Reading fastq files from subfolder

[YoavLub]

I'm trying to run crispressobatch however my fastq files are in subfolders for each clone.
Is there a way to get the program to read them while running in the parent directory?
I tried specifying the complete path in the .batch file but no luck.
Thanks
Crispresso_batch_samplesheet.txt
.
That's the command I used
CRISPRessoBatch --batch_settings Crispresso_batch_samplesheet.batch --amplicon_seq CCCAGGTCGTTGTTTTTTCCAGCTTAGAAGCCATGGCGCACCTCCATTTTTGTGCGCTCTCCTAATGAGGTTTTTTTTTCCCCTTCCGGACCTGTTTTAGTATTA -g AGGAGAGCGCACAAAAATGG --expected_hdr_amplicon_seq cccaggtcgttgttttttccagcttagaagccatggcgcacctcGaAtAttgtgcgctctcctaatgaggtttttttttccccttccggacctgttttagtatta
Thanks.

[kclem]

Having data in folders shouldn't be a problem.

How are you running CRISPResso? Are you running this with docker or conda? What operating system are you on?

CRISPResso prints out the files it can 'see' in the current working directory -- does it print out the expected files?

You may try deleting the initial "./" from each of the paths. Does that work?

[YoavLub]

Thanks for replying.
I run conda on a linux server.
It doesn't see the files just the top folders.
The error I get is
ERROR: The specified file ‘’ cannot be opened.
Available files in current directory:
._batch_samplesheet1.batch
210816_A00929_0424_BHHGJTDRXY
210725_A00929_0393_AHG52KDRXY
Crispresso_batch_samplesheet.batch
batch_samplesheet1.batch
._Crispresso_batch_samplesheet.batch
If I copy the fastq files to a single folder and run in it then it runs just fine.

[kclem]

Your batch file has a few empty newlines at the end of it -- perhaps those are throwing it off -- if you delete those lines, does it work?

I'll put in a check to remove blank lines on imports in the future.

[YoavLub]

Removing the empty lines solved the problem.
Thanks