Issues with CopyRighter analysis

[Even Sannes Riiser]

Dear all,

I am currently performing a 16S amplicon sequencing experiment, and have been processing my sequences using Mothur. I want to use your software to correct for differences in 16S copy numbers, but are having some troubles getting it to work properly. I therefore (desperately) hope for your help.

The software seems to be installed correcly; when I run just the command «copyrighter» in the bash terminal on my Mac, I get the message «Missing required argument: -i <input>».

The mothur MiSeq SOP uses the Silva database for classification by default, but as CopyRighter requires a GreenGenes taxonomy, I performed the classification using this database. After a bit of modification, I ended up with a «generic» OTU table as shown in the attached file (OTU_table_test.txt). The columns are separated by tabs, the taxonomic levels are not (just whitespace).

My data file (data_ssu_cn.txt) contains two columns (separated by tabs); the taxonomic description and the copy numbers. See the attached file.

When I run the command «copyrighter -i OTU_table_test.txt -o OTU_table_copyrighted -d data_ssu_cn.txt -v», I get the message "Reading input file 'OTU_table_test_1.txt'
Can't locate object method "format" via package "Bio::Community::IO::Driver::generic" at /usit/abel/u1/evensr/perl5/bin/copyrighter line 229, <GEN1> line 5.»

This also goes for all the different formats I try to modify my OTU table into. Ideally, I would like to use the format as in the attached file «Example 2» (at least all its information, incl. the OTU names).

Does anyone have any idea what I may be doing wrong? I would be extremely happy for all help.. :)

Kind regards,

Even Sannes Riiser,
PhD candidate

Centre for Evolutionary and Ecological Synthesis (CEES),
University of Oslo,
Norway

[Florent Angly]

Hi Even,

There seem to be a problem with your file of copy numbers. Try again
using the file distributed with CopyRighter at
data/201210/ssu_img40_gg201210.txt

Hope this helps, regards,

Florent

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[Even Sannes Riiser]

Hi Florent,

Thank you for the answer, but this still doesn't do it.

To test the command once more, I copied both the "ssu_img40_gg201210.txt" file (from AmpliCopyrighter/data/201210) and the "otu_table.generic" (from AmpliCopyrighter/t/data) to the same folder, and executed this command from here:

copyrighter -i otu_table.generic -o output_table -d ssu_img40_gg201210.txt -v

I still get the error:

Reading input file 'otu_table.generic'
Can't locate object method "format" via package "Bio::Community::IO::Driver::generic" at /usit/abel/u1/evensr/perl5/bin/copyrighter line 229, <GEN1> line 6.

Can you think of any other reasons why I can't get this to work?

Kind regards,

Even

[Florent Angly]

Even,

There must be something wrong with the perl module versions that are
on your system. Could you please reinstall CopyRighter following this
procedure?
perl Makefile.PL
make
make test
sudo make install

Please note the module versions reported and make sure the 'make test'
step completes successfully.
Cheers,

Florent

> https://groups.google.com/d/msgid/copyrighter/7ca2f13e-c9f6-4d1f-9b31-96ca89d41222%40googlegroups.com.