Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-19T02:54:25.487Z
Answers.LastActivityDate: 2019-12-19T02:54:25.487Z
Answers.UserDisplayName: Tom Harrop
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-18T13:54:46.923Z
Comments.Text: Pore? Say, "R9.4.1"? This is the pore is the physical protein (mutant curlin G with helicase) on your chip that you used. It likely will be r941, unless you are trialing out the new R10 pores.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-18T14:18:22.953Z
Comments.Text: Yes I also believe the pore would be R9.4.1. Not sure about the `caller variant` now
Comments.UserDisplayName: BCArg
Tags: <nanopore><assembly><long-reads><base-calling>
Title: nanopore - where to retrieve information from the basecaller used
ThreadText: # nanopore - where to retrieve information from the basecaller used
  
  (Asked by: username_0 on 2019-12-18)
  
  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](https://github.com/nanoporetech/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](https://nanoporetech.github.io/medaka/installation.html)). But know I'd need to find out the `{pore}` and `{caller variant}`
  
  **Tags:** nanopore, assembly, long-reads, base-calling
  
  > **Comments:**
  > **username_1**: Pore? Say, "R9.4.1"? This is the pore is the physical protein (mutant curlin G with helicase) on your chip that you used. It likely will be r941, unless you are trialing out the new R10 pores.  
  > **username_0**: Yes I also believe the pore would be R9.4.1. Not sure about the `caller variant` now  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-12-19. Score: 2
  
  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" .
  
  ```
  
  
  ---
  
  