Question: VelvetOptimiser fails to operate
0
gravatar for El Niño
5 months ago by
El Niño10
El Niño10 wrote:

Dear all,

So I've run Velvet on my linux terminal and I also tried to install VelvetOptimiser on it. However, when I run VelvetOptimiser.pl "-short -fasta contigs.fa", I got the following message from the Terminal

Can't locate VelvetOpt/Assembly.pm in @INC (you may need to install the VelvetOpt::Assembly module) (@INC contains: /d/igr/TH19/TH19/directory1 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at VelvetOptimiser.pl line 37.
BEGIN failed--compilation aborted at VelvetOptimiser.pl line 37.

Now does anybody know the solution to this problem? I Googled before asking this question, but after spending the whole afternoon trying to find the answer, I got stuck because of failing to install Bioperl apparently.

I copied all the messages from the Terminal for you to see better the problem.

*nolock_cpan> force install B/BI/BIRNEY/bioperl-1.2.1.tar.gz
Fetching with LWP:
http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
LWP failed with code[404] message[Not Found]
Trying with
    /usr/bin/wget -O "/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970"
to get
    http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
--2019-05-24 16:33:00--  http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
Resolving www.cpan.org www.cpan.org)... 151.101.194.217, 151.101.130.217, 151.101.66.217, ...
Connecting to www.cpan.org www.cpan.org)|151.101.194.217|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2019-05-24 16:33:00 ERROR 404: Not Found.
    Function system("/usr/bin/wget -O "/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970" "http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz" ")
    returned status 8 (wstat 2048), left
/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970 with size 0
    Warning: no success downloading '/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970'. Giving up on it.
Fetching with LWP:
http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
LWP failed with code[404] message[Not Found]
Trying with
    /usr/bin/wget -O "/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970"
to get
    http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
--2019-05-24 16:33:00--  http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
Resolving www.cpan.org www.cpan.org)... 151.101.194.217, 151.101.130.217, 151.101.66.217, ...
Connecting to www.cpan.org www.cpan.org)|151.101.194.217|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2019-05-24 16:33:00 ERROR 404: Not Found.
    Function system("/usr/bin/wget -O "/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970" "http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz" ")
    returned status 8 (wstat 2048), left
/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970 with size 0
    Warning: no success downloading '/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970'. Giving up on it.
Trying with
    /usr/bin/wget -O "/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970"
to get
    http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
--2019-05-24 16:33:00--  http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
Resolving www.cpan.org www.cpan.org)... 151.101.194.217, 151.101.130.217, 151.101.66.217, ...
Connecting to www.cpan.org www.cpan.org)|151.101.194.217|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2019-05-24 16:33:01 ERROR 404: Not Found.
    Function system("/usr/bin/wget -O "/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970" "http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz" ")
    returned status 8 (wstat 2048), left
/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970 with size 0
    Warning: no success downloading '/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970'. Giving up on it.
No external ftp command available
Trying with
    /usr/bin/wget -O "/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970"
to get
    http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
--2019-05-24 16:33:01--  http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz
Resolving www.cpan.org www.cpan.org)... 151.101.194.217, 151.101.130.217, 151.101.66.217, ...
Connecting to www.cpan.org www.cpan.org)|151.101.194.217|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2019-05-24 16:33:01 ERROR 404: Not Found.
    Function system("/usr/bin/wget -O "/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970" "http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz" ")
    returned status 8 (wstat 2048), left
/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970 with size 0
    Warning: no success downloading '/home/fox/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz.tmp18970'. Giving up on it.
No external ftp command available
Please check, if the URLs I found in your configuration file
(http://www.cpan.org/) are valid. The urllist can be edited. E.g. with 'o
conf urllist push ftp://myurl/'
Could not fetch authors/id/B/BI/BIRNEY/bioperl-1.2.1.tar.gz*

ANY HELP WILL BE HIGHLY APPRECIATED!!!

bioperl assembly • 239 views
ADD COMMENTlink modified 5 months ago by h.mon28k • written 5 months ago by El Niño10

Did you follow this advice?

Can't locate VelvetOpt/Assembly.pm in @INC (**you may need to install the VelvetOpt::Assembly module**)
ADD REPLYlink written 5 months ago by ATpoint25k

Hi ATpoint,

I Googled for this whole problem and it turned out what I need was install Bioperl. So I follow this tutorial and got stuck at the last step, which I pasted all the error details on my post. Best regards,

ADD REPLYlink written 5 months ago by El Niño10
1

I would just try conda install -c bioconda perl-velvetoptimiser, see here, maybe make a separate conda environment just for this.

ADD REPLYlink modified 5 months ago • written 5 months ago by ATpoint25k

Velvet hasn't really been an up to date assembler for quite a few years, you might get more mileage out of Spades, Soap2denovo or others.

ADD REPLYlink written 5 months ago by colindaven1.8k

In fact, my genome was assembled using SOAPdenovo (1st version) and after that the problem is there are two many contigs and too many gaps that I need to link them together for a single circular genome so that I can draw a genome map. Do you have any idea how to do this?

Thank you a bunch in advance!

ADD REPLYlink written 5 months ago by El Niño10

What kind of data and coverage do you have? Single circular genomes are only commonly obtained with PacBio or Nanopore sequencing. Short sequencing alone (454, Illumina or Ion Torrent) is not enough to close most genomes.

ADD REPLYlink written 5 months ago by h.mon28k

In fact, it was not me who did the genome assembly but that was done by another lab. Based on their data, this genome contains 630,302,822 bp with 6,240,622 reads. Genome assembly gives 201 contigs with total number of bases of 5,830,249. They did paired-end sequencing and what I got was fna, gbk, gff,..files together with an annotation report.

They did genome sequencing using Illumina SBS technology.

What else do you need to know? I can send you the whole genome sequencing report via email if you wish.

ADD REPLYlink written 5 months ago by El Niño10

I can send you the whole genome sequencing report via email if you wish.

This is a bit hasty, as we didn't even discuss my consultant fees. ;-)

With the raw sequencing data you have, I believe currently SPAdes (or maybe Shovil) will generate the best assembly. You will not get a single, circular chromosome. You will get a closed genome only with manual finishing (PCRs + Sanger / PacBio / NanoPore sequencing), or with additional PAcBio or NanoPore shotgun sequencing.

P.S.: the consultant fees comment is just a joke. But this is a volunteer forum, there is only so much I can do.

ADD REPLYlink written 5 months ago by h.mon28k

Thank you so much. I will give SPAdes a shot now.

ADD REPLYlink written 5 months ago by El Niño10

You are trying to install a very old version of BioPerl, follow the BioPerl documentation instead: BIOPERL INSTALLATION or Beginners HOWTO.

Or use the conda package manager as already suggested.

ADD REPLYlink written 5 months ago by h.mon28k
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