying to replicate.