Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ERROR: file [DRR016125_2.fastq.gz] does not appear to exist! #963

Open
ElToronjas opened this issue Oct 1, 2024 · 0 comments
Open

ERROR: file [DRR016125_2.fastq.gz] does not appear to exist! #963

ElToronjas opened this issue Oct 1, 2024 · 0 comments

Comments

@ElToronjas
Copy link

Hi,
I just installed salmon using conda. I tried to execute the sample test that comes on the main page: https://combine-lab.github.io/salmon/getting_started/

When I try to run the quantification code
#!/bin/bash
for fn in data/DRR0161{25..40};
do
samp=basename ${fn}
echo "Processing sample ${samp}"
salmon quant -i athal_index -l A
-1 ${fn}/${samp}_1.fastq.gz
-2 ${fn}/${samp}_2.fastq.gz
-p 8 --validateMappings -o quants/${samp}_quant
done
even though the files are there, in the data directory, the tool seems to not recognize the fastq files and pops the following error for every DRR0161xx_x.fastq.gz file:
ERROR: file [DRR016140_2.fastq.gz] does not appear to exist!

]
salmon quant was invoked improperly

Is this some common error or is it a new bug?
Thanks in advance for any response/suggestion on how to proceed here

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant