Inquiry about error message

[simonwisnovsky]

My lab has recently switched from Mageck to guide-counter for generating count tables, we find it a faster and more accurate alternative. We've processed a number of screens without problems. However, I've recently been trying to re-process some older data and keep getting this error message that we have not seen before, see command below:

(base) guide-counter count --input Sig9_C_R1_RC.fastq --library CRISPRilib-20-Top5.txt --output Sig9_C1_R1 [2023-10-27T18:36:57Z INFO guide_counter::guide] Loaded library with 103072 guides for 18787 genes; 0=essential, 0=nonessential, 0=control, 103072=other. [2023-10-27T18:36:57Z INFO guide_counter::commands::count] Building lookup. [2023-10-27T18:36:58Z INFO guide_counter::commands::count] Lookup built with 6285562 entries. thread 'main' panicked at 'range end index 20 out of range for slice of length 19', src/commands/count.rs:258:38 note: run with RUST_BACKTRACE=1 environment variable to display a backtrac

Any ideas as to what is going wrong here? The only difference between these fastq files and ones we have previously used successfully is that the read length is slightly shorter (21 bp vs. 25 bp). Otherwise conditions are exactly the same.

Thanks in advance!

[tfenne]

Thanks for the report @simonwisnovsky - I took a brief look at the code and it's not entirely obvious to me why this is occurring.

Would you be able to share some of your input data with me to help me diagnose? I suspect that the library file and the first few hundred lines of the input FASTQ would be sufficient (if that reproduces the error). I can provide contact info if you don't want to share them publicly but can share privately.

Also, can you please confirm you're using v1.0.3?

[simonwisnovsky]

Hi Tim, Of course, thanks very much. I've put a link below to one of the Fastq files and our library file, please let me know if that works. The library file has worked fine for other fastq files. https://www.dropbox.com/scl/fo/t0qgp17r2n3fbaeoxhwzq/h?rlkey=lde99q0lsrcw3kx4ahwflob61&dl=0 Cheers, Simon Prof. Simon Wisnovsky PhD (He, Him, His https://equity.ubc.ca/resources/gender-diversity/pronouns/) Assistant Professor Faculty of Pharmaceutical Sciences University of British Columbia | Vancouver Campus | Musqueam Traditional Territory 2405 Wesbrook Mall | Vancouver BC | V6T 1Z3 Canada @.***

On Mon, Oct 30, 2023 at 9:20 AM Tim Fennell @.***> wrote:

[CAUTION: Non-UBC Email]

Thanks for the report @simonwisnovsky https://github.com/simonwisnovsky

• I took a brief look at the code and it's not entirely obvious to me why this is occurring.

Would you be able to share some of your input data with me to help me diagnose? I suspect that the library file and the first few hundred lines of the input FASTQ would be sufficient (if that reproduces the error). I can provide contact info if you don't want to share them publicly but can share privately.

Also, can you please confirm you're using v1.0.3?

— Reply to this email directly, view it on GitHub https://github.com/fulcrumgenomics/guide-counter/issues/20#issuecomment-1785571301, or unsubscribe https://github.com/notifications/unsubscribe-auth/BDSJNGDH6HGKOTNLRUX2NGLYB7HULAVCNFSM6AAAAAA6THD6U2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBVGU3TCMZQGE . You are receiving this because you were mentioned.Message ID: @.***>

[tfenne]

Thanks @simonwisnovsky - I was able to replicate the error with version 0.1.2 but not 0.1.3. Could you please try 0.1.3? Thanks!

[simonwisnovsky]

Hi Tim, Ah ok thanks - is the 0.1.3 version on bioconda? I have run conda update and it tells me I already have the latest version. I believe I also did the initial installation after March 2022. Cheers, Simon Prof. Simon Wisnovsky PhD (He, Him, His https://equity.ubc.ca/resources/gender-diversity/pronouns/) Assistant Professor Faculty of Pharmaceutical Sciences University of British Columbia | Vancouver Campus | Musqueam Traditional Territory 2405 Wesbrook Mall | Vancouver BC | V6T 1Z3 Canada @.***

On Tue, Oct 31, 2023 at 7:51 AM Tim Fennell @.***> wrote:

[CAUTION: Non-UBC Email]

Thanks @simonwisnovsky https://github.com/simonwisnovsky - I was able to replicate the error with version 0.1.2 but not 0.1.3. Could you please try 0.1.3? Thanks!

— Reply to this email directly, view it on GitHub https://github.com/fulcrumgenomics/guide-counter/issues/20#issuecomment-1787377308, or unsubscribe https://github.com/notifications/unsubscribe-auth/BDSJNGGC65NNABYU6U3MN2TYCEGALAVCNFSM6AAAAAA6THD6U2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBXGM3TOMZQHA . You are receiving this because you were mentioned.Message ID: @.***>

[tfenne]

Yes - version 0.1.3 is on bioconda (see https://anaconda.org/bioconda/guide-counter). I'm not an expert on conda update, but I think if you run conda install -c bioconda guide-counter=0.1.3 directly it should force the update.