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# crisprseqs
Slackbot
11/12/2024, 8:59 AMThis message was deleted.
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Laurence Kuhlburger
11/12/2024, 9:54 AMCould you please paste the full error?
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Dominik Beck
11/13/2024, 7:02 AMHi Laurence,
Thank you so much for your reply and trying to help out ! Sorry for replying at odd times, I’m located in Sydney. I have no updated to crisprseq v 2.30 and run through all possible parameters on the test dataset provided on your website as well as my own dataset. See comparison attached. I’m running it issue with RRA and MLE.
Dominik Beck
11/13/2024, 7:12 AMIt seems that with RRA I’m running into issue when I have more than two datasets (i.e. on control and one treatment vs 3 control and 3 treatments). I wonder if I have the samplesheet.csv wrong ? This is how I used it ?
Dominik Beck
11/13/2024, 7:15 AMWhen I use MLE essentially the error comes from NFCORE_CRISPRSEQCRISPRSEQ SCREENINGMAGECK_FLUTEMLE and I have no idea how where its coming from :o I wonder if you might be able to guess and then I can try to fix it ?
Dominik Beck
11/13/2024, 7:16 AMWith Bagle2 I only have an error on my own dataset :0 It looks rather complicated :0
Dominik Beck
11/13/2024, 7:17 AMSorry to bombard you with all of this, I understand if you don't have time to answer ! Thanks, dominik !
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Laurence Kuhlburger
11/13/2024, 8:34 AMCould you try making your own design matrix and running mle with
--mle_design_matrixLaurence Kuhlburger
11/13/2024, 8:35 AMIn your sample sheet, could you give unique condition names in the condition column ? eg “control_1"control_2 ” and adapt the contrast file accordingly?
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Dominik Beck
11/14/2024, 6:19 AMHi Laurence,
I did run it with a design matrix (see attached) and the command below on your test dataset but I’m still getting the same error message (see attached). The design matrix that I used to run the command looks exactly like the design matrix generated by the code (“control_vs_treatment”).
This was the command:
Copy code
nextflow run nf-core/crisprseq --analysis screening --input samplesheet_test.csv --library brunello_target_sequence.txt --contrasts rra_contrasts.txt --mle --mle_design_matrix design_matrix.txt --outdir test_mle -profile dockerl
Laurence Kuhlburger
11/14/2024, 8:48 AMis there anyway you can also send me the .command.err log from your work directory
work/b0/625f42Laurence Kuhlburger
11/14/2024, 8:49 AMi don’t understand what is making FluteMLE to fail. Are you running it with conda, docker or singularity?
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Dominik Beck
11/15/2024, 7:25 AMHi Laurence, I just looked at the folder, and surprisingly enough it contains a number of graphs and data. I put them in a zip file, its quite large so will try to send this here. Lets see if it sends 🙂
Dominik Beck
11/15/2024, 7:26 AMI'm running it on singularity 🙂
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Laurence Kuhlburger
11/15/2024, 7:26 AMokay i’m not sure why the pipeline fails at this step then 😕
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Dominik Beck
11/15/2024, 7:42 AMOk thanks for your help though 🙂 Is there a way to possibly deactivate the MAGeCKFlute part so that the rest runs through ?
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Laurence Kuhlburger
11/15/2024, 7:45 AMNot yet but if you’d like to contribute you’re more than welcome 🙂 I was thinking about implementing something like this
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Dominik Beck
11/15/2024, 7:49 AMI'd love to, but I'm probably not a good enough programmer 😂
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Laurence Kuhlburger
11/15/2024, 7:51 AMIt’d be adding one optional parameter and if clauses, it’s actually a pretty good beginner issue 🙂
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Dominik Beck
11/15/2024, 8:07 AMI guess, but I wouldn't know where the code is, or how to compile it 😅
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