Instead of pointing to a specific file you use ~a ...
# genomeassemblern
Niklas Schandry
04/10/2025, 6:28 PMInstead of pointing to a specific file you use a wildcard, if all your fq.gz files are in one folder you use a folder
/some/folder/*.fq.gzNiklas Schandry
04/10/2025, 6:31 PMIn your case maybe put all
trim_pudu_HAC_ONT*.fastq.gzONTONT/Niklas Schandry
04/10/2025, 6:37 PMSorry, its been a while since I used that option
m
Maria Bárbara Borges
04/10/2025, 6:54 PMAhh I see
Maria Bárbara Borges
04/10/2025, 6:55 PMI’ll try this. Thank you
Maria Bárbara Borges
04/10/2025, 8:11 PM Copy code
* --input (./pudu/samplesheet.csv): Validation of file failed:
-> Entry 1: Error for field 'ontreads' (/home/vmaracaja/pudu/ONT/): ONT reads cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'
-> Entry 1: Error for field 'ontreads' (/home/vmaracaja/pudu/ONT/): ONT reads cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'Maria Bárbara Borges
04/10/2025, 8:12 PMDoesn't work
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Niklas Schandry
04/11/2025, 6:54 AMI see, that is a problem that needs to be fixed. Until that happens, I would suggest you collect the reads yourself. You can probably do something like
zcat trim_pudu_HAC_ONT*.fastq.gz | gzip > trim_pudu_HAC_ONT_all.fastq.gzm
Maria Bárbara Borges
04/11/2025, 9:46 AMNo problem! That's what I am doing
Maria Bárbara Borges
04/11/2025, 9:46 AMThanks a lot for the help!
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