[shaohua.fan]

Marten, thanks for your quick reply. I editted my configure file as you suggested and run goBambus again, but still failed.
I used the .conf as:
# Priorities
priority ALL 1
# The following lines can be un-commented to specify certain
# per-library settings

# Redundancies
# redundancy lib_some 1

# allowed error
# error MUMmer 0.5

# overlaps allowed
# overlaps MUMmer Y

# Global redundancy
redundancy 2

# min group size
mingroupsize 0

The log information for goBambus is :
Parsing links out of input file
Step 100: running detective
Combining XML files
Step 200: making the xmls
starting
Done
Step 300: Preparing contig links
starting
Done
Step 400: Running scaffolder
Grommit(/home/aubsxl/bin/bambus/bin/grommit -i ctg2660_BES_mapping_704.inp -o ctg2660_BES_mapping_704.out.xml -C c
tg2660_BES_mapping_704.grommit.conf --append --logfile goBambus.log --debug 1) script failed

The error information from goBambus.error file is:
20100712|123807| 10451| Grommit(/home/aubsxl/bin/bambus/bin/grommit -i ctg2660_BES_mapping_704.inp -o ctg2660_BES_
mapping_704.out.xml -C ctg2660_BES_mapping_704.grommit.conf --append --logfile goBambus.log --debug 1) script fail
ed

The first several lines from my mates files is:
library libname 200 500
HWUSI-EAS1665_0002:2:1:1022:18088#0/1 HWUSI-EAS1665_0002:2:1:1022:18088#0/2 libname
HWUSI-EAS1665_0002:2:1:1029:11872#0/1 HWUSI-EAS1665_0002:2:1:1029:11872#0/2 libname
HWUSI-EAS1665_0002:2:1:1029:11034#0/1 HWUSI-EAS1665_0002:2:1:1029:11034#0/2 libname
HWUSI-EAS1665_0002:2:1:1030:19457#0/1 HWUSI-EAS1665_0002:2:1:1030:19457#0/2 libname
HWUSI-EAS1665_0002:2:1:1031:12133#0/1 HWUSI-EAS1665_0002:2:1:1031:12133#0/2 libname

Marten, could you look at these information and point out what's wrong with this? I have no idea. Thanks a lot,

Kevin

Hi, Catfisher,

I met the exact same question as you. Have you found any solution of this question?

[elisadouzi]

Hi shouhua,
I also have the same err as you. Have you figured out?

Thanks!

[rahularjun86]

HI all,
I have a question regarding the mate file. I ran velvet(with no scaffolding option) and get 4-5 nice assemblies with different k-mer's. Then I merged all these 4 assemblies into a single one using minimus2 Amos. Now I have .contig file and .bnk/ file. How can I generate the .mate file? should I use the sed command discussed in some posts. but the Id's of my .mate file and .contig file are not showing any link. My .contig file has id: #NODE_1_length_1305_cov_18.627586(0) from velvet and the .mate is with Illumina id's @HWUSI-EAS100R:6:73:941:1973#0/1 @HWUSI-EAS100R:6:73:941:1973#0/2. How can I link this information. Anybody please help.
Regards,
Rahul

[sabiha]

Hii,,
I am trying to run bambus on velvet contigs..
i have generated .afg while assembling using velvet.. and then used the following command lines... as suggested by some forum ...
/amos-3.0.1/src/Bank/bank-transact -cf -b j99.bnk -m velvet_asm.afg

/amos-3.0.1/src/Bambus/Bundler/clk -b j99.bnk/

/amos-3.0.1/src/Bambus/Bundler/Bundler -b j99.bnk

/amos-3.0.1/src/Bambus/Bundler/MarkRepeats -b j99.bnk -redundancy 2 -agressive >repeat_fi

/amos-3.0.1/src/Bambus/Bundler/OrientContigs -b j99.bnk -prefix j99scaff -redundancy 2 -repeats repeat_fi -all -agressive -linearize

perl /amos-3.0.1/src/Bambus/Untangler/untangle.pl -e j99scaff.evidence.xml -s j99scaff.out.xml -o j99scaff.untangle.xml

/amos-3.0.1/src/Bank/bank2fasta -d -b j99.bnk >bambus_contigs.fa

perl /amos-3.0.1/src/Bambus/Untangler/printScaff.pl -e j99scaff.evidence.xml -s j99scaff.untangle.xml -l j99scaff.library -f bambus_contigs.fa -merge -o bambus_scaff

and it has generated the following stats..

no. valid links: 0
no. incorrect len. links: 0
no. incorrect ori. links: 0
no. unchecked links: 18129

I can see that no scaffolding is being done, since there are no valid links...
can anyone tell me if my approach is right ... and if it is a must to use mates file

[relipmoc]

Hii,,
I am trying to run bambus on velvet contigs..
i have generated .afg while assembling using velvet.. and then used the following command lines... as suggested by some forum ...

Why don't try SSPACE? For more details, please see http://seqanswers.com/forums/showthread.php?t=8350

and

Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D. and Pirovano, W. (2011) Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, 27, 578-579.

[sabiha]

.. I ve already tried SSpace. Just wanted to see how bambus wrks... as it does hierarchical scaffolding

[MeganS]

sabiha,

Does the stdout from bank-transact report any "Objects added"?

Are your .xml files links of some sort (paired reads, etc)? I have gotten bambus to work, but used the .xml link information much earlier. Before running bambus, I used toAmos with fasta reads, a TIGR .contig file, and xml link information. Then I generated an amos bank using bank-transact on the resulting .afg file. Then ran bambus (via the goBambus script) on the bank.

[sabiha]

MeganS,

Thank you for helping me out. stdout from bank-transact reported the following.
Messages read: 4963548
Objects added: 4963548
Objects deleted: 0
Objects replaced: 0

I have Illumina paired end reads in fastq format, which has quality scores included in the same file. I am planning to split the sequences and the quality into two files and will try using these files.

How did u generate the xml link information??