# Albacore basecalling running but outputs 0 reads

I am trying to basecall data produced by the MinION using the SQK-LSK109 kit and FLO-MIN106 flowcell via the command-line. My version of albacore is the latest (v2.3.4). I tried running using the following command-line (the name of the sequencing run and fast5s are different and are default from machine output):

python3.6 /home/dkennetz/.local/bin/read_fast5_basecaller.py -i ./seqrun/fast5/ -t 1 -s ./good_reads/ -f FLO-MIN106 -k SQK-LSK109 -r -o fastq


-t 1 is just for this test. It is running and finishing almost instantly with 0 errors but outputting no reads. I have previously run this same command-line using the SQK-LSK108 kit and had no problems.

I then went on to validate the fast5s using the h5_validate tool:

python3.6 /home/dkennetz/.local/bin/h5_validate /home/dkennetz/.local/lib/python3.6/site-packages/h5_validator/schemas/single_read_fast5.yaml seqrun/fast5/0/seqrun.fast5 -v


The output from this is:

    Matcher <'UniqueGlobalKey', type=group match_type=exact count=
{'minimum_count': 1, 'maximum_count': 1}> was not satisfied after matching <HDF5 file "seqrun.fast5" (mode r)>

Error at /:

{'minimum_count': 1, 'maximum_count': 1}> was not satisfied after matching <HDF5 file "seqrun.fast5" (mode r)>


I read on the community page that this may be because the header is missing some relevant meta-data information? Any help on how to fix this would be greatly appreciated!

This is cross-posted on the community page for ONT here:

https://community.nanoporetech.com/posts/albacore-basecalling-runni

\$multi_to_single_fast5 -i /path/to/fast5/ -s /path/to/save/output/