text: user3452: 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}
  
  user1021: 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" .
  
  
original_text: 3452: <p>Where can I find information about the basecaller used in a specific nanopore run (we have a Gridion machine)? </p>
  
  <p>I know already that we have <code>Guppy v. 3.0.3</code>, which I found out by clicking on the <code>about</code> tab on the MinKNOW GUI).</p>
  
  <p>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 <code>final_summary.txt</code> and it does not contain such information. I also checked the head of the <code>fastq</code> files and no further details.</p>
  
  <p>My ultimate goal for the moment is to run <a href="https://github.com/nanoporetech/medaka" rel="nofollow noreferrer">medaka</a> on a draft genome assembly. But for that I'd need to specify the <code>medaka model</code>. From <code>medaka_consensus -h</code> I see that the options available and defaults are:</p>
  
  <pre><code>-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'.
  </code></pre>
  
  <p>Therefore I already know that my option should contain <code>min</code> and <code>g303</code> (format of the models available described <a href="https://nanoporetech.github.io/medaka/installation.html" rel="nofollow noreferrer">here</a>). But know I'd need to find out the <code>{pore}</code> and <code>{caller variant}</code></p>
   1021: <p>I basecall separately with guppy. In the output folder specified by <code>--save_path</code> or <code>-s</code> there are a whole bunch of .log files.</p>
  
  <pre><code>$ 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
  </code></pre>
  
  <p>The information you need for <code>medaka</code> is at the top of the <strong>first</strong> log file (alphabetically, and by creation date).</p>
  
  <pre><code>$ 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
  </code></pre>
  
  <p>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.</p>
  
  <pre><code>grep -nr "^model file" .
  </code></pre>
  