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Old 08-23-2011, 07:58 PM   #1
Kennels
Senior Member
 
Location: Sydney

Join Date: Feb 2011
Posts: 149
Default AMOS: problem getting hawkeye to view bambus output

Hi,

Does anyone have an idea what my problem is? I've just installed and learning to use AMOS.
I'm using AMOS's minimus to assemble some .fasta reads, make scaffold by Bambus2, and try to visualize in hawkeye.

My workflow was:
1. toAmos -s myreads.fa -o myreads.afg
2. minimus myreads.afg
3. goBambus2 myreads.bnk/ myScaff

Everything ran with no problem up to this point. Then,

4. hawkeye myreads.bnk

I got the follow error:

Opening myreads.bnk/... [0.00s]
Indexing Contigs .......... [0.00s] 712 reads in 15 contigs
Indexing Scaffolds [0.00s] 0 contigs in 0 scaffolds
Indexing Libraries .......... [0.00s] 2 libraries
Indexing Mates .......... [0.00s] 22 mated reads in 772 fragments
Indexing Reads .......... [0.00s] 714 reads
Features not available
Initialize Display .ERROR: WHAT: Cannot stream fetch: beyond end of stream
LINE: 147
FILE: BankStream_AMOS.cc

My fasta sequence reads is just a compilation of reads from various lanes of illumina data. It may not have pair end information for all reads.
Is my error due to not having paired end information? If so why did Bambus2 run with no errors?

Thanks
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Old 08-24-2011, 08:55 AM   #2
suryasaha
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Location: New York

Join Date: Mar 2011
Posts: 27
Default

You might try asking this on AMOS HELP <amos-help@lists.sourceforge.net>. You can sign up here.

-S.
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Old 08-24-2011, 05:07 PM   #3
Kennels
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Location: Sydney

Join Date: Feb 2011
Posts: 149
Default

I have, but still waiting for reply, and hoped to reach a wider audience here.
Anyone any ideas?
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Old 08-24-2011, 08:49 PM   #4
Kennels
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Location: Sydney

Join Date: Feb 2011
Posts: 149
Default

Problem solved.

I was assuming that paired information was deduced and included in the amos .afg file during its generation, but actually the paired information must be explicitly provided in a separate .mates file. Once this was included in the .afg file generation, I could run minimus -> bambus -> hawkeye to view any scaffolds.

I found a really helpful site which provided a script to parse out the mate pair information from your input .fasta file here http://compbio.korea.ac.kr/wiki/inde...ina_for_bambus which is this:

Code:
cat my.fasta |grep ">" |sed s/\>//g |sed 's/\/1*$/./g;s/\/2*$/./g'|awk -F "." '{print $1}' |sort |uniq -c |awk '{if ($1 == 2) print $2"/1\t"$2"/2\tsmall"}' > mates.txt
One just needs to adjust and add the library name and insert sizes at the top of the generated file.
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