Re: SAMSA2 - DIAMOND

[Sam Westreich]

Hi Jeroen,

Good catch, thanks for bringing this to my attention.  Since --fast is default, I've removed the explicit declaration from the commands, on both the bash_scripts/master_script.sh and setup_and_test/test_of_master_script_tiny.sh .  

Best,

Sam

On Tue, Jun 12, 2018 at 4:51 AM, <jvde...@centrescientifique.mc> wrote:

Hi Sam,

Of course I meant the test_of_master_script_tiny.bash script.

I saw you had just modified it 2 weeks ago.

Cheers,

Jeroen

 

De : jvdewater@centrescientifique.mc [mailto:jvdewater@centrescientifique.mc]
Envoyé : Tuesday, June 12, 2018 1:48 PM
À : 'swest...@gmail.com'
Objet : SAMSA2 - DIAMOND

 

Dear Sam,

 

I was giving your SAMSA2 pipeline a try today, but I encountered a problem with the test run.

It seems that you added the option --fast for DIAMOND, but it doesn’t recognize it and gives an error.

Based on the DIAMOND manual the only sensitivity and speed options currently available are –sensitive, --more-sensitive and --band #.

They do make a mention that they used --fast as default, however.

 

When I remove --fast from your test_of_master_script.sh, the test runs successfully.

It also runs successfully when I run the test with the options --sensitive and --more-sensitive.

 

I just wanted to let you know about this issue, and that it can be easily fixed.

 

All the best,

 

Jeroen van de Water

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Post-doctoral Research Fellow

Centre Scientifique de Monaco

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E-mail: jvdewater@centrescientifique.mc

 

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--

Sam Westreich

Microbiome Scientist, DNAnexus, 

http://www.mosaicbiome.com