nanopore - where to retrieve information from the basecaller used

Question

Where can I find information about the basecaller used in a specific nanopore run (we have a Gridion machine)?

I know already that we have Guppy v. 3.0.3, which I found out by clicking on the about tab on the MinKNOW GUI).

I was wondering, though, if additional information about the basecaller is outputted in any of the files generated when the run is finished? I checked already the final_summary.txt and it does not contain such information. I also checked the head of the fastq files and no further details.

My ultimate goal for the moment is to run medaka on a draft genome assembly. But for that I'd need to specify the medaka model. From medaka_consensus -h I see that the options available and defaults are:

-m  medaka model, (default: r941_min_high_g330).
        Available: r941_min_fast_g303, r941_min_high_g303, r941_min_high_g330, r941_prom_fast_g303, r941_prom_high_g303, r941_prom_high_g330, r10_min_high_g303, r10_min_high_g340, r941_prom_diploid_snp, r941_min_high_g340_rle.
        Alternatively a .hdf file from 'medaka train'.

Therefore I already know that my option should contain min and g303 (format of the models available described here). But know I'd need to find out the {pore} and {caller variant}

Answer 1

I basecall separately with guppy. In the output folder specified by --save_path or -s there are a whole bunch of .log files.

$ ls -l *.log | head
-rw-r--r-- 1 tom tom 5242714 Dec  3 11:04 guppy_basecaller_log-2019-12-02_22-02-36.log
-rw-r--r-- 1 tom tom 5242718 Dec  3 11:06 guppy_basecaller_log-2019-12-02_22-04-38.log
-rw-r--r-- 1 tom tom 5242730 Dec  3 11:08 guppy_basecaller_log-2019-12-02_22-06-41.log
-rw-r--r-- 1 tom tom 5242879 Dec  3 11:11 guppy_basecaller_log-2019-12-02_22-08-50.log
-rw-r--r-- 1 tom tom 5242811 Dec  3 11:13 guppy_basecaller_log-2019-12-02_22-11-06.log
-rw-r--r-- 1 tom tom 5242817 Dec  3 11:15 guppy_basecaller_log-2019-12-02_22-13-28.log
-rw-r--r-- 1 tom tom 5242880 Dec  3 11:18 guppy_basecaller_log-2019-12-02_22-15-47.log
-rw-r--r-- 1 tom tom 5242816 Dec  3 11:20 guppy_basecaller_log-2019-12-02_22-18-09.log
-rw-r--r-- 1 tom tom 5242777 Dec  3 11:22 guppy_basecaller_log-2019-12-02_22-20-30.log
-rw-r--r-- 1 tom tom 5242742 Dec  3 11:25 guppy_basecaller_log-2019-12-02_22-22-47.log

The information you need for medaka is at the top of the first log file (alphabetically, and by creation date).

$ head -n 13 guppy_basecaller_log-2019-12-02_22-02-36.log 
2019-12-02 22:02:36.255793 [guppy/message] ONT Guppy basecalling software version 3.4.1+ad4f8b9
config file:        /opt/ont/guppy/data/dna_r9.4.1_450bps_hac.cfg
model file:         /opt/ont/guppy/data/template_r9.4.1_450bps_hac.jsn
input path:         raw/minion
save path:          test_341/minion
chunk size:         1000
chunks per runner:  512
minimum qscore:     7
records per file:   4000
num basecallers:    1
gpu device:         cuda:0
kernel path:        
runners per device: 4

If you ran live basecalling and you don't have those log files you could also try a recursive grep from the output folder, e.g.

grep -nr "^model file" .