Filtering error although reads are good quality

[clarazourray]

Hi, I have tried to run CRISPResso2 on batch mode using Ubuntu and paired-end reads fastq files. It is able to combine the reads using the FLASH command but I then get a filtering error saying that no reads have survived the quality filtering. However I have checked my reads using FASTQC and all my reads have a quality score above 30.

This is the error I get. I am also getting a strange 'exec gzip: Exec format error' which I am not sure where it's coming from as I unzipped the .gz files before running them...

Debug output

Thanks for your help!

[Colelyman]

Hi @clarazourray,

Thanks for using CRISPResso2! This seems like a strange error. It doesn't look like there is an error with your reads, but I suspect there is an issue unzipping the results from FLASH (thereby resulting in no reads).

Do you happen to be running CRISPResso2 under WSL? If so, it looks like there is an issue with a specific version of gzip (see here and here). If you are using WSL, could you try and run this command to install a (hopefully) working version of gzip?

apt install gzip=1.10-4ubuntu1

Alternatively, you can download the .deb file here gzip 1.10-4ubuntu1. After installing, you can try and rerun CRISPResso to see if that makes a difference.

If you would rather not go through this trouble, an other option is to run CRISPResso in the Docker container which won't be affected by this issue.

Good luck, Cole

[clarazourray]

Hi Cole,

Thanks for the quick reply.

It appears that that version of gzip is no longer available (perhaps as Linux Impish is no longer supported?), however, changing from WSL Version 1 to WSL Version 2 fixed the gzip problem and everything is working smoothly now!

Thanks again for your help :)

[Colelyman]

Glad to hear that you got it working! Good luck analyzing your experiments.

On Sep 12, 2022, at 4:18 AM, clarazourray @.***> wrote:

Hi Cole,

Thanks for the quick reply.

It appears that that version of gzip is no longer available (perhaps as Linux Impish is no longer supported?), however, changing from WSL Version 1 to WSL Version 2 fixed the gzip problem and everything is working smoothly now!

Thanks again for your help :)

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