Closed Nikita-Sharaev closed 1 year 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?
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
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!
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