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rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
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It didn't generate any output files #55

Closed HaeWon-chung closed 4 years ago

HaeWon-chung commented 4 years ago

Hi,

I finally run mirdeep2 with my data but it doesn't seem to generate any output file. I checked mirdeep_runs folder and there are subfolders but it doesn't contain any output files. There is 1 parameter file and tmp folder. I have attached report log for your review.

report.log

HaeWon-chung commented 4 years ago

I found expression folder which contains html and csv files. But there is single miRNA in miRBase.mrd. Is it what it looks like in general? I'm looking for output.mrd file which I was trying to use for miPIE. But mirdeep2 doesn't seem to generate output.mrd, right?

Drmirdeep commented 4 years ago

Did the tutorial run without errors?

HaeWon-chung commented 4 years ago

The tutorial runs OK. It generated output files. I'll take a closer look why it failed with my files.

mschilli87 commented 4 years ago

@HaeWon-chung: Any update on this? If the tutorial works but you pipeline fails, it's likely an error on you side. Still I'd like to make sure before we relaese a new version of miRDeep2. This is the only issue standing between non-git users and the improvements made to miRDeep2 since February. :wink:

HaeWon-chung commented 4 years ago

I removed and re-installed the software - install.pl works this time. And it seems like working well with my data. It generated csv, html, and output.mrd files. Thanks!

mschilli87 commented 4 years ago

@HaeWon-chung: Thx for updating us. @Drmirdeep: Anything holding back a new release now?

Drmirdeep commented 4 years ago

This is a bug tracker and not a private messaging service! Please use other channels to reach me. And yes, you can do ++ if you like