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pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
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CRISPResso2_Pooled #188

Closed Nikita-Sharaev closed 1 year ago

Nikita-Sharaev commented 2 years ago

Hello, I use the CRISPRessoPooled command to analyze several cleavage sites in the bacterial genome. Previously, it was ok, but the Pooled version stopped working at some point. Now I get only this message:

ERROR: invalid literal for int() with base 10: b''

And CRISPRessoPooled interrupts after it. Please, can you explain how to fix it? The log file, file with amplicons, and command are applied. Thanks!

Command: CRISPRessoPooled -r1 NSh_11_S75_R1_001.fastq -r2 NSh_11_S75_R2_001.fastq -f amplicons_pooled.txt --name NSh_11_1

amplicons_pooled.txt CRISPRessoPooled_RUNNING_LOG.txt

kclem commented 2 years ago

Hi @Nikita-Sharaev,

Thanks for using CRISPResso. It looks like the error is coming from bowtie2 not being able to index your input file.

It appears that your amplicons_pooled.txt file is space-separated. Can you try to change the spaces to tabs and run again?

If that doesn't work, can you try running the command bowtie2-build --wrapper basic-0 CRISPRessoPooled_on_NSh_11_1/AMPLICONS.fa CRISPRessoPooled_on_NSh_11_1/CUSTOM_BOWTIE2_INDEX to see if there is more detailed output?

kclem commented 2 years ago

Hi @Nikita-Sharaev,

Did this solve your problem? If so, would you mind giving an update in case others have this same problem?

Thanks,

Kendell

kclem commented 1 year ago

We're closing this issue because it hasn't been updated recently. If this issue still exists, please reopen this issue and we'll look into it!