NanoR reporting 0 for Fast5 files

davidebolo1993 / NanoR

Nanopore data analysis in R

GNU Lesser General Public License v3.0

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NanoR reporting 0 for Fast5 files #18

Closed kuskovich closed 3 years ago

kuskovich commented 3 years ago

When I load my sequencing data from the MinION sequencer and try to run NanoPrepareM, I see this message: Passed FAST5: 0 Failed FAST5: 0 Skipped FAST5: 0 Done

I am not sure whether it is not working because of the directory (I have attached a picture). Any suggestions would be greatly appreciated!

davidebolo1993 commented 3 years ago

Hi @kuskovich,

sorry, but it's hard to tell if this issue is somehow related to the content of your directory. Which directory are you actually giving as input to DataPass/DataFail (data_1st?). NanoPrepareM finds .fast5 files recursively, but maybe there is something wrong with the content of those "barcode*" folders. Can you also try to pass something like "/path/to/fast5_fail/barcode1" as DataFail and "/path/to/fast5_pass/barcode1" to DataPass?

Thanks,

Davide

davidebolo1993 commented 3 years ago

Any updates on this?

kuskovich commented 3 years ago

Hello,

The issue seems to have resolved itself. I think it was an issue with my computer not having the capacity to run such a large data set. I'm working with a team on this project and they were able to successfully run the commands and generate the graphs. Thanks very much!

davidebolo1993 commented 3 years ago

Glad it works!

Best,

Davide