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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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SVM.py gives error #36

Closed sem0036 closed 4 years ago

sem0036 commented 4 years ago

Command: ~/EpiNano/scripts/SVM.py -a -t mod.tsv.per.site.var.csv -p unm.tsv.per.site.var.csv -cl 1-5 -mc 11 -o test

gives the error message "IndexError: single positional indexer is out-of-bounds" and I'm unclear on how to fix this issue

Huanle commented 4 years ago

Hi @sem0036 , Are you using python3? it seems you are training with only modified sample, min telling me why is that? Normally the error mesage will include the line number of the script. Maybe you did not copy the complete error message. can you confirm?

enovoa commented 4 years ago

hi @sem0036 please let us know if using python3 solved the issue. thanks! Eva

sem0036 commented 4 years ago

Even with python3 it still is giving me this error.

enovoa commented 4 years ago

Hi @sem0036 - have you tried using the data in the example folder?

sem0036 commented 4 years ago

I've tried with the example data (my first question was the modified vs unmodified) and with my own data, both give me the same Index Error.

Huanle commented 4 years ago

Hi @sem0036, would you mind sending your data to me so that i can have a test and help to figure out what has been going 'wrong'? Thanks.

enovoa commented 4 years ago

Huanle - i think @sem0036's problem is unrelated to the data, as she has tried with the fast5 in the repo. @sem0036 if you could provide a more descriptive explanation of your error (e.g. versions that you currently have in your environment etc) that would be the best to troubleshoot. Index errors in my experience are related to problems in python versions used. Best, Eva

Huanle commented 4 years ago

@sem0036, @enovoa, I only see the command using @sem0036 's own data but not the one with example inputs. 

python3.6 scripts/SVM.py -a -t examples/svm_input/sample1.csv -p examples/svm_input/sample2.csv -cl 3 -mc 11 -o test

The above command with example inputs work on my machine. BTW, it is doing training with sample1 and testing with sample2. So, it would be nice if you can: 1) send me the command you are using with example inputs; 2) let me know your python version, mine is python3.6, under which I coded SVM.py; 3) run pip3 freeze and double check if you have all requested versions of python modules installed ?

Thanks a lot.

sem0036 commented 4 years ago

Thank you for all the quick responses, @enovoa was correct in that is was incomplete python installation!