Maintain input folder hierarchy on conversion to/from fast5 about pod5-file-format HOT 6 CLOSED

Hello - it seems like you already have files in the output location, or alternatively files named the same thing in your input?

Can you show me the tree of files you are trying to convert in the input/output, and the exact command you are running?

Thanks,

• George

from pod5-file-format.

Hi, yes files in the input are named the same, that was the point I was making. It is (was?) done so by default when minknow splits reads into fast5_fail and fast5_pass.

I couldn't find any documentation on if it is better to keep 4000 reads/file or if it is better to store more reads per pod5 file?

from pod5-file-format.

In this case input files are named like this:
20191118_1537_MN19470_FAK64715_2f44e93d/fast5_fail/FAK64715_3b9c09954054f5908e63cf500553a769d9b98cea_0.fast5
20191118_1537_MN19470_FAK64715_2f44e93d/fast5_pass/FAK64715_3b9c09954054f5908e63cf500553a769d9b98cea_0.fast5

So I assumed this is what caused the error but it could also be from duplicated folders.

from pod5-file-format.

OK - I'll have a look at respecting the input hierarchy shortly.

I couldn't find any documentation on if it is better to keep 4000 reads/file or if it is better to store more reads per pod5 file?

Its really up to you and how you want to use the data, there is no performance downside to putting all the data into one file.

If you are doing the conversion to archive the data, it may be more convenient to have one large file.

• George

from pod5-file-format.

Ok, thanks. Having too many reads per file was a problem for some tools with fast5 but perhaps this is one of the reasons for the format being replaced. For large runs it may still be better to split reads into multiple files, so would be good if there was an option to define how many reads to store per pod5 file.

from pod5-file-format.

Hi @olawa,

Please try the latest release, where the conversion scripts now have --file-read-count as an option, and to maintain the input folder hierarchy.

• George

from pod5-file-format.