Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • ymc
    Senior Member
    • Mar 2010
    • 496

    #1

    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

Latest Articles

Collapse

  • SEQadmin2
    16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by SEQadmin2





    NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
    10-30-2026, 06:46 AM
  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 07:59 AM
0 responses
13 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-05-2026, 09:25 AM
0 responses
32 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-03-2026, 11:54 AM
0 responses
45 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
170 views
0 reactions
Last Post SEQadmin2  
Working...