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  • blast2 problem

    Hi,


    I've a problem with a blast. Here's my command

    blast2 -p blastn -i s3_grouped_min100.fasta -d ../../../../database/blast/ncRNA.fasta -W 7 -e 0.0001 -o s3_ncRNA_min100_tab.blast -m 8

    it doesn't work ...

    but it worked without the -m 8 parameter .

    I don't understand why it doesn't work ?

    *** stack smashing detected ***: blast2 terminated
    ======= Backtrace: =========
    /lib/libc.so.6(__fortify_fail+0x37)[0x7fcdd5956217]
    /lib/libc.so.6(__fortify_fail+0x0)[0x7fcdd59561e0]
    /usr/lib/libncbitool.so.6(+0x12f496)[0x7fcdd6902496]
    /usr/lib/libncbitool.so.6(BlastPrintTabulatedResultsEx+0x4a)[0x7fcdd69024ea]
    /usr/lib/libncbitool.so.6(BlastPrintTabulatedResults+0x41)[0x7fcdd6902531]
    /usr/lib/libblastapi.so.6(BLAST_FormatResults+0x58c)[0x7fcdd6df01dc]
    blast2(Nlm_Main+0xc17)[0x404247]
    /usr/lib/libncbi.so.6(main+0x20)[0x7fcdd5e125c0]
    /lib/libc.so.6(__libc_start_main+0xfd)[0x7fcdd5875c4d]
    blast2[0x4034c9]
    ======= Memory map: ========
    00400000-00408000 r-xp 00000000 08:06 11017147 /usr/bin/blast2
    00607000-00608000 r--p 00007000 08:06 11017147 /usr/bin/blast2
    00608000-00609000 rw-p 00008000 08:06 11017147 /usr/bin/blast2
    0099f000-011ef000 rw-p 00000000 00:00 0 [heap]
    7fcdc0000000-7fcdc013a000 rw-p 00000000 00:00 0
    7fcdc013a000-7fcdc4000000 ---p 00000000 00:00 0
    7fcdc4000000-7fcdc4277000 rw-p 00000000 00:00 0
    7fcdc4277000-7fcdc8000000 ---p 00000000 00:00 0
    7fcdc89f1000-7fcdcc000000 r--p 00000000 08:06 5505275 /home/nicolas/bordet/database/blast/ncRNA.fasta.nhr
    7fcdcc000000-7fcdcc1f6000 rw-p 00000000 00:00 0
    7fcdcc1f6000-7fcdd0000000 ---p 00000000 00:00 0
    7fcdd0a09000-7fcdd0a1f000 r-xp 00000000 08:06 2883664 /lib/libgcc_s.so.1
    7fcdd0a1f000-7fcdd0c1e000 ---p 00016000 08:06 2883664 /lib/libgcc_s.so.1
    7fcdd0c1e000-7fcdd0c1f000 r--p 00015000 08:06 2883664 /lib/libgcc_s.so.1
    7fcdd0c1f000-7fcdd0c20000 rw-p 00016000 08:06 2883664 /lib/libgcc_s.so.1
    7fcdd0c20000-7fcdd25aa000 r--p 00000000 08:06 5505276 /home/nicolas/bordet/database/blast/ncRNA.fasta.nsq
    7fcdd25aa000-7fcdd25ab000 ---p 00000000 00:00 0
    7fcdd25ab000-7fcdd2dab000 rw-p 00000000 00:00 0
    7fcdd2dab000-7fcdd2dac000 ---p 00000000 00:00 0
    7fcdd2dac000-7fcdd35ac000 rw-p 00000000 00:00 0
    7fcdd35ac000-7fcdd35ad000 ---p 00000000 00:00 0
    7fcdd35ad000-7fcdd3dad000 rw-p 00000000 00:00 0
    7fcdd3dad000-7fcdd3dae000 ---p 00000000 00:00 0
    7fcdd3dae000-7fcdd45ae000 rw-p 00000000 00:00 0
    7fcdd45ae000-7fcdd4b85000 r--p 00000000 08:06 5505277 /home/nicolas/bordet/database/blast/ncRNA.fasta.nin
    7fcdd4b85000-7fcdd4b91000 r-xp 00000000 08:06 2889201 /lib/libnss_files-2.11.1.so
    7fcdd4b91000-7fcdd4d90000 ---p 0000c000 08:06 2889201 /lib/libnss_files-2.11.1.so
    7fcdd4d90000-7fcdd4d91000 r--p 0000b000 08:06 2889201 /lib/libnss_files-2.11.1.so
    7fcdd4d91000-7fcdd4d92000 rw-p 0000c000 08:06 2889201 /lib/libnss_files-2.11.1.so
    7fcdd4d92000-7fcdd4d9c000 r-xp 00000000 08:06 2889220 /lib/libnss_nis-2.11.1.so
    7fcdd4d9c000-7fcdd4f9b000 ---p 0000a000 08:06 2889220 /lib/libnss_nis-2.11.1.so
    7fcdd4f9b000-7fcdd4f9c000 r--p 00009000 08:06 2889220 /lib/libnss_nis-2.11.1.so
    7fcdd4f9c000-7fcdd4f9d000 rw-p 0000a000 08:06 2889220 /lib/libnss_nis-2.11.1.so
    7fcdd4f9d000-7fcdd4fb4000 r-xp 00000000 08:06 2889195 /lib/libnsl-2.11.1.so
    7fcdd4fb4000-7fcdd51b3000 ---p 00017000 08:06 2889195 /lib/libnsl-2.11.1.so
    7fcdd51b3000-7fcdd51b4000 r--p 00016000 08:06 2889195 /lib/libnsl-2.11.1.so
    7fcdd51b4000-7fcdd51b5000 rw-p 00017000 08:06 2889195 /lib/libnsl-2.11.1.so
    7fcdd51b5000-7fcdd51b7000 rw-p 00000000 00:00 0
    7fcdd51b7000-7fcdd51bf000 r-xp 00000000 08:06 2889196 /lib/libnss_compat-2.11.1.so
    7fcdd51bf000-7fcdd53be000 ---p 00008000 08:06 2889196 /lib/libnss_compat-2.11.1.so
    7fcdd53be000-7fcdd53bf000 r--p 00007000 08:06 2889196 /lib/libnss_compat-2.11.1.so
    7fcdd53bf000-7fcdd53c0000 rw-p 00008000 08:06 2889196 /lib/libnss_compat-2.11.1.so
    7fcdd53c0000-7fcdd53d3000 r-xp 00000000 08:06 11015457 /usr/lib/libblastcompadj.so.6.1.20090809
    7fcdd53d3000-7fcdd55d2000 ---p 00013000 08:06 11015457 /usr/lib/libblastcompadj.so.6.1.20090809
    7fcdd55d2000-7fcdd55d3000 r--p 00012000 08:06 11015457 /usr/lib/libblastcompadj.so.6.1.20090809
    7fcdd55d3000-7fcdd55d4000 rw-p 00013000 08:06 11015457 /usr/lib/libblastcompadj.so.6.1.20090809
    7fcdd55d4000-7fcdd5656000 r-xp 00000000 08:06 2889193 /lib/libm-2.11.1.so
    7fcdd5656000-7fcdd5855000 ---p 00082000 08:06 2889193 /lib/libm-2.11.1.so
    7fcdd5855000-7fcdd5856000 r--p 00081000 08:06 2889193 /lib/libm-2.11.1.so
    7fcdd5856000-7fcdd5857000 rw-p 00082000 08:06 2889193 /lib/libm-2.11.1.so
    7fcdd5857000-7fcdd59d1000 r-xp 00000000 08:06 2889188 /lib/libc-2.11.1.so
    7fcdd59d1000-7fcdd5bd0000 ---p 0017a000 08:06 2889188 /lib/libc-2.11.1.so
    7fcdd5bd0000-7fcdd5bd4000 r--p 00179000 08:06 2889188 /lib/libc-2.11.1.so
    7fcdd5bd4000-7fcdd5bd5000 rw-p 0017d000 08:06 2889188 /lib/libc-2.11.1.so
    7fcdd5bd5000-7fcdd5bda000 rw-p 00000000 00:00 0
    7fcdd5bda000-7fcdd5bf2000 r-xp 00000000 08:06 2889223 /lib/libpthread-2.11.1.so
    7fcdd5bf2000-7fcdd5df1000 ---p 00018000 08:06 2889223 /lib/libpthread-2.11.1.so
    7fcdd5df1000-7fcdd5df2000 r--p 00017000 08:06 2889223 /lib/libpthread-2.11.1.so
    7fcdd5df2000-7fcdd5df3000 rw-p 00018000 08:06 2889223 /lib/libpthread-2.11.1.so
    7fcdd5df3000-7fcdd5df7000 rw-p 00000000 00:00 0
    7fcdd5df7000-7fcdd5e88000 r-xp 00000000 08:06 11016323 /usr/lib/libncbi.so.6.1.20090809
    7fcdd5e88000-7fcdd6087000 ---p 00091000 08:06 11016323 /usr/lib/libncbi.so.6.1.20090809
    7fcdd6087000-7fcdd608a000 r--p 00090000 08:06 11016323 /usr/lib/libncbi.so.6.1.20090809
    7fcdd608a000-7fcdd608d000 rw-p 00093000 08:06 11016323 /usr/lib/libncbi.so.6.1.20090809
    7fcdd608d000-7fcdd609f000 rw-p 00000000 00:00 0
    7fcdd609f000-7fcdd6515000 r-xp 00000000 08:06 11016349 /usr/lib/libncbiobj.so.6.1.20090809
    7fcdd6515000-7fcdd6715000 ---p 00476000 08:06 11016349 /usr/lib/libncbiobj.so.6.1.20090809
    7fcdd6715000-7fcdd6721000 r--p 00476000 08:06 11016349 /usr/lib/libncbiobj.so.6.1.20090809Abandon

  • #2
    You're using the NCBI 'legacy' BLAST, right? You could try the new blastn executable which can do FASTA vs FASTA.

    Comment


    • #3
      I am having the same problem. Some times shows this error, some times shows "Segmentation fault", sometimes both errors take more time to appear, sometimes appears as soon as I start the process... I do not understand.
      Do you have some information?

      Comment

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