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Isaac Genome Alignment Software
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xmlTextReaderRead failed #17

Closed grendon closed 10 years ago

grendon commented 10 years ago

I am just trying to reproduce the results with the NA12878 dataset that you included in your paper. I obtained the input dataset from the GATK bundle dataset. It is in bam format. I used the parameters described in the paper.

Execution aborted with the message xmlTextReaderRead failed

I have not seen this kind of error before. What causes it? How can I correct the problem?

This is the error log

[grendon@vlad-hm]$ more ../tmp/isaac_aligner_NA12878_w_parms_from_paper_thr8_mem150 2014-10-18 18:43:19 [7f3f776017c0] Forcing LC_ALL to C 2014-10-18 18:43:19 [7f3f776017c0] Version: iSAAC-01.14.04.17 2014-10-18 18:43:19 [7f3f776017c0] argc: 25 argv: /home/grendon/bin/iSAAC-i nstall/bin/isaac-align -r /home/genome/build/HG19_WholeGenome/HG19WholeGenome.f a -m 150 -b /home/grendon/reads/NA12878/NA12878.hiseq.wgs.bwa.raw.bam --base-cal ls-format bam -j 8 --base-quality-cutoff 15 --pf-only 1 --keep-duplicates 1 --ke ep-unaligned back --stats-image-format none --barcode-mismatches 1 --use-bases-m ask Y100n,Y100n 2014-10-18 18:43:19 [7f3f776017c0] Opened bam stream on "/home/grendon/read s/NA12878/NA12878.hiseq.wgs.bwa.raw.bam" 2014-10-18 18:43:19 [7f3f74fca700] BAM Header skipped 2014-10-18 18:43:19 [7f3f74fca700] Will need to skip 45 reference sequences 2014-10-18 18:43:19 [7f3f74fca700] BAM References skipped 2014-10-18 18:43:19 [7f3f74fca700] suspending on thread 0 unparsed: 2 lastU nparsedBytes:0 2014-10-18 18:43:19 [7f3f74fca700] BamLoader::returnParseSlot nextParserThr ead_:0 2014-10-18 18:43:19 [7f3f776017c0] use bases mask: yyyyyyyyyyyyyyyyyyyyyyyy yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn,yy yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy yyyyyyyyyyyyyyyyyyn 2014-10-18 18:43:19 [7f3f776017c0] reads parsed: 2 2014-10-18 18:43:19 [7f3f776017c0] Discovered data read: ReadMetadata(1, 10 0 [1, 100], 0id, 0off,1frc) 2014-10-18 18:43:19 [7f3f776017c0] Discovered data read: ReadMetadata(2, 10 0 [102, 201], 1id, 100off,102frc) 2014-10-18 18:43:19 [7f3f776017c0] constructed extremity seed SeedMetadata( 0, 32, 0, 0) 2014-10-18 18:43:19 [7f3f776017c0] constructed extremity seed SeedMetadata( 68, 32, 0, 1) 2014-10-18 18:43:19 [7f3f776017c0] constructed SeedMetadata(32, 32, 0, 2) 2014-10-18 18:43:19 [7f3f776017c0] constructed overlapping SeedMetadata(16, 32, 0, 3) 2014-10-18 18:43:19 [7f3f776017c0] constructed extremity seed SeedMetadata( 0, 32, 1, 4) 2014-10-18 18:43:19 [7f3f776017c0] constructed extremity seed SeedMetadata( 68, 32, 1, 5) 2014-10-18 18:43:19 [7f3f776017c0] constructed SeedMetadata(32, 32, 1, 6) 2014-10-18 18:43:19 [7f3f776017c0] constructed overlapping SeedMetadata(16, 32, 1, 7) 2014-10-18 18:43:19 [7f3f776017c0] Generated 'none' barcode: BarcodeMetadat a(20FUKAAXX100202,1,default,none,(0), 4294967295) 2014-10-18 18:43:19 [7f3f776017c0] align: Setting memory limit to 161061273 600 bytes. :1: parser error : Document is empty

chrM ^ Error: 2014-Oct-18 18:43:19: Success: /home/grendon/bin/isaac_aligner-master/src /c++/lib/xml/XmlReader.cpp(333): Throw in function bool isaac::xml::XmlReader::r ead() Dynamic exception type: boost::exception_detail::clone_impl<isaac::xml::XmlReade rException> std::exception::what: xmlTextReaderRead failed : xmlTextReaderRead failed [grendon@vlad-hm scripts]$ emacs isaac_align_NA12878.sh [grendon@vlad-hm scripts]$ more ../tmp/isaac_aligner_NA12878_w_parms_from_paper_thr8_mem150 2014-10-18 18:43:19 [7f3f776017c0] Forcing LC_ALL to C 2014-10-18 18:43:19 [7f3f776017c0] Version: iSAAC-01.14.04.17 2014-10-18 18:43:19 [7f3f776017c0] argc: 25 argv: /home/grendon/bin/iSAAC-i nstall/bin/isaac-align -r /home/genome/build/HG19_WholeGenome/HG19WholeGenome.f a -m 150 -b /home/grendon/reads/NA12878/NA12878.hiseq.wgs.bwa.raw.bam --base-cal ls-format bam -j 8 --base-quality-cutoff 15 --pf-only 1 --keep-duplicates 1 --ke ep-unaligned back --stats-image-format none --barcode-mismatches 1 --use-bases-m ask Y100n,Y100n 2014-10-18 18:43:19 [7f3f776017c0] Opened bam stream on "/home/grendon/read s/NA12878/NA12878.hiseq.wgs.bwa.raw.bam" 2014-10-18 18:43:19 [7f3f74fca700] BAM Header skipped 2014-10-18 18:43:19 [7f3f74fca700] Will need to skip 45 reference sequences 2014-10-18 18:43:19 [7f3f74fca700] BAM References skipped 2014-10-18 18:43:19 [7f3f74fca700] suspending on thread 0 unparsed: 2 lastU nparsedBytes:0 2014-10-18 18:43:19 [7f3f74fca700] BamLoader::returnParseSlot nextParserThr ead_:0 2014-10-18 18:43:19 [7f3f776017c0] use bases mask: yyyyyyyyyyyyyyyyyyyyyyyy yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn,yy yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy yyyyyyyyyyyyyyyyyyn 2014-10-18 18:43:19 [7f3f776017c0] reads parsed: 2 2014-10-18 18:43:19 [7f3f776017c0] Discovered data read: ReadMetadata(1, 10 0 [1, 100], 0id, 0off,1frc) 2014-10-18 18:43:19 [7f3f776017c0] Discovered data read: ReadMetadata(2, 10 0 [102, 201], 1id, 100off,102frc) 2014-10-18 18:43:19 [7f3f776017c0] constructed extremity seed SeedMetadata( 0, 32, 0, 0) 2014-10-18 18:43:19 [7f3f776017c0] constructed extremity seed SeedMetadata( 68, 32, 0, 1) 2014-10-18 18:43:19 [7f3f776017c0] constructed SeedMetadata(32, 32, 0, 2) 2014-10-18 18:43:19 [7f3f776017c0] constructed overlapping SeedMetadata(16, 32, 0, 3) 2014-10-18 18:43:19 [7f3f776017c0] constructed extremity seed SeedMetadata( 0, 32, 1, 4) 2014-10-18 18:43:19 [7f3f776017c0] constructed extremity seed SeedMetadata( 68, 32, 1, 5) 2014-10-18 18:43:19 [7f3f776017c0] constructed SeedMetadata(32, 32, 1, 6) 2014-10-18 18:43:19 [7f3f776017c0] constructed overlapping SeedMetadata(16, 32, 1, 7) 2014-10-18 18:43:19 [7f3f776017c0] Generated 'none' barcode: BarcodeMetadat a(20FUKAAXX100202,1,default,none,(0), 4294967295) 2014-10-18 18:43:19 [7f3f776017c0] align: Setting memory limit to 161061273 600 bytes. :1: parser error : Document is empty chrM ^ Error: 2014-Oct-18 18:43:19: Success: /home/grendon/bin/isaac_aligner-master/src /c++/lib/xml/XmlReader.cpp(333): Throw in function bool isaac::xml::XmlReader::r ead() Dynamic exception type: boost::exception_detail::clone_impl<isaac::xml::XmlReade rException> std::exception::what: xmlTextReaderRead failed : xmlTextReaderRead failed

rpetrovski commented 10 years ago

grendon, isaac-align -r requires path to sorted-reference.xml, not an .fa file. You need to use isaac-sort-reference to produce the proper files from .fa input.

Roman.