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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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Nothing will be generate by Epinano_Variants.py #99

Closed JeremyQuo closed 2 years ago

JeremyQuo commented 2 years ago

Hello, I am running some samples in test_data, and it comes some problems. Here is my command

python ../../Epinano_Variants.py -R ref.fa -b ko.bam -n 6 -T t -s ../../misc/sam2tsv.jar

And the log shows like,

koTMP already exists, will overwrite it

No error log and it seems like finished. But nothing generated by this cmd,although readme illustrated that it will generate xxx.var.csv and xxxx.5mer.csv.

Can you help me to solve it please? Thanks

JeremyQuo commented 2 years ago

I find the reason. In readme file , it said these two files can be generated by Epinano_Variants.

However , it just only generate per.site.files. Slide_Variants.py need to deal with it after Epinano_Variants like below,

python ../../misc/Slide_Variants.py ko.plus_strand.per.site.csv 5

And finally, we get it.