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  • Tophat fusion crashed for unknown reason

    My tophat fusion crashed. My OS is Ubuntu 12.04. What's going on here? Thanks

    -------------------------------------------
    [2013-06-21 18:42:53] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie (2/3)
    *** glibc detected *** /tank/rnaseq/tophat-2.0.8b.Linux_x86_64/fix_map_ordering: free(): invalid next size (normal): 0x000000016b5681d0 ***
    ======= Backtrace: =========
    /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f501ee74b96]
    /tank/rnaseq/tophat-2.0.8b.Linux_x86_64/fix_map_ordering[0x412c14]
    /tank/rnaseq/tophat-2.0.8b.Linux_x86_64/fix_map_ordering[0x40a3e3]
    /tank/rnaseq/tophat-2.0.8b.Linux_x86_64/fix_map_ordering[0x40b5cc]
    /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f501ee1776d]
    /tank/rnaseq/tophat-2.0.8b.Linux_x86_64/fix_map_ordering[0x4094a9]
    ======= Memory map: ========
    00400000-0049f000 r-xp 00000000 08:22 53231 /tank/rnaseq/tophat-2.0.8b.Linux_x86_64/fix_map_ordering
    0069e000-006a6000 rw-p 0009e000 08:22 53231 /tank/rnaseq/tophat-2.0.8b.Linux_x86_64/fix_map_ordering
    006a6000-006ba000 rw-p 00000000 00:00 0
    0075f000-175182000 rw-p 00000000 00:00 0 [heap]
    7f4f87c37000-7f4fa7c38000 rw-p 00000000 00:00 0
    7f4fb6085000-7f4fbc086000 rw-p 00000000 00:00 0
    7f4fbc086000-7f4fdeeec000 rw-p 00000000 00:00 0
    7f4fdeeec000-7f4ffeeed000 rw-p 00000000 00:00 0
    7f5002850000-7f5005851000 rw-p 00000000 00:00 0
    7f5006451000-7f5007452000 rw-p 00000000 00:00 0
    7f5007c53000-7f500d5e1000 rw-p 00000000 00:00 0
    7f500d5e1000-7f50135e2000 rw-p 00000000 00:00 0
    7f50135e2000-7f50165e3000 rw-p 00000000 00:00 0
    7f5016cf5000-7f5016d0a000 r-xp 00000000 fc:02 134628 /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f5016d0a000-7f5016f09000 ---p 00015000 fc:02 134628 /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f5016f09000-7f5016f0a000 r--p 00014000 fc:02 134628 /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f5016f0a000-7f5016f0b000 rw-p 00015000 fc:02 134628 /lib/x86_64-linux-gnu/libgcc_s.so.1
    7f5016f0b000-7f50192e7000 rw-p 00000000 00:00 0
    7f5019468000-7f501edf6000 rw-p 00000000 00:00 0
    7f501edf6000-7f501efab000 r-xp 00000000 fc:02 134548 /lib/x86_64-linux-gnu/libc-2.15.so
    7f501efab000-7f501f1aa000 ---p 001b5000 fc:02 134548 /lib/x86_64-linux-gnu/libc-2.15.so
    7f501f1aa000-7f501f1ae000 r--p 001b4000 fc:02 134548 /lib/x86_64-linux-gnu/libc-2.15.so
    7f501f1ae000-7f501f1b0000 rw-p 001b8000 fc:02 134548 /lib/x86_64-linux-gnu/libc-2.15.so
    7f501f1b0000-7f501f1b5000 rw-p 00000000 00:00 0
    7f501f1b5000-7f501f1cd000 r-xp 00000000 fc:02 134551 /lib/x86_64-linux-gnu/libpthread-2.15.so
    7f501f1cd000-7f501f3cc000 ---p 00018000 fc:02 134551 /lib/x86_64-linux-gnu/libpthread-2.15.so
    7f501f3cc000-7f501f3cd000 r--p 00017000 fc:02 134551 /lib/x86_64-linux-gnu/libpthread-2.15.so
    7f501f3cd000-7f501f3ce000 rw-p 00018000 fc:02 134551 /lib/x86_64-linux-gnu/libpthread-2.15.so
    7f501f3ce000-7f501f3d2000 rw-p 00000000 00:00 0
    7f501f3d2000-7f501f4cd000 r-xp 00000000 fc:02 134563 /lib/x86_64-linux-gnu/libm-2.15.so
    7f501f4cd000-7f501f6cc000 ---p 000fb000 fc:02 134563 /lib/x86_64-linux-gnu/libm-2.15.so
    7f501f6cc000-7f501f6cd000 r--p 000fa000 fc:02 134563 /lib/x86_64-linux-gnu/libm-2.15.so
    7f501f6cd000-7f501f6ce000 rw-p 000fb000 fc:02 134563 /lib/x86_64-linux-gnu/libm-2.15.so
    7f501f6ce000-7f501f6e4000 r-xp 00000000 fc:02 134718 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
    7f501f6e4000-7f501f8e3000 ---p 00016000 fc:02 134718 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
    7f501f8e3000-7f501f8e4000 r--p 00015000 fc:02 134718 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
    7f501f8e4000-7f501f8e5000 rw-p 00016000 fc:02 134718 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
    7f501f8e5000-7f501f907000 r-xp 00000000 fc:02 134580 /lib/x86_64-linux-gnu/ld-2.15.so
    7f501fae3000-7f501fae7000 rw-p 00000000 00:00 0
    7f501fb01000-7f501fb07000 rw-p 00000000 00:00 0
    7f501fb07000-7f501fb08000 r--p 00022000 fc:02 134580 /lib/x86_64-linux-gnu/ld-2.15.so
    7f501fb08000-7f501fb0a000 rw-p 00023000 fc:02 134580 /lib/x86_64-linux-gnu/ld-2.15.so
    7fffac2df000-7fffac300000 rw-p 00000000 00:00 0 [stack]
    7fffac3ff000-7fffac400000 r-xp 00000000 00:00 0 [vdso]
    ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
    [FAILED]
    Error running:
    gzip -cd< tophat_P3Tf/tmp/left_kept_reads_seg2.fq.z|/usr/bin/bowtie -q -v 2 -k 40 -m 40 -S -p 6 --sam-nohead --max /dev/null tophat_P3Tf/tmp/segment_juncs -|/tank/rnaseq/tophat-2.0.8b.Linux_x86_64/fix_map_ordering --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile tophat_P3Tf/tmp/left_kept_reads_seg2.to_spliced.bam.index --bowtie1 --sam-header tophat_P3Tf/tmp/segment_juncs.bwt.samheader.sam - tophat_P3Tf/tmp/left_kept_reads_seg2.to_spliced.bam

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