Samplesheet for nanopore reads not working

[hutchinsonmiri]

Hi! I am attempting to use a samplesheet for some nanopore reads but Cecret seems to interpreting the reads as paired-end. I am able to run the pipeline just fine when the fastqs are in a directory. My sample sheet is formatted as follows:
sample,fastq_1,fastq_2
2024028971,/Projects/Research/Cecret/Cecret_v3.12.20240227_nano/nanopore/2024028971.fastq.gz,nanopore
2024028978,/Projects/Research/Cecret/Cecret_v3.12.20240227_nano/nanopore/2024028978.fastq.gz,nanopore
2024028980,/Projects/Research/Cecret/Cecret_v3.12.20240227_nano/nanopore/2024028980.fastq.gz,nanopore

The pipeline reports that paired-end reads were found:
Paired-end Fastq files found : 2024028971
Paired-end Fastq files found : 2024028978
Paired-end Fastq files found : 2024028980

And then fails at the fastqc step.

Do you have any advice? Thanks so much in advance!!

[erinyoung]

!!!

It looks like the documentation doesn't match what the sample sheet is actually supposed to contain. (meaning, this is my issue, not yours)

What happens if you use ont for column 3 (the fastq_2 column) instead of nanopore?

sample,fastq_1,fastq_2
2024028971,/Projects/Research/Cecret/Cecret_v3.12.20240227_nano/nanopore/2024028971.fastq.gz,ont
2024028978,/Projects/Research/Cecret/Cecret_v3.12.20240227_nano/nanopore/2024028978.fastq.gz,ont
2024028980,/Projects/Research/Cecret/Cecret_v3.12.20240227_nano/nanopore/2024028980.fastq.gz,ont

[hutchinsonmiri]

Thanks! Strangely when I try that, it seems to be interpreting 'ont' as the name of one of the reads as artic begins to proceed (according to the command error):

usage: artic [-h] [-v]
{extract,basecaller,demultiplex,minion,gather,guppyplex,filter,rampart,export,run}
...
artic: error: unrecognized arguments: ont]

Also, I am getting this error (repeated for each of the samples):
[4f/64a662] NOTE: Missing output file(s) artic/2024028971_filtered.fastq.gz expected by process CECRET:cecret:artic_read_filtering (2024028971) -- Execution is retried (1)

Thanks again for your help!!

[erinyoung]

I'm going to have to look into this. My kiddo is home because of a school break, but I'm confident I can fix this by tomorrow.

[hutchinsonmiri]

Thanks a bunch!!! I really appreciate it.

…

On Mon, Oct 21, 2024 at 12:19 PM Young ***@***.***> wrote: I'm going to have to look into this. My kiddo is home because of a school break, but I'm confident I can fix this by tomorrow. — Reply to this email directly, view it on GitHub <#375 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJBA2KGD7L3GKPKYVL43VGTZ4VARPAVCNFSM6AAAAABQGLPF2CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRXGQYTCMJSGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[erinyoung]

I've created a PR that should fix the issue: #378

Basically, the nanopore file was read in with an extra string which was causing the error.

This PR is currently undergoing testing, but once testing is finished, version 3.15.24296 will be released and shouldn't have that extra string that is throwing the error.

[erinyoung]

It should be fixed now. Let me know if you run into issues!

[hutchinsonmiri]

Thanks!!!! Appreciate your assistance!!

…

On Tue, Oct 22, 2024 at 4:48 PM Young ***@***.***> wrote: I've created a PR that should fix the issue: #378 <#378> Basically, the nanopore file was read in with an extra string which was causing the error. This PR is currently undergoing testing, but once testing is finished, version 3.15.24296 will be released and shouldn't have that extra string that is throwing the error. — Reply to this email directly, view it on GitHub <#375 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJBA2KCDFUTLM36JVHDJQLDZ43I4BAVCNFSM6AAAAABQGLPF2CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZQGQ2TMMRVGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>