I think MinKNOW's local 1D base calling (albacore?) saves data in the fast5 files differently to metrichor / nanonet basecalling.
Indeed, when trying to run many poretools commands, I get similar errors that seem to relate to different attribute nomenclature in the fast5 files.
For example:
poretools 0.6.0
$ poretools yield_plot ./pass/
WARNING:poretools:No start time for ./pass/MinION_20161031_FNFAD24075_MN19348_sequencing_run_sample_57684_ch100_read2727_strand.fast5!
[same error for all reads]
Traceback (most recent call last):
File "/Users/noncodo/miniconda2/bin/poretools", line 9, in <module>
load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()
File "/Users/noncodo/miniconda2/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg/poretools/poretools_main.py", line 533, in main
args.func(parser, args)
File "/Users/noncodo/miniconda2/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg/poretools/poretools_main.py", line 55, in run_subtool
submodule.run(parser, args)
File "/Users/noncodo/miniconda2/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg/poretools/yield_plot.py", line 75, in run
start_time = fast5.get_start_time()
File "/Users/noncodo/miniconda2/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg/poretools/Fast5File.py", line 541, in get_start_time
node = self.find_event_timing_block()
File "/Users/noncodo/miniconda2/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg/poretools/Fast5File.py", line 507, in find_event_timing_block
path = fastq_paths[self.version]['template'] % (self.group)
KeyError: 'template'
$ h5ls -r ./pass/MinION_20161031_FNFAD24075_MN19348_sequencing_run_sample_57684_ch100_read2727_strand.fast5
/ Group
/Analyses Group
/Analyses/Basecall_1D_000 Group
/Analyses/Basecall_1D_000/BaseCalled_template Group
/Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR}
/Analyses/Basecall_1D_000/Summary Group
/Analyses/Basecall_1D_000/Summary/basecall_1d_template Group
/Raw Group
/Raw/Reads Group
/Raw/Reads/Read_968 Group
/Raw/Reads/Read_968/Signal Dataset {48979/Inf}
/UniqueGlobalKey Group
/UniqueGlobalKey/channel_id Group
/UniqueGlobalKey/context_tags Group
/UniqueGlobalKey/tracking_id Group
I think MinKNOW's local 1D base calling (albacore?) saves data in the fast5 files differently to metrichor / nanonet basecalling. Indeed, when trying to run many poretools commands, I get similar errors that seem to relate to different attribute nomenclature in the fast5 files.
For example: