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sequencing / isaac_aligner

Isaac Genome Alignment Software
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xmlTextReaderRead failed #23

Open wuxiaohong12 opened 4 years ago

wuxiaohong12 commented 4 years ago

2020-04-07 13:36:47 [7f9c73d0a7c0] Forcing LC_ALL to C 2020-04-07 13:36:47 [7f9c73d0a7c0] Version: iSAAC-01.15.04.01 2020-04-07 13:36:47 [7f9c73d0a7c0] argc: 9 argv: isaac-align -r isaac_aligner/hs37d5.fa -b Fastq -m 40 --base-calls-format fastq-gz 2020-04-07 13:36:47 [7f9c73d0a7c0] Opened fastq stream on isaac_aligner/Fastq/lane1_read1.fastq.gz 2020-04-07 13:36:47 [7f9c73d0a7c0] Opened fastq stream on isaac_aligner/Fastq/lane1_read2.fastq.gz 2020-04-07 13:36:47 [7f9c73d0a7c0] FastqFlowcellInfo(1,76:76,[1 ]) 2020-04-07 13:36:47 [7f9c73d0a7c0] use bases mask: yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn,yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyn 2020-04-07 13:36:47 [7f9c73d0a7c0] reads parsed: 2 2020-04-07 13:36:47 [7f9c73d0a7c0] Discovered data read: ReadMetadata(1, 75 [1, 75], 0id, 0off,1frc) 2020-04-07 13:36:47 [7f9c73d0a7c0] Discovered data read: ReadMetadata(2, 75 [77, 151], 1id, 75off,77frc) 2020-04-07 13:36:47 [7f9c73d0a7c0] constructed extremity seed SeedMetadata(0, 32, 0, 0) 2020-04-07 13:36:47 [7f9c73d0a7c0] constructed extremity seed SeedMetadata(43, 32, 0, 1) 2020-04-07 13:36:47 [7f9c73d0a7c0] constructed extremity seed SeedMetadata(0, 32, 1, 2) 2020-04-07 13:36:47 [7f9c73d0a7c0] constructed extremity seed SeedMetadata(43, 32, 1, 3) 2020-04-07 13:36:47 [7f9c73d0a7c0] Generated 'none' barcode: BarcodeMetadata(1,1,default,none,(0), 4294967295) 2020-04-07 13:36:47 [7f9c73d0a7c0] align: Setting memory limit to 42949672960 bytes. :1: parser error : Document is empty

chr1 dna:chromosome chromosome:GRCh37:1:1:249250621:1 ^ Error: 2020-Apr-07 13:36:47: Success: /root/isaac_aligner/src/c++/lib/xml/XmlReader.cpp(330): Throw in function bool isaac::xml::XmlReader::read() Dynamic exception type: boost::exception_detail::clone_impl std::exception::what: xmlTextReaderRead failed : xmlTextReaderRead failed

rpetrovski commented 4 years ago

iSAAC-01 does not support fasta as input and has been discontinued ages ago. For latest Isaac aligner please go to https://github.com/Illumina/Isaac4 For most recent Illumina data processing offering please visit https://emea.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html