poretools not finding fastq after subsequent albacore basecalling

[biorover]

I ran a rapid library kit (RAD002) with basecalling, but stopped it before it could catch up. I then basecalled the skip folder using albacore. Poretools can find the sequences of the fast5 files basecalled by MinKNOW, but can't find the sequences basecalled by albacore. Upon inspection with h5ls, I found that Albacore had written the basecalls to Analyses/Basecall_1D_001/BaseCalled_template/ (Analyses/Basecall_1D_000/ only contains "Summary" group). However, from my cursory glance at Fast5File.py, it should be able to find basecalls no matter what the numbers on the end of "Basecall_1D_***" are. Any idea what's going on? Sample fast5 file attached. albacorecalledread.fast5.zip

[nickloman]

Use --group 1

[biorover]

Works perfectly, thanks!

[AhmedAbdelfattah]

Thanks, this was helpful