oligotype no cluster and nmds graphs in the output dirctory

Yaping Wang

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Mar 9, 2016, 10:13:14 PM3/9/16

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hi all

I got a problem when do oligotyping. There was no cluster

and nmds graphs in the HTML-OUTPUT directory. This is the script I

employed: oligotype aligned.fasta-TRIMMED aligned.fasta-

TRIMMED-ENTROPY -c 1 -s 4 -M 12.

the attechment shows all the files in the output directory.

Any ideas on what might have caused this?

Thanks a lot

Yaping

20160310111119.png

A. Murat Eren

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Mar 9, 2016, 10:33:11 PM3/9/16

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What does the log file say?

Probably your R installation is missing some libraries.

Best,

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Yaping Wang

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Mar 9, 2016, 11:05:13 PM3/9/16

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Hi Eren
I don't know where the log file is. is the attachment what u want to check?

在 2016年3月10日星期四 UTC+8上午11:13:14，Yaping Wang写道：

result.txt

A. Murat Eren

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Mar 9, 2016, 11:14:56 PM3/9/16

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It is called RUNINFO.

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Yaping Wang

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Mar 10, 2016, 12:51:27 AM3/10/16

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i checked it. as u said the R installation missed some libraries. Thank u very much

Best wishes

Yaping

在 2016年3月10日星期四 UTC+8上午11:13:14，Yaping Wang写道：

hi all

Yaping Wang

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Mar 10, 2016, 8:11:18 AM3/10/16

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hello Eren, sorry to trouble u again. After the first round oligotyping (oligotype aligned.fasta-TRIMMED aligned.fasta-TRIMMED-ENTROPY -c 1 -s 4 -M 15), i checked the index.html file and found the site for oligotype is site 113. this is not in line with the highest peak site in the entropy figure. then i checked the ENTROPY file which showed site 113 was the peak and the entropy figure of the 4 oligotypes showed the entropy value of site 113 was not zero.

Here is the question: which site (113 or 114) i should trust and what to do about the following compont chosen.

thanks a lot for your patience

have a nice day

Yaping

2928-ENTROPY.pdf

00000_T_unique.png

00001_G_unique.png

00002_A_unique.png

00003_C_unique.png

2928-ENTROPY

Message has been deleted

Hilary Morrison

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Jul 8, 2016, 3:21:52 PM7/8/16

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Having the same problem and I would not expect missing libraries in our system :)

empty files:

./FIGURES/date/heatmap_analysis

./FIGURES/site/heatmap_analysis

./FIGURES/__default__/bars

./FIGURES/__default__/lines

Hilary Morrison

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Jul 8, 2016, 3:25:30 PM7/8/16

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A. Murat Eren

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Jul 9, 2016, 12:47:53 AM7/9/16

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What does the RUNINFO.log file says? Are there any errors in it during the creation of some of these files?

Best,

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A. Murat Eren (meren)
http://merenlab.org :: gpg

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