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giesselmann / STRique

Nanopore raw signal repeat detection pipeline
MIT License
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Error Reading fast5 #3

Closed mattdmem closed 5 years ago

mattdmem commented 5 years ago

Hello,

I get error reading fast5 when trying to run your tool. Any ideas? We are using MinIT and the latest version of MinKnow (19). I think these are multi read fast5s? is this a problem?

Thanks

Matt

LynnLy commented 5 years ago

Multi fast5s were released relatively recently, so I don't think they are compatible with this tool. You can use multi_to_single_fast5 from ONT fast5 api to convert your files to the old single fast5 format and then use STRique.

giesselmann commented 5 years ago

@LynnLy is right, so far we support only the single read fast5 format. I think I can patch it in, possibly next week. Pay

mattdmem commented 5 years ago

Patching it in would be great! Thanks!

mattdmem commented 5 years ago

@LynnLy's method worked - although there were so many fast5s it was taking FOREVER, so I grabbed the relevant read ids from the alignment and just put them in a separate folder.

giesselmann commented 5 years ago

@mattdmem With version v0.2.0 we now support bulk-fast5. I had to change the format of the fast5Index, any index.json generated with previous STRique versions won't work. The reworked command line now requires an index file instead of the raw directory. The index is compatible with the one generated from our nanopype pipeline. Since I also changed the location of the submodules, I would recommend starting with a clean installation as documented in the README. Apologize for that. Please also note that we now provide a Docker container to address the installation / dependency issues around pomegranate and networkx.