View Single Post
Old 03-18-2011, 07:51 AM   #2
Vincenzo
Junior Member
 
Location: Barcellona

Join Date: Feb 2011
Posts: 4
Default

Dears,
this is my config file.
I have not a sam file in the output, but only some sh script: match.sh, localign.sh, postprocess.sh, sam.sh.
I don't know what is the next step because, as i write you, it's sometimes hard to guess which parameter name in the schema stands for which in the BFAST programs.
A suggestion:
if you have any validation errors with eclipse don't worry, they're not preclude the running of bfast.
I am a beginner so i don't know if this can help you. I hope..
Anyway, this is the BASIC xml version to run it:
<?xml version="1.0" encoding="UTF-8"?>
<bfastConfig xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="BfastConfig_5.xsd">
<globalOptions>
<bfastBin>/cbbl/users/vincenzo/bin/</bfastBin>
<samtoolsBin>/cbbl/users/vincenzo/bin/</samtoolsBin>
<qsubBin>/cbbl/users/vincenzo/bin/run_parallel/</qsubBin>
<fastaFileName>/cbbl/users/vincenzo/bin/run_parallel/DH10B.fa</fastaFileName>
<runDirectory>/cbbl/users/vincenzo/bin/run_parallel/</runDirectory>
<readsDirectory>/cbbl/users/vincenzo/bin/run_parallel/</readsDirectory>
<outputDirectory>/cbbl/users/vincenzo/bin/run_parallel/</outputDirectory>
<tmpDirectory>/cbbl/users/vincenzo/bin/run_parallel/</tmpDirectory>
<outputID>result</outputID>
<cleanUsedIntermediateFiles>0</cleanUsedIntermediateFiles>
<numReadsPerFASTQ localalignSplit="20" matchSplit="20">20</numReadsPerFASTQ>
<timing>ON</timing>
<queueType>SGE</queueType>
<space>NT</space>
</globalOptions>
<matchOptions>
<readCompression>gz</readCompression>
<threads>1</threads>
</matchOptions>
<localalignOptions>
<threads>1</threads>
</localalignOptions>
<postprocessOptions>
<threads>1</threads>
</postprocessOptions>
<samOptions>
<samtools>1</samtools>
</samOptions>
</bfastConfig>

To add any parameter, you can inspire from XSD and from bfast.submit.pl.
If you solved it, please share your code.
Thanks a lot.
Vincenzo
Vincenzo is offline   Reply With Quote