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base calling error

Open oohas2000 opened this issue 1 year ago • 1 comments

Hi, I have this following error while executing preprocess: [9c/129f0f] process > baseCalling (guppy-RedOak_WGA-0) [100%] 1 of 1, failed: 1 ✘ [- ] process > concatenateFastQFiles - [- ] process > QC - [- ] process > fastQC - [- ] process > mapping - [- ] process > counting - [- ] process > joinCountQCs - [- ] process > alnQC - [- ] process > joinAlnQCs - [- ] process > alnQC2 - [- ] process > multiQC - Skipping the email

MultiFast5 files detected! WARN: The echo directive has been deprecated - use to debug instead Error executing process > 'baseCalling (guppy-RedOak_WGA-0)'

Caused by: Process baseCalling (guppy-RedOak_WGA-0) terminated with an error exit status (255)

Command executed:

guppy_basecaller --flowcell FLO-MIN106 --kit SQK-LSK109 --fast5_out -i ./ --save_path ./0_out --cpu_threads_per_caller 1 --gpu_runners_per_device 1 --num_callers 8 cat 0_out/.fastq >> 0.fastq rm 0_out/.fastq gzip 0.fastq

Command exit status: 255

Command output: (empty)

Command error: Unexpected token '--fast5_out' on command-line. Try 'guppy_basecaller --help' for more information.

Work dir: /nfs/data/projects/Xylella/master_of_pores/NanoPreprocess/work/9c/129f0ff9f8a6d830a50964470517c3

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

oohas2000 avatar Sep 08 '23 09:09 oohas2000