Closed maximilianmordig closed 10 months ago
Hey,
we will have a look a the fast5 data, but how old are these fast5 files, and does it happen with all fast5 files, or only some?
Cheers, James
Thanks for looking into it. I think they are quite old. 30/89 files pass.
Hi @maximilianmordig
We have downloaded that dataset and inspected it. It is another weird form of FAST5 files (probably the 100th different type of FAST5 we have come across). This time, it identifies as a single fast5 based on the file version but is multi-fast5.
There are two ways to get these sort of files converted:
wget -O ERR9127551_RefStrains210914_NK_barcode02.blow5 https://unsw-my.sharepoint.com/:u:/g/personal/z5136909_ad_unsw_edu_au/Ecag7i1h41xFnmOQTbUhqLkBtUtkCdoorBtQgfgxT1IWng?download=1
wget -O ERR9127551_RefStrains210914_NK_barcode02.blow5.idx https://unsw-my.sharepoint.com/:u:/g/personal/z5136909_ad_unsw_edu_au/EcOqgJWo-1VAh21NUk8ZGD4BBKw0rMTwRIDUgecCk_MDsg?download=1
Hey @maximilianmordig,
Thank you reporting this.
The fast5 files you have shared don't have file version
or file type
attributes. Hence, the program cannot detect them as multi-fast5
and decides them as the default single-fast5
files. This causes the problems you faced.
I added verbose lines to print what the program decides the file types to be (slow5tools --verbose 7 f2s ...
).
Additionally, I introduced an enforce-multi-fast5
feature (slow5tools f2s --enforce-multi-fast5 ...
) this will enforce the program to handle files as multi-fast5
. Use this branch.
If a conversion fails, use verbose output to check if the program has failed detect the correct file type. If so, then use --enforce-multi-fast5
if appropriate. This flag is not visible in the f2s
help message, as this is not a common scenario.
@maximilianmordig has this issue been resolved?
@hasindu2008 @hiruna72 Sorry for the slow reply, I wasn't feeling well recently. I checked the tool and it works now! Thank you very much.
I am trying to convert data to slow5 and get the following error:
The archive is big, so you can stop after encountering one file.
The output from slow5tools v1.1.0 is:
Running with
lossless
:I don't know which field is missing, it would be helpful to add this to the error message.
Btw, the help seems to be incorrect:
lossless takes an argument.