Unfamiliar output from bcbio

[gnvalbuena]

I was running a smallRNA analysis on bcbio, and was expecting the output to be like previous analyses I have carried out, where each isomir is specified according to your naming convention. However, the results of my most recent analysis has been the following, which isn't particularly informative

counts.txt

Is this expected? And if it isn't what's likely to be causing it?

[lpantano]

Hi,

sorry about the issues. Not sure exactly what is going on. Can you send me the files inside log folder and the ls of the final folder?

That file is the count for the seqcluster tool that is a general characterization of the data on the genome. It should be inside seqcluster folder.

I am guessing you are not getting any miRNA files?

If you send me those file I may have a better idea of what is going on.

cheers

[gnvalbuena]

Yes, I did take it from the seqcluster folder. in this instance, there weren't any other outputs in the main final folder. I had attached a truncated copy of the file, but there are more columns in the file corresponding to the samples analysed, sorry.

I'm attaching the contents of the log folder here: log.zip

ls of the final folder is here: finalfolderls.txt

Thanks!

[lpantano]

Hi,

I think you don't have the small RNA data installed.

Can I ask whether you are using bcbio_nextgen.py directly or using bcbio through other wrapper, like bcbio_vm.py, etc?

To have the small RNA data installed you can do:

bcbio_nextgen.py upgrade -u development --tools --datatarget smallrna

That assuming you can control that. If you are running bcbio through other tool, let me know and I can ping Brad to ask how to get it installed.

thanks