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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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Issue when performing 'nanodisco characterize' #30

Closed lorenzocasbarra closed 1 year ago

lorenzocasbarra commented 2 years ago

Dear Dr. Tourancheau, I'm a phd student approaching for the first time to nanopore sequencing and DNA methylation characterization. I was trying to use nanodisco out of curiosity and everything proceeded fine until the typing and fine mapping step. In this step I performed the following call: # nanodisco characterize -p 20 -b Ecoli -d dataset/EC_subset_difference.RDS -o analysis/motif_detection/Ecoli_motifs -m CTGRYG,AWTMWTKAWAAAWR,CRCCAKCWGCGCRA,CTKCTCGKYAAAAC,ACWTCGMTCCSKGC -t nn,rf,knn -r reference/Escherichia_coli_ATCC_35218.fasta Which returned the following error: Error in { : task 2 failed - "arguments imply differing number of rows: 1, 0" Calls: find.signature.center -> %do% -> Execution halted # I also tried the following: nanodisco characterize -p 20 -b Ecoli -d dataset/EC_subset_difference.RDS -o analysis/motif_detection/Ecoli_motifs -m CTGRYG -t nn,rf,knn -r reference/Escherichia_coli_ATCC_35218.fasta Which returned the following error: Error in { : task 2 failed - "arguments imply differing number of rows: 1, 0" Calls: find.signature.center -> %do% -> Execution halted # Hoping that you can help me with some advice, I provide a txt file explaining more in detail the calls I performed in my pipeline (https://drive.google.com/file/d/1ZMJxPnyO_ioS6wL1YQEofnq8mRjJMBv6/view?usp=sharing). You can also find my workspace compressed at the following link (which is approximatly 1GB): https://drive.google.com/file/d/1rtiDOthSBrA_j6-VrqxxgowXvjBcs1rv/view?usp=sharing Thank you for your time and attention. Kind regards, Lorenzo Casbarra

touala commented 2 years ago

Hello Lorenzo,

I'd like to apologize for making you wait for so long and thank you for sending your workspace.

Looking at the fast5 shared, I can see that the genome must be only shallowly covered. Is this the full dataset? If it is, nanodisco won't be able to work as it require at least 5x to compute statistics. This results in dataset/EC_subset_difference.RDS being mostly empty (many NA for all statistics). Otherwise, after a quick look, I think the commands are fine.

Alan

lorenzocasbarra commented 2 years ago

Hello Alan, Sorry for my late response and thank you for your help, I really appreciate it. Effectively, the fast5 used doesn't represent the full dataset. I just tried out nanodisco with it, since it is the only basecalled fast5 at my disposal. I'm hoping to basecall the others in a matter of time and I'll let you know if any other issues arise. Thanks again!

Il giorno mer 1 dic 2021 alle ore 23:43 touala @.***> ha scritto:

Hello Lorenzo,

I'd like to apologize for making you wait for so long and thank you for sending your workspace.

Looking at the fast5 shared, I can see that the genome must be only shallowly covered. Is this the full dataset? If it is, nanodisco won't be able to work as it require at least 5x to compute statistics. This results in dataset/EC_subset_difference.RDS being mostly empty (many NA for all statistics). Otherwise, after a quick look, I think the commands are fine.

Alan

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