Scaffolding of 454 data

[gorysko]

Hi for everyone
I've got one problem

After making assembly of 454 data by mira I've file with contings, I've tried to scaffold this data by
SSPACE, but it failed because of bowtie error at the file mapwithBowtie ( I've updated bowtie)

By Bambus -- it fails because of "detective failed"

SO what Could You recommend for me for making scaffold?

[nickloman]

Honestly? Just use Newbler.

[gorysko]

So maybe You could give me link to it? because I can\t find

[boetsie]

Hi Gorysko,

can you specify the bowtie error of SSPACE? Try to set the user rights of Bowtie in SSPACE folder. Go to the Bowtie folder in the terminal and type chmod 777 *

At the moment i'm making a new version of SSPACE which includes BWA-sw and BWA as optional read aligners. This should help to align 454 data.

Regards,
Boetsie

[nickloman]

So maybe You could give me link to it? because I can\t find

Ask your sequencing provider for it, or request a copy here:

http://my454.com/products/analysis-software/index.asp

[gorysko]

Thank You)

[gorysko]

The page with request is broken

[flxlex]

No it is not :-) http://my454.com/contact-us/software-request.asp

[dnusol]

Dear boetsie,

how long can SSPACE take for about 500K fasta entries? It's been running on for about 17hours. (params: -x 1)

[gorysko]

Hi boetsie
The error is 256 at mapwithBowtie.pl line 44
"
Bowtie error; 256 at /home/gorysko/SSPACE-1.2_linux-x86_64/bin/mapWithBowtie.pl line 44.
**************************************************

Process 'mapping reads' failed on Thu Nov 17 12:41:17 2011

"

[dnusol]

gorysko,

change the permissions for the bowtie directory

chmod a+x bowtie/*

hth

D.

[gorysko]

With permissions everything ok

[boetsie]

Well, that should not be the case... I know the extension can be slow, but not that slow. Can you maybe look in the intermediate_results file, is there a file *extendedcontigs.fa? Have you tried to run it with -x 0? Please ask the question in the SSPACE thread next time

Dear boetsie,

how long can SSPACE take for about 500K fasta entries? It's been running on for about 17hours. (params: -x 1)

Boetsie

[dnusol]

Dear boetsie,

thanks for your quick answer. Yes, there is a *extendedconfigs.fasta file.

I captured the stderr and stdout and at the moment the last entry says:

Wed Nov 16 18:00:35 2011: Contig extension initiated


And no, I have not tried -x 0

D.

[boetsie]

Ok, problems could be that the memory limit (check the memory consumption, e.g. with 'top' in linux.) has reached or it is at an infinite loop (check file size of the file *.extendedcontigs.fasta). Third option could just be that it is too slow Maybe check with 'top' if only perl is running, or that Bowtie is still mapping the reads.

-x 0 could give you satisfying results as well, maybe check this first..

Boetsie

Dear boetsie,

thanks for your quick answer. Yes, there is a *extendedconfigs.fasta file.

I captured the stderr and stdout and at the moment the last entry says:

Wed Nov 16 18:00:35 2011: Contig extension initiated


And no, I have not tried -x 0

D.