Bfast parallel running

[Vincenzo]

Dear,
i am a beginner.
I have a question about the running of bfast in parallel way.
_i downloaded the XML schema.
_ i have all files for the running: .brg, .bif, .fai.,reads.fastq
My cluster is SGE.
The input is in the NT space.(from Illumina).
When i launch ./bfast.submit.pl -config schema.xml the result is:

"Unable to recognise encoding of this document at /soft/lib/perl5/site_perl/5.8.8/XML/SAX/PurePerl/EncodingDetect.pm line 100.
The global options were not found."

The schema.xml is(i modified it for my job):


<?xml version="1.0"?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="bfastConfig">
<xs:complexType>
<xs:sequence>
<xs:element name="globalOptions">
<xs:complexType>
<xs:sequence>
<xs:element name="bfastBin" type="directoryPath" value="bfast.submit.pl"/>
<xs:element name="samtoolsBin" type="directoryPath" value="samtools"/>
<xs:element name="qsubBin" type="directoryPath"/>
<xs:element name="FastaFileName" value="phi.x.174.fa" type="filePath" use="required"/>
<xs:element name="runDirectory" type="directoryPath" use="required"/>
<xs:element name="readsDirectory" type="directoryPath" use="required"/>
<xs:element name="outputDirectory" type="directoryPath" use="required"/>
<xs:element name="tmpDirectory" type="directoryPath" use="required"/>
<xs:element name="outputID" type="xs:string" use="required"/>
<xs:element name="cleanUsedIntermediateFiles" type="xs:integer" use="required"/>
<xs:element name="numReadsPerFASTQ" type="integer" value="1">
<xs:complexType>
<xs:attribute name="matchSplit" type="positiveInteger" use="required"/>
<xs:attribute name="localalignSplit" type="positiveInteger" use="required"/>
</xs:complexType>
</xs:element>
<xs:element name="timing">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="ON"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="queueType" use="required">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="SGE"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="space" use="required">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="NT"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="matchOptions">
<xs:complexType>
<xs:sequence>
<xs:element name="mainIndexes" type="xs:string"/>
<xs:element name="secondaryIndexes" type="xs:string"/>
<xs:element name="offsets" type="xs:string"/>
<xs:element name="loadAllIndexes" type="xs:integer"/>
<xs:element name="readCompression">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="none"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="keySize" type="positiveInteger"/>
<xs:element name="maxKeyMatches" type="positiveInteger"/>
<xs:element name="maxNumMatches" type="positiveInteger"/>
<xs:element name="strand">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="BOTH"/>
<xs:enumeration value="FORWARD"/>
<xs:enumeration value="REVERSE"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="threads" type="positiveInteger" value="2"/>
<xs:element name="mergeSeparate" type="xs:integer"/>
<xs:element name="qsubQueue" type="xs:string"/>
<xs:element name="qsubArgs" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="localalignOptions">
<xs:complexType>
<xs:sequence>
<xs:element name="offset" type="nonNegativeInteger"/>
<xs:element name="threads" type="integer" value="2"/>
<xs:element name="pairedEndLength" type="xs:integer"/>
<xs:element name="mirrorType" type="xs:integer"/>
<xs:element name="forceMirror">
<xs:simpleType>
<xs:restriction base="xs:integer">
<xs:minInclusive value="0"/>
<xs:maxInclusive value="3"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="qsubQueue" type="xs:string"/>
<xs:element name="qsubArgs" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="postprocessOptions">
<xs:complexType>
<xs:sequence>
<xs:element name="algorithm">
<xs:simpleType>
<xs:restriction base="xs:integer">
<xs:minInclusive value="0"/>
<xs:maxInclusive value="3"/>
</xs:restriction>
</xs:simpleType>
</xs:element>
<xs:element name="outputFormat" type="xs:integer"/>
<xs:element name="threads" type="positiveInteger" value="2"/>
<xs:element name="qsubQueue" type="xs:string"/>
<xs:element name="qsubArgs" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="samOptions">
<xs:complexType>
<xs:sequence>
<xs:element name="samtools" type="integer" use="required"/>
<xs:element name="qsubQueue" type="xs:string"/>
<xs:element name="qsubArgs" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:simpleType name="filePath">
<xs:restriction base="xs:string">
<xsattern value="/home/vincenzo/run_parallel"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="directoryPath">
<xs:restriction base="xs:string">
<xsattern value="/home/vincenzo/run_parallel"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="nonNegativeInteger">
<xs:restriction base="xs:integer">
<xs:minInclusive value="0"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="positiveInteger">
<xs:restriction base="xs:integer">
<xs:minInclusive value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:schema>

Thanks a lot.
Please tell me if there is a clear tutorial about this phase of running.
This is my first post, i hope is clear.
Bye

[nilshomer]

There is no tutorial about this script and is meant for advanced users. You have not converted the XML schema into a valid XML file. You should first read a tutorial about XML and creating an XML file from an XML schema. For example,

<xs:element name="qsubQueue" type="xs:string"/>

should be

<qsubQueue>SGE</qsubQueue>

.

[Vincenzo]

Can you share a complete file.xml to inspire and help me in the develop of this config file?
For example a file.xml that you used to run your jobs.
Thanks a lot

[nilshomer]

Please email the mailing list for further questions: [email protected]. There may be someone on the list who can share their xml configuration file with you.