[svtoolkit-help] Mismatched read pair records

[yw <yw...@gm...>]

Hi there,
I have been tried to run Genome-STRIP with my data these days. I believe
I have successfully installed the software. The install test was okay.
And I tried with 30 BAM files and got the results. However, When I came
to more BAM files, something went wrong.
I can't figure out what is wrong with my BAM files. Anyone has any
suggestions? Thx.

Here is the error message:

java -Xmx4g
-Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir
-cp
/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar
-verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R
/home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I
/home/wbxie/wild_rice/bwa_map/100.bam -I
/home/wbxie/wild_rice/bwa_map/100.bam -I
/home/wbxie/wild_rice/bwa_map/101.bam -I
/home/wbxie/wild_rice/bwa_map/102.bam -I
/home/wbxie/wild_rice/bwa_map/103.bam -I
/home/wbxie/wild_rice/bwa_map/104.bam -I
/home/wbxie/wild_rice/bwa_map/105.bam -I
/home/wbxie/wild_rice/bwa_map/106.bam -I
/home/wbxie/wild_rice/bwa_map/107.bam -I
/home/wbxie/wild_rice/bwa_map/108.bam -I
/home/wbxie/wild_rice/bwa_map/109.bam -I
/home/wbxie/wild_rice/bwa_map/10.bam -I
/home/wbxie/wild_rice/bwa_map/110.bam -I
/home/wbxie/wild_rice/bwa_map/111.bam -I
/home/wbxie/wild_rice/bwa_map/112.bam -I
/home/wbxie/wild_rice/bwa_map/113.bam -I
/home/wbxie/wild_rice/bwa_map/114.bam -I
/home/wbxie/wild_rice/bwa_map/115.bam -I
/home/wbxie/wild_rice/bwa_map/116.bam -I
/home/wbxie/wild_rice/bwa_map/117.bam -I
/home/wbxie/wild_rice/bwa_map/118.bam -I
/home/wbxie/wild_rice/bwa_map/119.bam -I
/home/wbxie/wild_rice/bwa_map/11.bam -I
/home/wbxie/wild_rice/bwa_map/120.bam -I
/home/wbxie/wild_rice/bwa_map/121.bam -I
/home/wbxie/wild_rice/bwa_map/122.bam -I
/home/wbxie/wild_rice/bwa_map/123.bam -I
/home/wbxie/wild_rice/bwa_map/124.bam -I
/home/wbxie/wild_rice/bwa_map/125.bam -I
/home/wbxie/wild_rice/bwa_map/126.bam -I
/home/wbxie/wild_rice/bwa_map/127.bam -I
/home/wbxie/wild_rice/bwa_map/128.bam -I
/home/wbxie/wild_rice/bwa_map/129.bam -I
/home/wbxie/wild_rice/bwa_map/12.bam -I
/home/wbxie/wild_rice/bwa_map/130.bam -I
/home/wbxie/wild_rice/bwa_map/132.bam -I
/home/wbxie/wild_rice/bwa_map/133.bam -I
/home/wbxie/wild_rice/bwa_map/134.bam -I
/home/wbxie/wild_rice/bwa_map/135.bam -I
/home/wbxie/wild_rice/bwa_map/13.bam -I
/home/wbxie/wild_rice/bwa_map/14.bam -I
/home/wbxie/wild_rice/bwa_map/15.bam -I
/home/wbxie/wild_rice/bwa_map/16.bam -I
/home/wbxie/wild_rice/bwa_map/17.bam -I
/home/wbxie/wild_rice/bwa_map/18.bam -I
/home/wbxie/wild_rice/bwa_map/19.bam -I
/home/wbxie/wild_rice/bwa_map/1.bam -I
/home/wbxie/wild_rice/bwa_map/20.bam -I
/home/wbxie/wild_rice/bwa_map/21.bam -I
/home/wbxie/wild_rice/bwa_map/22.bam -I
/home/wbxie/wild_rice/bwa_map/23.bam -I
/home/wbxie/wild_rice/bwa_map/24.bam -I
/home/wbxie/wild_rice/bwa_map/25.bam -I
/home/wbxie/wild_rice/bwa_map/26.bam -I
/home/wbxie/wild_rice/bwa_map/27.bam -I
/home/wbxie/wild_rice/bwa_map/28.bam -I
/home/wbxie/wild_rice/bwa_map/29.bam -I
/home/wbxie/wild_rice/bwa_map/2.bam -I
/home/wbxie/wild_rice/bwa_map/30.bam -I
/home/wbxie/wild_rice/bwa_map/31.bam -I
/home/wbxie/wild_rice/bwa_map/32.bam -I
/home/wbxie/wild_rice/bwa_map/33.bam -I
/home/wbxie/wild_rice/bwa_map/34.bam -I
/home/wbxie/wild_rice/bwa_map/35.bam -I
/home/wbxie/wild_rice/bwa_map/36.bam -I
/home/wbxie/wild_rice/bwa_map/37.bam -I
/home/wbxie/wild_rice/bwa_map/38.bam -I
/home/wbxie/wild_rice/bwa_map/39.bam -I
/home/wbxie/wild_rice/bwa_map/3.bam -I
/home/wbxie/wild_rice/bwa_map/40.bam -I
/home/wbxie/wild_rice/bwa_map/41.bam -I
/home/wbxie/wild_rice/bwa_map/42.bam -I
/home/wbxie/wild_rice/bwa_map/43.bam -I
/home/wbxie/wild_rice/bwa_map/44.bam -I
/home/wbxie/wild_rice/bwa_map/45.bam -I
/home/wbxie/wild_rice/bwa_map/46.bam -I
/home/wbxie/wild_rice/bwa_map/47.bam -I
/home/wbxie/wild_rice/bwa_map/48.bam -I
/home/wbxie/wild_rice/bwa_map/49.bam -I
/home/wbxie/wild_rice/bwa_map/4.bam -I
/home/wbxie/wild_rice/bwa_map/50.bam -I
/home/wbxie/wild_rice/bwa_map/51.bam -I
/home/wbxie/wild_rice/bwa_map/52.bam -I
/home/wbxie/wild_rice/bwa_map/53.bam -I
/home/wbxie/wild_rice/bwa_map/54.bam -I
/home/wbxie/wild_rice/bwa_map/55.bam -I
/home/wbxie/wild_rice/bwa_map/56.bam -I
/home/wbxie/wild_rice/bwa_map/57.bam -I
/home/wbxie/wild_rice/bwa_map/58.bam -I
/home/wbxie/wild_rice/bwa_map/59.bam -I
/home/wbxie/wild_rice/bwa_map/5.bam -I
/home/wbxie/wild_rice/bwa_map/60.bam -I
/home/wbxie/wild_rice/bwa_map/61.bam -I
/home/wbxie/wild_rice/bwa_map/62.bam -I
/home/wbxie/wild_rice/bwa_map/63.bam -I
/home/wbxie/wild_rice/bwa_map/64.bam -I
/home/wbxie/wild_rice/bwa_map/65.bam -I
/home/wbxie/wild_rice/bwa_map/66.bam -I
/home/wbxie/wild_rice/bwa_map/67.bam -I
/home/wbxie/wild_rice/bwa_map/68.bam -I
/home/wbxie/wild_rice/bwa_map/69.bam -I
/home/wbxie/wild_rice/bwa_map/6.bam -I
/home/wbxie/wild_rice/bwa_map/70.bam -I
/home/wbxie/wild_rice/bwa_map/71.bam -I
/home/wbxie/wild_rice/bwa_map/72.bam -I
/home/wbxie/wild_rice/bwa_map/73.bam -I
/home/wbxie/wild_rice/bwa_map/74.bam -I
/home/wbxie/wild_rice/bwa_map/75.bam -I
/home/wbxie/wild_rice/bwa_map/76.bam -I
/home/wbxie/wild_rice/bwa_map/77.bam -I
/home/wbxie/wild_rice/bwa_map/78.bam -I
/home/wbxie/wild_rice/bwa_map/79.bam -I
/home/wbxie/wild_rice/bwa_map/7.bam -I
/home/wbxie/wild_rice/bwa_map/80.bam -I
/home/wbxie/wild_rice/bwa_map/81.bam -I
/home/wbxie/wild_rice/bwa_map/83.bam -I
/home/wbxie/wild_rice/bwa_map/84.bam -I
/home/wbxie/wild_rice/bwa_map/85.bam -I
/home/wbxie/wild_rice/bwa_map/86.bam -I
/home/wbxie/wild_rice/bwa_map/87.bam -I
/home/wbxie/wild_rice/bwa_map/88.bam -I
/home/wbxie/wild_rice/bwa_map/89.bam -I
/home/wbxie/wild_rice/bwa_map/8.bam -I
/home/wbxie/wild_rice/bwa_map/90.bam -I
/home/wbxie/wild_rice/bwa_map/91.bam -I
/home/wbxie/wild_rice/bwa_map/92.bam -I
/home/wbxie/wild_rice/bwa_map/93.bam -I
/home/wbxie/wild_rice/bwa_map/94.bam -I
/home/wbxie/wild_rice/bwa_map/95.bam -I
/home/wbxie/wild_rice/bwa_map/96.bam -I
/home/wbxie/wild_rice/bwa_map/97.bam -I
/home/wbxie/wild_rice/bwa_map/98.bam -I
/home/wbxie/wild_rice/bwa_map/99.bam -I
/home/wbxie/wild_rice/bwa_map/9.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W01.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W02.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W03.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W04.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W05.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W06.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W07.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W08.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W09.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W10.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W11.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W12.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W13.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W14.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W15.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W16.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W17.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W18.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W19.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W20.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W21.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W22.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W23.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W24.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W25.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W26.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W27.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W28.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W29.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W30.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W31.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W32.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W33.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W34.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W35.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W36.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W37.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W38.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W39.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W40.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W41.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W42.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W43.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W44.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W45.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W46.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W47.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W48.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W49.bam -I
/home/wbxie/wild_rice/wangwen/bwa_map/W50.bam -I
/home/wbxie/bam_file_MSUv7/C001.bam -I
/home/wbxie/bam_file_MSUv7/C002.bam -I
/home/wbxie/bam_file_MSUv7/C003.bam -I
/home/wbxie/bam_file_MSUv7/C004.bam -I
/home/wbxie/bam_file_MSUv7/C005.bam -I
/home/wbxie/bam_file_MSUv7/C006.bam -I
/home/wbxie/bam_file_MSUv7/C007.bam -I
/home/wbxie/bam_file_MSUv7/C008.bam -I
/home/wbxie/bam_file_MSUv7/C009.bam -I
/home/wbxie/bam_file_MSUv7/C010.bam -I
/home/wbxie/bam_file_MSUv7/C011.bam -I
/home/wbxie/bam_file_MSUv7/C012.bam -I
/home/wbxie/bam_file_MSUv7/C013.bam -I
/home/wbxie/bam_file_MSUv7/C014.bam -I
/home/wbxie/bam_file_MSUv7/C015.bam -I
/home/wbxie/bam_file_MSUv7/C016.bam -I
/home/wbxie/bam_file_MSUv7/C017.bam -I
/home/wbxie/bam_file_MSUv7/C018.bam -I
/home/wbxie/bam_file_MSUv7/C019.bam -I
/home/wbxie/bam_file_MSUv7/C020.bam -I
/home/wbxie/bam_file_MSUv7/C021.bam -I
/home/wbxie/bam_file_MSUv7/C022.bam -I
/home/wbxie/bam_file_MSUv7/C023.bam -I
/home/wbxie/bam_file_MSUv7/C024.bam -I
/home/wbxie/bam_file_MSUv7/C025.bam -I
/home/wbxie/bam_file_MSUv7/C026.bam -I
/home/wbxie/bam_file_MSUv7/C027.bam -I
/home/wbxie/bam_file_MSUv7/C028.bam -I
/home/wbxie/bam_file_MSUv7/C029.bam -I
/home/wbxie/bam_file_MSUv7/C030.bam -I
/home/wbxie/bam_file_MSUv7/C031.bam -I
/home/wbxie/bam_file_MSUv7/C032.bam -I
/home/wbxie/bam_file_MSUv7/C033.bam -I
/home/wbxie/bam_file_MSUv7/C034.bam -I
/home/wbxie/bam_file_MSUv7/C035.bam -I
/home/wbxie/bam_file_MSUv7/C036.bam -I
/home/wbxie/bam_file_MSUv7/C037.bam -I
/home/wbxie/bam_file_MSUv7/C038.bam -I
/home/wbxie/bam_file_MSUv7/C039.bam -I
/home/wbxie/bam_file_MSUv7/C040.bam -I
/home/wbxie/bam_file_MSUv7/C041.bam -I
/home/wbxie/bam_file_MSUv7/C042.bam -I
/home/wbxie/bam_file_MSUv7/C043.bam -I
/home/wbxie/bam_file_MSUv7/C044.bam -I
/home/wbxie/bam_file_MSUv7/C045.bam -I
/home/wbxie/bam_file_MSUv7/C046.bam -I
/home/wbxie/bam_file_MSUv7/C047.bam -I
/home/wbxie/bam_file_MSUv7/C048.bam -I
/home/wbxie/bam_file_MSUv7/C049.bam -I
/home/wbxie/bam_file_MSUv7/C050.bam -I
/home/wbxie/bam_file_MSUv7/C051.bam -I
/home/wbxie/bam_file_MSUv7/C052.bam -I
/home/wbxie/bam_file_MSUv7/C053.bam -I
/home/wbxie/bam_file_MSUv7/C054.bam -I
/home/wbxie/bam_file_MSUv7/C055.bam -I
/home/wbxie/bam_file_MSUv7/C056.bam -I
/home/wbxie/bam_file_MSUv7/C057.bam -I
/home/wbxie/bam_file_MSUv7/C058.bam -I
/home/wbxie/bam_file_MSUv7/C059.bam -I
/home/wbxie/bam_file_MSUv7/C060.bam -I
/home/wbxie/bam_file_MSUv7/C061.bam -I
/home/wbxie/bam_file_MSUv7/C062.bam -I
/home/wbxie/bam_file_MSUv7/C063.bam -I
/home/wbxie/bam_file_MSUv7/C064.bam -I
/home/wbxie/bam_file_MSUv7/C065.bam -I
/home/wbxie/bam_file_MSUv7/C066.bam -I
/home/wbxie/bam_file_MSUv7/C067.bam -I
/home/wbxie/bam_file_MSUv7/C068.bam -I
/home/wbxie/bam_file_MSUv7/C069.bam -I
/home/wbxie/bam_file_MSUv7/C070.bam -I
/home/wbxie/bam_file_MSUv7/C071.bam -I
/home/wbxie/bam_file_MSUv7/C072.bam -I
/home/wbxie/bam_file_MSUv7/C073.bam -I
/home/wbxie/bam_file_MSUv7/C074.bam -I
/home/wbxie/bam_file_MSUv7/C075.bam -I
/home/wbxie/bam_file_MSUv7/C076.bam -I
/home/wbxie/bam_file_MSUv7/C077.bam -I
/home/wbxie/bam_file_MSUv7/C078.bam -I
/home/wbxie/bam_file_MSUv7/C079.bam -I
/home/wbxie/bam_file_MSUv7/C080.bam -I
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/home/wbxie/bam_file_MSUv7/C082.bam -I
/home/wbxie/bam_file_MSUv7/C083.bam -I
/home/wbxie/bam_file_MSUv7/C084.bam -I
/home/wbxie/bam_file_MSUv7/C085.bam -I
/home/wbxie/bam_file_MSUv7/C086.bam -I
/home/wbxie/bam_file_MSUv7/C087.bam -I
/home/wbxie/bam_file_MSUv7/C088.bam -I
/home/wbxie/bam_file_MSUv7/C089.bam -I
/home/wbxie/bam_file_MSUv7/C090.bam -I
/home/wbxie/bam_file_MSUv7/C091.bam -I
/home/wbxie/bam_file_MSUv7/C092.bam -I
/home/wbxie/bam_file_MSUv7/C093.bam -I
/home/wbxie/bam_file_MSUv7/C094.bam -I
/home/wbxie/bam_file_MSUv7/C095.bam -I
/home/wbxie/bam_file_MSUv7/C096.bam -I
/home/wbxie/bam_file_MSUv7/C097.bam -I
/home/wbxie/bam_file_MSUv7/C098.bam -I
/home/wbxie/bam_file_MSUv7/C099.bam -I
/home/wbxie/bam_file_MSUv7/C100.bam -I
/home/wbxie/bam_file_MSUv7/C101.bam -I
/home/wbxie/bam_file_MSUv7/C102.bam -I
/home/wbxie/bam_file_MSUv7/C103.bam -I
/home/wbxie/bam_file_MSUv7/C104.bam -I
/home/wbxie/bam_file_MSUv7/C105.bam -I
/home/wbxie/bam_file_MSUv7/C106.bam -I
/home/wbxie/bam_file_MSUv7/C107.bam -I
/home/wbxie/bam_file_MSUv7/C108.bam -I
/home/wbxie/bam_file_MSUv7/C109.bam -I
/home/wbxie/bam_file_MSUv7/C110.bam -I
/home/wbxie/bam_file_MSUv7/C111.bam -I
/home/wbxie/bam_file_MSUv7/C112.bam -I
/home/wbxie/bam_file_MSUv7/C113.bam -I
/home/wbxie/bam_file_MSUv7/C114.bam -I
/home/wbxie/bam_file_MSUv7/C115.bam -I
/home/wbxie/bam_file_MSUv7/C116.bam -I
/home/wbxie/bam_file_MSUv7/C117.bam -I
/home/wbxie/bam_file_MSUv7/C118.bam -I
/home/wbxie/bam_file_MSUv7/C119.bam -I
/home/wbxie/bam_file_MSUv7/C120.bam -I
/home/wbxie/bam_file_MSUv7/C121.bam -I
/home/wbxie/bam_file_MSUv7/C122.bam -I
/home/wbxie/bam_file_MSUv7/C123.bam -I
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/home/wbxie/bam_file_MSUv7/W239.bam -I
/home/wbxie/bam_file_MSUv7/W240.bam -I
/home/wbxie/bam_file_MSUv7/W241.bam -I
/home/wbxie/bam_file_MSUv7/W242.bam -I
/home/wbxie/bam_file_MSUv7/W243.bam -I
/home/wbxie/bam_file_MSUv7/W244.bam -I
/home/wbxie/bam_file_MSUv7/W245.bam -I
/home/wbxie/bam_file_MSUv7/W246.bam -I
/home/wbxie/bam_file_MSUv7/W247.bam -I
/home/wbxie/bam_file_MSUv7/W248.bam -I
/home/wbxie/bam_file_MSUv7/W249.bam -I
/home/wbxie/bam_file_MSUv7/W250.bam -I
/home/wbxie/bam_file_MSUv7/W251.bam -I
/home/wbxie/bam_file_MSUv7/W252.bam -I
/home/wbxie/bam_file_MSUv7/W253.bam -I
/home/wbxie/bam_file_MSUv7/W254.bam -I
/home/wbxie/bam_file_MSUv7/W255.bam -I
/home/wbxie/bam_file_MSUv7/W256.bam -I
/home/wbxie/bam_file_MSUv7/W257.bam -I
/home/wbxie/bam_file_MSUv7/W258.bam -I
/home/wbxie/bam_file_MSUv7/W259.bam -I
/home/wbxie/bam_file_MSUv7/W260.bam -I
/home/wbxie/bam_file_MSUv7/W261.bam -I
/home/wbxie/bam_file_MSUv7/W262.bam -I
/home/wbxie/bam_file_MSUv7/W263.bam -I
/home/wbxie/bam_file_MSUv7/W264.bam -I
/home/wbxie/bam_file_MSUv7/W265.bam -I
/home/wbxie/bam_file_MSUv7/W266.bam -I
/home/wbxie/bam_file_MSUv7/W267.bam -I
/home/wbxie/bam_file_MSUv7/W268.bam -I
/home/wbxie/bam_file_MSUv7/W269.bam -I
/home/wbxie/bam_file_MSUv7/W270.bam -I
/home/wbxie/bam_file_MSUv7/W271.bam -I
/home/wbxie/bam_file_MSUv7/W272.bam -I
/home/wbxie/bam_file_MSUv7/W273.bam -I
/home/wbxie/bam_file_MSUv7/W274.bam -I
/home/wbxie/bam_file_MSUv7/W275.bam -I
/home/wbxie/bam_file_MSUv7/W276.bam -I
/home/wbxie/bam_file_MSUv7/W277.bam -I
/home/wbxie/bam_file_MSUv7/W278.bam -I
/home/wbxie/bam_file_MSUv7/W279.bam -I
/home/wbxie/bam_file_MSUv7/W280.bam -I
/home/wbxie/bam_file_MSUv7/W281.bam -I
/home/wbxie/bam_file_MSUv7/W282.bam -I
/home/wbxie/bam_file_MSUv7/W283.bam -I
/home/wbxie/bam_file_MSUv7/W284.bam -I
/home/wbxie/bam_file_MSUv7/W285.bam -I
/home/wbxie/bam_file_MSUv7/W286.bam -I
/home/wbxie/bam_file_MSUv7/W287.bam -I
/home/wbxie/bam_file_MSUv7/W288.bam -I
/home/wbxie/bam_file_MSUv7/W289.bam -I
/home/wbxie/bam_file_MSUv7/W290.bam -I
/home/wbxie/bam_file_MSUv7/W291.bam -I
/home/wbxie/bam_file_MSUv7/W292.bam -I
/home/wbxie/bam_file_MSUv7/W293.bam -I
/home/wbxie/bam_file_MSUv7/W294.bam -I
/home/wbxie/bam_file_MSUv7/W295.bam -I
/home/wbxie/bam_file_MSUv7/W296.bam -I
/home/wbxie/bam_file_MSUv7/W297.bam -I
/home/wbxie/bam_file_MSUv7/W298.bam -I
/home/wbxie/bam_file_MSUv7/W299.bam -I
/home/wbxie/bam_file_MSUv7/W300.bam -I
/home/wbxie/bam_file_MSUv7/W301.bam -I
/home/wbxie/bam_file_MSUv7/W302.bam -I
/home/wbxie/bam_file_MSUv7/W303.bam -I
/home/wbxie/bam_file_MSUv7/W304.bam -I
/home/wbxie/bam_file_MSUv7/W305.bam -I
/home/wbxie/bam_file_MSUv7/W306.bam -I
/home/wbxie/bam_file_MSUv7/W307.bam -I
/home/wbxie/bam_file_MSUv7/W308.bam -I
/home/wbxie/bam_file_MSUv7/W309.bam -I
/home/wbxie/bam_file_MSUv7/W310.bam -I
/home/wbxie/bam_file_MSUv7/W311.bam -I
/home/wbxie/bam_file_MSUv7/W312.bam -I
/home/wbxie/bam_file_MSUv7/W313.bam -I
/home/wbxie/bam_file_MSUv7/W314.bam -I
/home/wbxie/bam_file_MSUv7/W315.bam -I
/home/wbxie/bam_file_MSUv7/W316.bam -I
/home/wbxie/bam_file_MSUv7/W317.bam -I
/home/wbxie/bam_file_MSUv7/W318.bam -I
/home/wbxie/bam_file_MSUv7/W319.bam -I
/home/wbxie/bam_file_MSUv7/W320.bam -I
/home/wbxie/bam_file_MSUv7/W321.bam -I
/home/wbxie/bam_file_MSUv7/W322.bam -I
/home/wbxie/bam_file_MSUv7/W323.bam -I
/home/wbxie/bam_file_MSUv7/W324.bam -I
/home/wbxie/bam_file_MSUv7/W325.bam -I
/home/wbxie/bam_file_MSUv7/W326.bam -I
/home/wbxie/bam_file_MSUv7/W327.bam -I
/home/wbxie/bam_file_MSUv7/W328.bam -I
/home/wbxie/bam_file_MSUv7/W329.bam -I
/home/wbxie/bam_file_MSUv7/W330.bam -O
/home/wbxie/software/svtoolkit/installtest/wild_rice_test2/P0001.discovery.vcf
-md wild_rice_test2/metadata -disableGATKTraversal -configFile
conf/genstrip_installtest_parameters.txt -runDirectory wild_rice_test2
-genomeMaskFile data/rice_all_genomes_v7.mask.fasta -partitionName P0001
-filePrefix P0001 -L chr13:1-490520 -searchLocus chr13:1-490520
-searchWindow chr13:1-490520 -searchMinimumSize 100 -searchMaximumSize
1000000
org.broadinstitute.sting.queue.util.JobExitException: Failed to run job.
Command line:
sh
/home/wbxie/software/svtoolkit/installtest/all_tmpdir/.exec5645035130960711054
Exit code: 1
Standard error contained:
[GC 524288K->73003K(2009792K), 0.1090360 secs]
INFO 18:49:12,251 HelpFormatter -
-----------------------------------------------------------------------------------

INFO 18:49:12,255 HelpFormatter - The Genome Analysis Toolkit (GATK)
v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29
INFO 18:49:12,255 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 18:49:12,255 HelpFormatter - Please view our documentation at
http://www.broadinstitute.org/gsa/wiki
INFO 18:49:12,256 HelpFormatter - For support, please view our support
site at http://getsatisfaction.com/gsa
INFO 18:49:12,256 HelpFormatter - Program Args: -T SVDiscovery -R
/home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -O
/home/wbxie/software/svtoolkit/installtest/wild_rice_test2/P0001.discovery.vcf
-md wild_rice_test2/metadata -disableGATKTraversal -configFile
conf/genstrip_installtest_parameters.txt -runDirectory wild_rice_test2
-genomeMaskFile data/rice_all_genomes_v7.mask.fasta -partitionName P0001
-filePrefix P0001 -L chr13:1-490520 -searchLocus chr13:1-490520
-searchWindow chr13:1-490520 -searchMinimumSize 100 -searchMaximumSize
1000000
INFO 18:49:12,256 HelpFormatter - Date/Time: 2012/10/31 18:49:12
INFO 18:49:12,256 HelpFormatter -
-----------------------------------------------------------------------------------

INFO 18:49:12,257 HelpFormatter -
-----------------------------------------------------------------------------------

INFO 18:49:12,295 GenomeAnalysisEngine - Strictness is SILENT
INFO 18:49:24,911 SVDiscovery - Initializing SVDiscovery ...
INFO 18:49:25,602 SVDiscovery - Opening reference sequence ...
INFO 18:49:25,604 SVDiscovery - Opened reference sequence.
INFO 18:49:25,604 SVDiscovery - Opening genome mask ...
INFO 18:49:25,605 SVDiscovery - Opened genome mask.
INFO 18:49:25,605 SVDiscovery - Initializing input data set ...
[GC 597291K->77188K(2534080K), 0.1140310 secs]
INFO 18:50:10,322 SVDiscovery - Initialized data set: 714 files, 811
read groups, 713 samples.
INFO 18:50:10,322 SVDiscovery - Opening metadata from
wild_rice_test2/metadata ...
INFO 18:50:10,324 SVDiscovery - Opened metadata.
INFO 18:50:10,327 SVDiscovery - Initializing discovery algorithm ...
INFO 18:50:10,329 SVDiscovery - Loading insert size histograms ...
[GC 1125764K->95799K(2534080K), 0.0965770 secs]
[GC 1144375K->25378K(2708864K), 0.0264040 secs]
[GC 1248738K->22178K(2592448K), 0.0159070 secs]
INFO 18:50:28,991 SVDiscovery - Loaded 713 histograms.
INFO 18:50:29,246 SVDiscovery - Discovery alt home filtering is disabled.
INFO 18:50:34,300 SVDiscovery - Processing locus:
chr13:1-490520:100-1000000
INFO 18:50:34,300 SVDiscovery - Locus search window: chr13:1-490520
INFO 18:50:34,300 SVDiscovery - Selecting read pairs ...
INFO 18:50:34,302 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/100.bam ...
[GC 1202722K->116136K(2642176K), 0.0972580 secs]
INFO 18:50:35,591 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/100.bam ...
INFO 18:50:36,210 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/101.bam ...
INFO 18:50:36,755 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/102.bam ...
INFO 18:50:37,831 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/103.bam ...
INFO 18:50:38,497 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/104.bam ...
INFO 18:50:39,044 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/105.bam ...
INFO 18:50:39,569 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/106.bam ...
[GC 1248488K->29382K(2503680K), 0.0308620 secs]
INFO 18:50:40,746 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/107.bam ...
INFO 18:50:41,388 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/108.bam ...
INFO 18:50:42,944 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/109.bam ...
[GC 1123078K->30510K(2550080K), 0.0262990 secs]
INFO 18:50:43,447 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/10.bam ...
INFO 18:50:44,718 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/110.bam ...
INFO 18:50:45,521 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/111.bam ...
INFO 18:50:46,216 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/112.bam ...
INFO 18:50:46,579 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/113.bam ...
INFO 18:50:46,991 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/114.bam ...
INFO 18:50:47,443 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/115.bam ...
[GC 1087278K->33903K(2429184K), 0.0333420 secs]
INFO 18:50:47,826 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/116.bam ...
INFO 18:50:48,614 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/117.bam ...
INFO 18:50:49,366 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/118.bam ...
INFO 18:50:49,807 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/119.bam ...
INFO 18:50:50,898 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/11.bam ...
[GC 1055407K->37127K(2479552K), 0.0348190 secs]
INFO 18:50:51,539 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/120.bam ...
INFO 18:50:52,165 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/121.bam ...
INFO 18:50:52,542 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/122.bam ...
INFO 18:50:53,271 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/123.bam ...
INFO 18:50:54,482 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/124.bam ...
[GC 1024903K->40183K(2358016K), 0.0309840 secs]
INFO 18:50:55,152 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/125.bam ...
INFO 18:50:55,815 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/126.bam ...
INFO 18:50:56,251 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/127.bam ...
INFO 18:50:57,213 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/128.bam ...
[GC 995703K->42367K(2412928K), 0.0230370 secs]
INFO 18:50:58,763 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/129.bam ...
INFO 18:51:00,579 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/12.bam ...
INFO 18:51:02,881 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/130.bam ...
INFO 18:51:05,376 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/132.bam ...
[GC 967039K->44807K(2297024K), 0.0225620 secs]
INFO 18:51:07,376 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/133.bam ...
INFO 18:51:09,755 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/134.bam ...
INFO 18:51:10,440 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/135.bam ...
INFO 18:51:11,409 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/13.bam ...
[GC 939975K->47447K(2348800K), 0.0217250 secs]
INFO 18:51:11,748 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/14.bam ...
INFO 18:51:12,472 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/15.bam ...
INFO 18:51:13,077 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/16.bam ...
INFO 18:51:13,996 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/17.bam ...
INFO 18:51:14,685 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/18.bam ...
INFO 18:51:15,072 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/19.bam ...
[GC 914391K->50271K(2242112K), 0.0236740 secs]
INFO 18:51:15,506 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/1.bam ...
INFO 18:51:16,303 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/20.bam ...
INFO 18:51:17,061 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/21.bam ...
INFO 18:51:17,511 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/22.bam ...
INFO 18:51:17,880 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/23.bam ...
[GC 890207K->52655K(2288448K), 0.0215040 secs]
INFO 18:51:18,447 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/24.bam ...
INFO 18:51:19,278 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/25.bam ...
INFO 18:51:19,718 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/26.bam ...
INFO 18:51:20,365 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/27.bam ...
INFO 18:51:21,014 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/28.bam ...
[GC 866735K->54951K(2191168K), 0.0215550 secs]
INFO 18:51:21,776 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/29.bam ...
INFO 18:51:22,405 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/2.bam ...
INFO 18:51:22,916 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/30.bam ...
INFO 18:51:23,825 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/31.bam ...
[GC 844327K->57087K(2232448K), 0.0223550 secs]
INFO 18:51:24,258 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/32.bam ...
INFO 18:51:24,620 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/33.bam ...
INFO 18:51:25,221 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/34.bam ...
INFO 18:51:27,655 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/35.bam ...
INFO 18:51:29,777 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/36.bam ...
INFO 18:51:31,625 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/37.bam ...
INFO 18:51:33,937 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/38.bam ...
[GC 822783K->60055K(2145280K), 0.0198480 secs]
INFO 18:51:36,299 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/39.bam ...
INFO 18:51:38,042 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/3.bam ...
INFO 18:51:38,595 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/40.bam ...
[GC 803031K->62319K(2180032K), 0.0218570 secs]
INFO 18:51:39,032 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/41.bam ...
INFO 18:51:39,434 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/42.bam ...
INFO 18:51:40,512 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/43.bam ...
INFO 18:51:40,980 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/44.bam ...
[GC 783535K->63991K(2101376K), 0.0191640 secs]
INFO 18:51:41,738 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/45.bam ...
INFO 18:51:41,999 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/46.bam ...
INFO 18:51:42,588 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/47.bam ...
INFO 18:51:43,510 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/48.bam ...
[GC 764343K->66415K(2131904K), 0.0176510 secs]
INFO 18:51:44,043 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/49.bam ...
INFO 18:51:44,662 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/4.bam ...
INFO 18:51:45,430 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/50.bam ...
INFO 18:51:46,094 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/51.bam ...
[GC 746799K->69015K(2063168K), 0.0198660 secs]
INFO 18:51:46,805 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/52.bam ...
INFO 18:51:47,480 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/53.bam ...
INFO 18:51:48,326 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/54.bam ...
[GC 730199K->71767K(2087232K), 0.0255990 secs]
INFO 18:51:49,781 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/55.bam ...
INFO 18:51:50,476 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/56.bam ...
INFO 18:51:50,996 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/57.bam ...
INFO 18:51:51,746 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/58.bam ...
INFO 18:51:52,313 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/59.bam ...
INFO 18:51:52,633 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/5.bam ...
[GC 714519K->75007K(2027520K), 0.0200360 secs]
INFO 18:51:53,613 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/60.bam ...
INFO 18:51:54,009 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/61.bam ...
INFO 18:51:54,334 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/62.bam ...
INFO 18:51:54,620 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/63.bam ...
INFO 18:51:54,958 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/64.bam ...
INFO 18:51:55,525 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/65.bam ...
[GC 700095K->77551K(2046016K), 0.0227850 secs]
INFO 18:51:56,376 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/66.bam ...
INFO 18:51:58,199 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/67.bam ...
[GC 685679K->78439K(1992384K), 0.0184230 secs]
INFO 18:51:59,867 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/68.bam ...
INFO 18:52:01,613 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/69.bam ...
INFO 18:52:04,087 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/6.bam ...
INFO 18:52:06,793 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/70.bam ...
INFO 18:52:08,640 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/71.bam ...
INFO 18:52:08,878 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/72.bam ...
INFO 18:52:09,110 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/73.bam ...
INFO 18:52:09,286 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/74.bam ...
INFO 18:52:09,462 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/75.bam ...
INFO 18:52:09,662 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/76.bam ...
[GC 670247K->82111K(2008256K), 0.0173290 secs]
INFO 18:52:09,787 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/77.bam ...
INFO 18:52:09,909 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/78.bam ...
INFO 18:52:10,160 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/79.bam ...
INFO 18:52:10,365 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/7.bam ...
INFO 18:52:10,806 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/80.bam ...
INFO 18:52:10,981 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/81.bam ...
INFO 18:52:11,188 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/83.bam ...
INFO 18:52:11,778 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/84.bam ...
INFO 18:52:13,377 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/85.bam ...
[GC 658239K->83943K(1963136K), 0.0213960 secs]
INFO 18:52:13,975 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/86.bam ...
INFO 18:52:14,539 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/87.bam ...
INFO 18:52:15,016 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/88.bam ...
INFO 18:52:15,953 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/89.bam ...
[GC 645031K->85199K(1974016K), 0.0175260 secs]
INFO 18:52:16,641 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/8.bam ...
INFO 18:52:18,498 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/90.bam ...
INFO 18:52:19,025 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/91.bam ...
[GC 631823K->86495K(1933248K), 0.0156370 secs]
INFO 18:52:20,446 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/92.bam ...
INFO 18:52:21,345 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/93.bam ...
[GC 619231K->88839K(1942272K), 0.0189790 secs]
INFO 18:52:22,029 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/94.bam ...
INFO 18:52:23,056 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/95.bam ...
INFO 18:52:23,844 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/96.bam ...
[GC 608199K->91399K(1908224K), 0.0195950 secs]
INFO 18:52:24,434 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/97.bam ...
INFO 18:52:25,537 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/98.bam ...
INFO 18:52:26,093 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/99.bam ...
[GC 597895K->92807K(1913280K), 0.0195380 secs]
INFO 18:52:26,842 SVDiscovery - Reading input file
/home/wbxie/wild_rice/bwa_map/9.bam ...
INFO 18:52:27,546 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W01.bam ...
[GC 586887K->94023K(1882304K), 0.0151020 secs]
[GC 576135K->95615K(1886848K), 0.0141770 secs]
INFO 18:52:32,415 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W02.bam ...
[GC 566207K->97127K(1859520K), 0.0161000 secs]
[GC 556647K->98523K(1862272K), 0.0137530 secs]
INFO 18:52:36,124 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W03.bam ...
[GC 547355K->99171K(1838272K), 0.0115450 secs]
[GC 537699K->99659K(1839616K), 0.0117330 secs]
INFO 18:52:40,179 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W04.bam ...
[GC 528203K->100363K(1818624K), 0.0099520 secs]
[GC 519307K->100739K(1818496K), 0.0117450 secs]
INFO 18:52:42,661 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W05.bam ...
[GC 510403K->101891K(1800512K), 0.0096000 secs]
[GC 502595K->102099K(1797888K), 0.0104900 secs]
[GC 494163K->102451K(1783040K), 0.0106100 secs]
INFO 18:52:48,203 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W06.bam ...
[GC 486131K->102859K(1777728K), 0.0093240 secs]
INFO 18:52:50,169 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W07.bam ...
[GC 478475K->103851K(1767744K), 0.0113390 secs]
[GC 471659K->104819K(1759936K), 0.0115180 secs]
[GC 465075K->105355K(1752512K), 0.0084150 secs]
INFO 18:52:54,024 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W08.bam ...
[GC 458315K->105947K(1745600K), 0.0108320 secs]
[GC 451867K->107763K(1739712K), 0.0148410 secs]
[GC 446835K->108827K(1732224K), 0.0133290 secs]
INFO 18:52:58,657 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W09.bam ...
[GC 441243K->109427K(1725824K), 0.0099850 secs]
[GC 435443K->110123K(1719552K), 0.0125140 secs]
[GC 429931K->111403K(1713728K), 0.0132940 secs]
[GC 425195K->112755K(1707776K), 0.0126480 secs]
INFO 18:53:03,392 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W10.bam ...
[GC 420723K->113411K(1702080K), 0.0116380 secs]
[GC 415683K->115003K(1697152K), 0.0144650 secs]
[GC 411771K->115963K(1691200K), 0.0118830 secs]
[GC 407419K->116899K(1685888K), 0.0140450 secs]
INFO 18:53:07,985 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W11.bam ...
[GC 403171K->117723K(1681024K), 0.0091770 secs]
[GC 399003K->118555K(1675968K), 0.0090400 secs]
INFO 18:53:10,884 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W12.bam ...
[GC 394971K->119403K(1671552K), 0.0109490 secs]
[GC 391083K->119803K(1666560K), 0.0125700 secs]
[GC 386875K->120619K(1662208K), 0.0103530 secs]
[GC 383211K->121315K(1657792K), 0.0087830 secs]
[GC 379555K->121003K(1652928K), 0.0070150 secs]
INFO 18:53:15,392 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W13.bam ...
[GC 375019K->121907K(1649344K), 0.0075980 secs]
[GC 371827K->121587K(1644672K), 0.0083340 secs]
[GC 367475K->122051K(1641088K), 0.0085640 secs]
[GC 364035K->122659K(1637504K), 0.0106830 secs]
[GC 360867K->122451K(1633344K), 0.0078820 secs]
[GC 356947K->122499K(1629632K), 0.0085530 secs]
[GC 353411K->122579K(1626048K), 0.0074810 secs]
[GC 349971K->122667K(1622656K), 0.0092880 secs]
INFO 18:53:23,301 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W14.bam ...
[GC 346667K->122843K(1619456K), 0.0069360 secs]
[GC 343515K->123171K(1616128K), 0.0086260 secs]
[GC 340579K->123147K(1612864K), 0.0101090 secs]
[GC 337419K->123387K(1609920K), 0.0091570 secs]
[GC 334587K->123555K(1606976K), 0.0083170 secs]
[GC 331747K->123611K(1603968K), 0.0059730 secs]
[GC 328859K->123419K(1600832K), 0.0110960 secs]
INFO 18:53:28,636 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W15.bam ...
[GC 325787K->123867K(1598400K), 0.0076520 secs]
[GC 323419K->124083K(1595648K), 0.0094950 secs]
[GC 320947K->123923K(1592768K), 0.0073860 secs]
INFO 18:53:31,667 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W16.bam ...
[GC 318163K->124355K(1590464K), 0.0098310 secs]
[GC 315971K->124495K(1587776K), 0.0061800 secs]
[GC 313551K->124343K(1584960K), 0.0093670 secs]
[GC 310903K->124687K(1582720K), 0.0069470 secs]
[GC 308815K->124839K(1580480K), 0.0090590 secs]
[GC 306599K->125007K(1578240K), 0.0102340 secs]
[GC 304463K->125039K(1575872K), 0.0065920 secs]
[GC 302255K->125111K(1573632K), 0.0078390 secs]
INFO 18:53:38,514 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W17.bam ...
[GC 300151K->125255K(1571520K), 0.0067460 secs]
[GC 298119K->125543K(1569472K), 0.0068200 secs]
[GC 296295K->125623K(1567360K), 0.0073280 secs]
[GC 294327K->125887K(1565440K), 0.0082320 secs]
[GC 292543K->125919K(1563328K), 0.0097040 secs]
[GC 290591K->125831K(1596096K), 0.0093780 secs]
INFO 18:53:42,258 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W18.bam ...
[GC 323463K->126335K(1593792K), 0.0075270 secs]
[GC 321279K->126479K(1591040K), 0.0058870 secs]
[GC 318799K->126600K(1588480K), 0.0087120 secs]
[GC 316360K->127015K(1586240K), 0.0071740 secs]
[GC 314279K->126751K(1583424K), 0.0072950 secs]
[GC 311583K->127095K(1581248K), 0.0068910 secs]
[GC 309559K->126991K(1578752K), 0.0081580 secs]
[GC 307151K->127247K(1576576K), 0.0061810 secs]
[GC 305167K->127408K(1574464K), 0.0083500 secs]
[GC 303088K->127415K(1572160K), 0.0084700 secs]
[GC 300919K->127471K(1569984K), 0.0074520 secs]
[GC 298863K->127544K(1567872K), 0.0073890 secs]
INFO 18:53:51,206 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W19.bam ...
[GC 296888K->127975K(1566144K), 0.0083840 secs]
[GC 295271K->127751K(1563776K), 0.0071630 secs]
[GC 293063K->127999K(1561984K), 0.0073520 secs]
[GC 291391K->127840K(1559872K), 0.0069980 secs]
[GC 289312K->128023K(1558144K), 0.0069980 secs]
[GC 287639K->128063K(1556288K), 0.0090880 secs]
INFO 18:53:55,175 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W20.bam ...
[GC 285823K->128639K(1554944K), 0.0083390 secs]
[GC 284607K->128400K(1552768K), 0.0067610 secs]
[GC 282640K->128623K(1551168K), 0.0066380 secs]
[GC 281135K->129087K(1581952K), 0.0086330 secs]
[GC 312127K->128999K(1618304K), 0.0095790 secs]
[GC 348647K->129792K(1615488K), 0.0079140 secs]
INFO 18:53:59,287 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W21.bam ...
[GC 346240K->130239K(1611904K), 0.0061660 secs]
[GC 343551K->130647K(1608960K), 0.0077450 secs]
[GC 340887K->130616K(1605824K), 0.0078470 secs]
[GC 337848K->130664K(1602880K), 0.0081610 secs]
[GC 335016K->130864K(1600192K), 0.0072030 secs]
[GC 332400K->131128K(1597632K), 0.0074790 secs]
[GC 329912K->131079K(1594752K), 0.0093360 secs]
INFO 18:54:04,595 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W22.bam ...
[GC 327175K->131456K(1592384K), 0.0100230 secs]
[GC 324928K->131656K(1589632K), 0.0079420 secs]
[GC 322568K->132040K(1587328K), 0.0072980 secs]
[GC 320456K->131944K(1584576K), 0.0078480 secs]
INFO 18:54:07,694 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W23.bam ...
[GC 317928K->132880K(1582784K), 0.0070040 secs]
[GC 316432K->133136K(1580032K), 0.0059220 secs]
[GC 314320K->133672K(1577920K), 0.0107030 secs]
[GC 312552K->133840K(1575680K), 0.0062960 secs]
[GC 310480K->134096K(1573440K), 0.0103420 secs]
[GC 308560K->134952K(1608832K), 0.0077280 secs]
[GC 344360K->135104K(1650560K), 0.0100510 secs]
INFO 18:54:12,690 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W24.bam ...
[GC 386432K->135544K(1646464K), 0.0079440 secs]
[GC 382840K->136144K(1642624K), 0.0081930 secs]
[GC 379536K->137216K(1639360K), 0.0104640 secs]
[GC 376768K->138488K(1635584K), 0.0121570 secs]
[GC 374328K->139056K(1631488K), 0.0088540 secs]
[GC 371248K->139008K(1627648K), 0.0077950 secs]
[GC 367680K->139832K(1648256K), 0.0138530 secs]
INFO 18:54:18,704 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W25.bam ...
[GC 387512K->140224K(1643200K), 0.0107090 secs]
[GC 383936K->140088K(1638784K), 0.0064150 secs]
[GC 379960K->140280K(1635072K), 0.0106940 secs]
[GC 376440K->140800K(1631616K), 0.0076590 secs]
[GC 373312K->140712K(1627776K), 0.0075550 secs]
[GC 369704K->141160K(1624576K), 0.0069120 secs]
INFO 18:54:24,299 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W26.bam ...
[GC 366696K->141264K(1621184K), 0.0069660 secs]
[GC 363472K->140984K(1617408K), 0.0094210 secs]
[GC 359928K->141456K(1614592K), 0.0063290 secs]
[GC 357200K->141552K(1611392K), 0.0085470 secs]
[GC 354160K->141560K(1608256K), 0.0073180 secs]
INFO 18:54:28,874 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W27.bam ...
[GC 351160K->142160K(1605760K), 0.0064920 secs]
[GC 348816K->142360K(1602752K), 0.0064730 secs]
[GC 346136K->142808K(1600064K), 0.0117680 secs]
[GC 343768K->142632K(1596928K), 0.0066200 secs]
[GC 340840K->142784K(1594176K), 0.0066150 secs]
[GC 338304K->142968K(1591616K), 0.0068720 secs]
INFO 18:54:33,196 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W28.bam ...
[GC 335864K->144032K(1589888K), 0.0061670 secs]
[GC 334368K->144648K(1587456K), 0.0105730 secs]
[GC 332488K->145240K(1584192K), 0.0073870 secs]
[GC 330648K->145920K(1582208K), 0.0072970 secs]
[GC 328960K->146184K(1579840K), 0.0083820 secs]
INFO 18:54:36,364 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W29.bam ...
[GC 326856K->147008K(1578048K), 0.0074540 secs]
[GC 325376K->146768K(1575040K), 0.0065350 secs]
[GC 322896K->146792K(1572736K), 0.0063310 secs]
[GC 320744K->146856K(1570496K), 0.0071200 secs]
[GC 318696K->147152K(1568512K), 0.0057730 secs]
[GC 316880K->147064K(1566272K), 0.0069300 secs]
INFO 18:54:39,808 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W30.bam ...
[GC 314744K->147800K(1564800K), 0.0087250 secs]
[GC 313496K->147760K(1597568K), 0.0075950 secs]
[GC 346608K->147840K(1621440K), 0.0080710 secs]
[GC 369344K->148240K(1638720K), 0.0084380 secs]
INFO 18:54:42,569 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W31.bam ...
[GC 387024K->148944K(1634432K), 0.0084980 secs]
[GC 384016K->148888K(1630144K), 0.0075110 secs]
[GC 380376K->149360K(1626944K), 0.0063560 secs]
[GC 377328K->149760K(1623680K), 0.0087050 secs]
[GC 374336K->150528K(1620736K), 0.0077600 secs]
[GC 371776K->150608K(1617216K), 0.0070980 secs]
INFO 18:54:46,624 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W32.bam ...
[GC 368592K->151104K(1614208K), 0.0087490 secs]
[GC 365888K->150952K(1610624K), 0.0069070 secs]
[GC 362664K->151592K(1608000K), 0.0077210 secs]
[GC 360296K->151512K(1604736K), 0.0067860 secs]
[GC 357272K->151864K(1601984K), 0.0085240 secs]
INFO 18:54:50,386 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W33.bam ...
[GC 354744K->152024K(1599104K), 0.0073760 secs]
[GC 352088K->152816K(1596736K), 0.0082600 secs]
[GC 350128K->152528K(1593536K), 0.0069810 secs]
[GC 347152K->152688K(1590848K), 0.0079070 secs]
[GC 344688K->152568K(1588096K), 0.0072750 secs]
[GC 342008K->152944K(1585792K), 0.0064030 secs]
INFO 18:54:54,281 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W34.bam ...
[GC 339888K->153344K(1583616K), 0.0092000 secs]
[GC 337856K->153352K(1580864K), 0.0073660 secs]
[GC 335496K->153968K(1579008K), 0.0070450 secs]
[GC 333808K->153872K(1576448K), 0.0064200 secs]
[GC 331472K->154232K(1574400K), 0.0089140 secs]
INFO 18:54:57,250 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W35.bam ...
[GC 329592K->154344K(1572160K), 0.0093050 secs]
[GC 327528K->154672K(1570048K), 0.0065730 secs]
[GC 325744K->154968K(1568064K), 0.0073720 secs]
[GC 323992K->154648K(1565568K), 0.0063200 secs]
[GC 321624K->154896K(1563648K), 0.0064870 secs]
[GC 319888K->155320K(1561984K), 0.0058860 secs]
INFO 18:55:01,935 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W36.bam ...
[GC 318392K->155872K(1560448K), 0.0079720 secs]
[GC 317024K->155816K(1558144K), 0.0066430 secs]
[GC 315112K->156088K(1556416K), 0.0090630 secs]
[GC 313528K->156136K(1554432K), 0.0077650 secs]
[GC 311784K->156288K(1552768K), 0.0079960 secs]
[GC 310208K->156376K(1550912K), 0.0065270 secs]
INFO 18:55:05,767 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W37.bam ...
[GC 308568K->156952K(1549696K), 0.0063830 secs]
[GC 307480K->156896K(1579456K), 0.0091980 secs]
[GC 337568K->157432K(1577472K), 0.0078280 secs]
[GC 335800K->157544K(1613056K), 0.0097640 secs]
[GC 371624K->158192K(1615104K), 0.0086260 secs]
INFO 18:55:08,556 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W38.bam ...
[GC 373936K->158528K(1612096K), 0.0062680 secs]
[GC 371136K->158176K(1608384K), 0.0079830 secs]
[GC 367776K->158224K(1605376K), 0.0076110 secs]
[GC 364880K->158424K(1602560K), 0.0060240 secs]
[GC 362200K->158568K(1599744K), 0.0069180 secs]
[GC 359528K->158488K(1596800K), 0.0072610 secs]
[GC 356696K->158664K(1594176K), 0.0061180 secs]
INFO 18:55:13,788 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W39.bam ...
[GC 354184K->159408K(1592128K), 0.0071710 secs]
[GC 352304K->159336K(1589184K), 0.0068170 secs]
[GC 349672K->159632K(1586752K), 0.0097900 secs]
[GC 347472K->159936K(1584384K), 0.0078110 secs]
[GC 345344K->160288K(1582080K), 0.0074270 secs]
[GC 343328K->160656K(1579776K), 0.0075370 secs]
[GC 341328K->160568K(1577088K), 0.0091460 secs]
INFO 18:55:18,008 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W40.bam ...
[GC 338936K->161224K(1575360K), 0.0062590 secs]
[GC 337352K->161744K(1610496K), 0.0119870 secs]
[GC 373136K->161816K(1646400K), 0.0085430 secs]
[GC 409368K->163008K(1643072K), 0.0083250 secs]
[GC 406592K->162616K(1637952K), 0.0055480 secs]
INFO 18:55:21,998 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W41.bam ...
[GC 402360K->163880K(1635392K), 0.0082890 secs]
[GC 399912K->164808K(1631936K), 0.0086170 secs]
[GC 397192K->164968K(1628160K), 0.0073300 secs]
[GC 393832K->165032K(1624384K), 0.0050900 secs]
INFO 18:55:24,964 SVDiscovery - Reading input file
/home/wbxie/wild_rice/wangwen/bwa_map/W42.bam ...
[GC 390440K->166320K(1621888K), 0.0080250 secs]
[GC 388400K->166304K(1617856K), 0.0068710 secs]
[GC 385120K...
 
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