Re: [Transdecoder-users] problems of installation

[Zhang, N. <Zh...@si...>]

Yes, the name is identical, but the sequence is different.
Something like that:
>Ampelocissus_ele_scaffold99_Locus_33_4_22.4
MGQKNSTHSTMEENCKWHKLLPRERERLMGTVGRRAIRSKLKNCRAMEVGIAATIRDQNG
TD*
>Ampelocissus_ele_scaffold99_Locus_33_4_22.4
MDRQNSFHESFPRSYRGKQFPFLQGPNPILPGTSVCQPLLDPSSASGNGSGGQKMFSDGL
NRVISSDRALSLLSSPLPETQEIGLSSMVQQNPIPPAQTLIPSLHYTGLSQYASSQGMGD
SVGSILVSDGSSNANLHCPAIFQLGPDGSSTNSSHQTLSFSWE*

There are many cases in my .pep file.
Ning

On Jan 30, 2014, at 8:06 PM, <Ale...@cs...<mailto:Ale...@cs...>>
 <Ale...@cs...<mailto:Ale...@cs...>> wrote:

Are they duplicate (two identical proteins) from one contig or two proteins (different coordinates) in a contig?

A

--
Alexie Papanicolaou
CSIRO Ecosystem Sciences

________________________________
From: Zhang, Ning
Sent: Thursday, 30 January 2014 9:56:19 PM
To: Papanicolaou, Alexie (CES, Black Mountain)
Cc: <tra...@li...<mailto:tra...@li...>>
Subject: Re: [Transdecoder-users] problems of installation

Hi, all:
I found that there are some duplicate peptides in *.transdecoder.pep.
What happened? How can I get only one peptide for each contig, maybe the longest one.
Thanks
Ning
On Jan 25, 2014, at 7:55 AM, Zhang, Ning wrote:

yes, I made it.
After installing this module, it works.
If you use Transdecoder on cluster, you had better install the module at your own path.
A module named local::lib which enables you install perl modules at your own path, so you needn't ask admin for help.
Ning
On Jan 25, 2014, at 1:33 AM, <Ale...@cs...<mailto:Ale...@cs...>>
 <Ale...@cs...<mailto:Ale...@cs...>> wrote:

It seems that you or your sysadmin will have to install the perl module:

$ cpan URI::Escape

If you are familiar with cpan, I'd recommend you do it yourself, otherwise pls ask your sysadmin

Brian: we may have to make a list of all the different module dependencies at some point and just create a CPAN bundle...
a

--
Dr. Alexie Papanicolaou

Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247
CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia

-- CSIRO profile<https://urldefense.proofpoint.com/v1/url?u=http://www.csiro.au/Organisation-Structure/Divisions/Ecosystem-Sciences/AlexiePapanicolaou.aspx&k=diZKtJPqj4jWksRIF4bjkw%3D%3D%0A&r=pLScI1VMNxHqdwIgs2R8Mg%3D%3D%0A&m=hN8coJf7sbIVLVZD%2FAqPfuOKF2zi7gdTl9WMkrF0MPw%3D%0A&s=48cc7bddc3e9fff5c131a2f4ca76b66cad324a17ff02929558bc2191336f1744>
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-- Bioinformatics is also an experimental science
________________________________
From: Zhang, Ning [Zh...@si...<mailto:Zh...@si...>]
Sent: Saturday, 25 January 2014 6:06 AM
To: tra...@li...<mailto:tra...@li...>
Subject: [Transdecoder-users] problems of installation

Hi, all:
I installed the latest Transdecoder with the command "make", however, when I run it, I got error message.

Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib /home/zhangn/localperl/lib/site_perl/5.16.3/x86_64-linux /home/zhangn/localperl/lib/site_perl/5.16.3 /home/zhangn/localperl/lib/5.16.3/x86_64-linux /home/zhangn/localperl/lib/5.16.3 .) at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15.
BEGIN failed--compilation aborted at /home/zhangn/software/transdecoder_rel16JAN2014/PerlLib/Gene_obj.pm line 15.
Compilation failed in require at ./TransDecoder line 102.
BEGIN failed--compilation aborted at ./TransDecoder line 102.

what is wrong with my installation.
Thanks.
Ning Zhang

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