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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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issue running BLASTN2SNP #89

Closed dhwani2410 closed 6 years ago

dhwani2410 commented 6 years ago

Verify

Subject of the issue

unable to execute BLASTN2SNP

Your environment

Steps to reproduce

dhwani@dhwani-VirtualBox:~/Desktop/new_miseq_kmer/ref_seq$ java -jar ./jvarkit/dist/blastn2snp.jar res_blastn_out.xml [INFO][BlastNToSnp]Reading from res_blastn_out.xml

Message: Content is not allowed in prolog. javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1] Message: Content is not allowed in prolog. at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:604) at com.sun.xml.internal.stream.XMLEventReaderImpl.peek(XMLEventReaderImpl.java:276) at com.github.lindenb.jvarkit.tools.blast.BlastNToSnp.peekIteration(BlastNToSnp.java:186) at com.github.lindenb.jvarkit.tools.blast.BlastNToSnp.run(BlastNToSnp.java:259) at com.github.lindenb.jvarkit.tools.blast.BlastNToSnp.doWork(BlastNToSnp.java:454) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:1164) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:1322) at com.github.lindenb.jvarkit.tools.blast.BlastNToSnp.main(BlastNToSnp.java:474)

query hit hit-index hsp-index query-POS hit-POS STRAND REF(hit) ALT(query) blast.align_length blast.hit.var blast.query.varblast.mid.var

[INFO][Launcher]blastn2snp Exited with failure (-1)

Expected behaviour

Tell us what should happen

Actual behaviour

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lindenb commented 6 years ago

sorry for my late answer, I don't receive my mail from github for an unknow reason...

lindenb commented 6 years ago

I suppose there is an error with your res_blastn_out.xml

Try to validate your xml with xmllint ( http://xmlsoft.org/xmllint.html )

xmllint res_blastn_out.xml

or open res_blastn_out.xml as a file in firefox.

dhwani2410 commented 6 years ago

Hello Sir

That is the output generated from BLAST with option -m 8 , to generate the result in XML format.

Regards Dhwani

On Sun, Nov 19, 2017 at 6:13 PM, Pierre Lindenbaum <notifications@github.com

wrote:

sorry for my late answer, I don't receive my mail from github for an unknow reason...

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lindenb/jvarkit/issues/89#issuecomment-345513737, or mute the thread https://github.com/notifications/unsubscribe-auth/Ac01fQPUzF3EoyIXEblPss68m1t_xSAZks5s4CKIgaJpZM4QaoKT .

lindenb commented 6 years ago

That is the output generated from BLAST with option -m 8 , to generate the result in XML format.

ok,

what is the output of 

xmllint res_blastn_out.xml

or can you open the xml file in firefox ?

dhwani2410 commented 6 years ago

This is the error

xmllint res_blastn_out.xml res_blastn_out.xml:1: parser error : Start tag expected, '<' not found read_1 HLA-A-Exon2 100.00 180 0 0 1 180 30 209 1e-103 357

On Mon, Nov 20, 2017 at 12:46 AM, Pierre Lindenbaum < notifications@github.com> wrote:

That is the output generated from BLAST with option -m 8 , to generate the result in XML format.

ok,

what is the output of

xmllint res_blastn_out.xml

or can you open the xml file in firefox ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lindenb/jvarkit/issues/89#issuecomment-345541796, or mute the thread https://github.com/notifications/unsubscribe-auth/Ac01fQCARw_o_aRNttYyXVUKwiI0fjawks5s4H54gaJpZM4QaoKT .

lindenb commented 6 years ago

ok, so your res_blastn_out.xml is not an XML file. It's a problem with the way your generated this file and it's not related to my software. closing.