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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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*** Break *** segmentation violation #112

Closed basharatbhat closed 6 years ago

basharatbhat commented 6 years ago

following error occurred while executing "cnvnator -root out.root -genome genome.fa -tree file.bam". Please help I have used root v5 and v6, but error is there

image

basharatbhat commented 6 years ago

Also,

image

is prompted

abyzov commented 6 years ago

Hi, looks like there could be a problem with you compiler. Which one are you using?

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

basharatbhat commented 6 years ago

administrator@PC:/opt/cnvnator-0.3.2$ cnvnator -root out.root -tree 23.sam Parsing file 23.sam ... Assuming SAM file ... Error in `/opt/cnvnator-0.3.2/bin/cnvnator-0.3.2': free(): invalid pointer: 0x00007ffc33978670 ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f594d34c7e5] /lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f594d35537a] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f594d35953c] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_MassignERKS4+0xaf)[0x7f594e11c3ef] /opt/cnvnator-0.3.2/bin/cnvnator-0.3.2[0x43604e] /opt/cnvnator-0.3.2/bin/cnvnator-0.3.2[0x40af19] /lib/x86_64-linux-gnu/libc.so.6(libc_start_main+0xf0)[0x7f594d2f5830] /opt/cnvnator-0.3.2/bin/cnvnator-0.3.2[0x40d029] ======= Memory map: ======== 00400000-004b2000 r-xp 00000000 08:01 2503372 /opt/cnvnator-0.3.2/bin/cnvnator-0.3.2 006b1000-006b2000 r--p 000b1000 08:01 2503372 /opt/cnvnator-0.3.2/bin/cnvnator-0.3.2 006b2000-006b3000 rw-p 000b2000 08:01 2503372 /opt/cnvnator-0.3.2/bin/cnvnator-0.3.2 006b3000-006b7000 rw-p 00000000 00:00 0 01a40000-01c3c000 rw-p 00000000 00:00 0 [heap] 7f5914000000-7f5914021000 rw-p 00000000 00:00 0 7f5914021000-7f5918000000 ---p 00000000 00:00 0 7f59185dc000-7f59186c6000 rw-p 00000000 00:00 0 7f59186c6000-7f5918747000 rw-p 00000000 00:00 0 7f5918747000-7f5918848000 rw-p 00000000 00:00 0 7f5918848000-7f594b6e3000 rw-p 00000000 00:00 0 7f594b6e3000-7f594b6ee000 r-xp 00000000 08:01 6585638 /lib/x86_64-linux-gnu/libnss_files-2.23.so 7f594b6ee000-7f594b8ed000 ---p 0000b000 08:01 6585638 /lib/x86_64-linux-gnu/libnss_files-2.23.so 7f594b8ed000-7f594b8ee000 r--p 0000a000 08:01 6585638 /lib/x86_64-linux-gnu/libnss_files-2.23.so 7f594b8ee000-7f594b8ef000 rw-p 0000b000 08:01 6585638 /lib/x86_64-linux-gnu/libnss_files-2.23.so 7f594b8ef000-7f594b8f5000 rw-p 00000000 00:00 0 7f594b8f5000-7f594b900000 r-xp 00000000 08:01 6585642 /lib/x86_64-linux-gnu/libnss_nis-2.23.so 7f594b900000-7f594baff000 ---p 0000b000 08:01 6585642 /lib/x86_64-linux-gnu/libnss_nis-2.23.so 7f594baff000-7f594bb00000 r--p 0000a000 08:01 6585642 /lib/x86_64-linux-gnu/libnss_nis-2.23.so 7f594bb00000-7f594bb01000 rw-p 0000b000 08:01 6585642 /lib/x86_64-linux-gnu/libnss_nis-2.23.so 7f594bb01000-7f594bb17000 r-xp 00000000 08:01 6585622 /lib/x86_64-linux-gnu/libnsl-2.23.so 7f594bb17000-7f594bd16000 ---p 00016000 08:01 6585622 /lib/x86_64-linux-gnu/libnsl-2.23.so 7f594bd16000-7f594bd17000 r--p 00015000 08:01 6585622 /lib/x86_64-linux-gnu/libnsl-2.23.so 7f594bd17000-7f594bd18000 rw-p 00016000 08:01 6585622 /lib/x86_64-linux-gnu/libnsl-2.23.so 7f594bd18000-7f594bd1a000 rw-p 00000000 00:00 0 7f594bd1a000-7f594bd22000 r-xp 00000000 08:01 6585633 /lib/x86_64-linux-gnu/libnss_compat-2.23.so 7f594bd22000-7f594bf21000 ---p 00008000 08:01 6585633 /lib/x86_64-linux-gnu/libnss_compat-2.23.so 7f594bf21000-7f594bf22000 r--p 00007000 08:01 6585633 /lib/x86_64-linux-gnu/libnss_compat-2.23.so 7f594bf22000-7f594bf23000 rw-p 00008000 08:01 6585633 /lib/x86_64-linux-gnu/libnss_compat-2.23.so 7f594bf23000-7f594bf47000 r-xp 00000000 08:01 6558263 /lib/x86_64-linux-gnu/libpng12.so.0.54.0 7f594bf47000-7f594c146000 ---p 00024000 08:01 6558263 /lib/x86_64-linux-gnu/libpng12.so.0.54.0 7f594c146000-7f594c147000 r--p 00023000 08:01 6558263 /lib/x86_64-linux-gnu/libpng12.so.0.54.0 7f594c147000-7f594c148000 rw-p 00024000 08:01 6558263 /lib/x86_64-linux-gnu/libpng12.so.0.54.0 7f594c148000-7f594c1fa000 r-xp 00000000 08:01 2505533 /opt/cnvnator-0.3.2/lib/root/libNet.so 7f594c1fa000-7f594c3fa000 ---p 000b2000 08:01 2505533 /opt/cnvnator-0.3.2/lib/root/libNet.so 7f594c3fa000-7f594c404000 r--p 000b2000 08:01 2505533 /opt/cnvnator-0.3.2/lib/root/libNet.so 7f594c404000-7f594c406000 rw-p 000bc000 08:01 2505533 /opt/cnvnator-0.3.2/lib/root/libNet.so 7f594c406000-7f594c409000 rw-p 00000000 00:00 0 7f594c409000-7f594c4ad000 r-xp 00000000 08:01 1573602 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1 7f594c4ad000-7f594c6ac000 ---p 000a4000 08:01 1573602 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1 7f594c6ac000-7f594c6b2000 r--p 000a3000 08:01 1573602 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1 7f594c6b2000-7f594c6b3000 rw-p 000a9000 08:01 1573602 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.12.1 7f594c6b3000-7f594c802000 r-xp 00000000 08:01 2505527 /opt/cnvnator-0.3.2/lib/root/libMatrix.so 7f594c802000-7f594ca02000 ---p 0014f000 08:01 2505527 /opt/cnvnator-0.3.2/lib/root/libMatrix.so 7f594ca02000-7f594ca09000 r--p 0014f000 08:01 2505527 /opt/cnvnator-0.3.2/lib/root/libMatrix.so 7f594ca09000-7f594ca0b000 rw-p 00156000 08:01 2505527 /opt/cnvnator-0.3.2/lib/root/libMatrix.so 7f594ca0b000-7f594ca10000 rw-p 00000000 00:00 0 7f594ca10000-7f594ca3b000 r-xp 00000000 08:01 2505550 /opt/cnvnator-0.3.2/lib/root/libThread.so 7f594ca3b000-7f594cc3a000 ---p 0002b000 08:01 2505550 /opt/cnvnator-0.3.2/lib/root/libThread.so 7f594cc3a000-7f594cc3d000 r--p 0002a000 08:01 2505550 /opt/cnvnator-0.3.2/lib/root/libThread.so 7f594cc3d000-7f594cc3e000 rw-p 0002d000 08:01 2505550 /opt/cnvnator-0.3.2/lib/root/libThread.so 7f594cc3e000-7f594cc3f000 rw-p 00000000 00:00 0 7f594cc3f000-7f594ccad000 r-xp 00000000 08:01 6558251 /lib/x86_64-linux-gnu/libpcre.so.3.13.2 7f594ccad000-7f594cead000 ---p 0006e000 08:01 6558251 /lib/x86_64-linux-gnu/libpcre.so.3.13.2 7f594cead000-7f594ceae000 r--p 0006e000 08:01 6558251 /lib/x86_64-linux-gnu/libpcre.so.3.13.2 7f594ceae000-7f594ceaf000 rw-p 0006f000 08:01 6558251 /lib/x86_64-linux-gnu/libpcre.so.3.13.2 7f594ceaf000-7f594ced0000 r-xp 00000000 08:01 6558189 /lib/x86_64-linux-gnu/liblzma.so.5.0.0 7f594ced0000-7f594d0cf000 ---p 00021000 08:01 6558189 /lib/x86_64-linux-gnu/liblzma.so.5.0.0 7f594d0cf000-7f594d0d0000 r--p 00020000 08:01 6558189 /lib/x86_64-linux-gnu/liblzma.so.5.0.0 7f594d0d0000-7f594d0d1000 rw-p 00021000 08:01 6558189 /lib/x86_64-linux-gnu/liblzma.so.5.0.0 7f594d0d1000-7f594d0d4000 r-xp 00000000 08:01 6585627 /lib/x86_64-linux-gnu/libdl-2.23.so 7f594d0d4000-7f594d2d3000 ---p 00003000 08:01 6585627 /lib/x86_64-linux-gnu/libdl-2.23.so 7f594d2d3000-7f594d2d4000 r--p 00002000 08:01 6585627 /lib/x86_64-linux-gnu/libdl-2.23.so 7f594d2d4000-7f594d2d5000 rw-p 00003000 08:01 6585627 /lib/x86_64-linux-gnu/libdl-2.23.so 7f594d2d5000-7f594d495000 r-xp 00000000 08:01 6585625 /lib/x86_64-linux-gnu/libc-2.23.so 7f594d495000-7f594d695000 ---p 001c0000 08:01 6585625 /lib/x86_64-linux-gnu/libc-2.23.so 7f594d695000-7f594d699000 r--p 001c0000 08:01 6585625 /lib/x86_64-linux-gnu/libc-2.23.so 7f594d699000-7f594d69b000 rw-p 001c4000 08:01 6585625 /lib/x86_64-linux-gnu/libc-2.23.so 7f594d69b000-7f594d69f000 rw-p 00000000 00:00 0 7f594d69f000-7f594d6b7000 r-xp 00000000 08:01 6585624 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f594d6b7000-7f594d8b6000 ---p 00018000 08:01 6585624 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f594d8b6000-7f594d8b7000 r--p 00017000 08:01 6585624 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f594d8b7000-7f594d8b8000 rw-p 00018000 08:01 6585624 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f594d8b8000-7f594d8bc000 rw-p 00000000 00:00 0 7f594d8bc000-7f594d8d2000 r-xp 00000000 08:01 6558160 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f594d8d2000-7f594dad1000 ---p 00016000 08:01 6558160 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f594dad1000-7f594dad2000 rw-p 00015000 08:01 6558160 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f594dad2000-7f594daf3000 r-xp 00000000 08:01 1576303 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 7f594daf3000-7f594dcf2000 ---p 00021000 08:01 1576303 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 7f594dcf2000-7f594dcf3000 r--p 00020000 08:01 1576303 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 7f594dcf3000-7f594dcf4000 rw-p 00021000 08:01 1576303 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 7f594dcf4000-7f594ddfc000 r-xp 00000000 08:01 6585620 /lib/x86_64-linux-gnu/libm-2.23.so 7f594ddfc000-7f594dffb000 ---p 00108000 08:01 6585620 /lib/x86_64-linux-gnu/libm-2.23.so 7f594dffb000-7f594dffc000 r--p 00107000 08:01 6585620 /lib/x86_64-linux-gnu/libm-2.23.so 7f594dffc000-7f594dffd000 rw-p 00108000 08:01 6585620 /lib/x86_64-linux-gnu/libm-2.23.so 7f594dffd000-7f594e16f000 r-xp 00000000 08:01 1574896 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 7f594e16f000-7f594e36f000 ---p 00172000 08:01 1574896 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 7f594e36f000-7f594e379000 r--p 00172000 08:01 1574896 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 7f594e379000-7f594e37b000 rw-p 0017c000 08:01 1574896 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 7f594e37b000-7f594e37f000 rw-p 00000000 00:00 0 7f594e37f000-7f594e591000 r-xp 00000000 08:01 2505410 /opt/cnvnator-0.3.2/lib/root/libMathCore.so 7f594e591000-7f594e791000 ---p 00212000 08:01 2505410 /opt/cnvnator-0.3.2/lib/root/libMathCore.so 7f594e791000-7f594e798000 r--p 00212000 08:01 2505410 /opt/cnvnator-0.3.2/lib/root/libMathCore.so 7f594e798000-7f594e79e000 rw-p 00219000 08:01 2505410 /opt/cnvnator-0.3.2/lib/root/libMathCore.so 7f594e79e000-7f594e7a7000 rw-p 00000000 00:00 0 7f594e7a7000-7f594e8e8000 r-xp 00000000 08:01 2505478 /opt/cnvnator-0.3.2/lib/root/libTree.so 7f594e8e8000-7f594eae8000 ---p 00141000 08:01 2505478 /opt/cnvnator-0.3.2/lib/root/libTree.so 7f594eae8000-7f594eaf6000 r--p 00141000 08:01 2505478 /opt/cnvnator-0.3.2/lib/root/libTree.so 7f594eaf6000-7f594eaf9000 rw-p 0014f000 08:01 2505478 /opt/cnvnator-0.3.2/lib/root/libTree.so 7f594eaf9000-7f594eafd000 rw-p 00000000 00:00 0 7f594eafd000-7f594eba2000 r-xp 00000000 08:01 2505475 /opt/cnvnator-0.3.2/lib/root/libGpad.so 7f594eba2000-7f594eda2000 ---p 000a5000 08:01 2505475 /opt/cnvnator-0.3.2/lib/root/libGpad.so 7f594eda2000-7f594edab000 r--p 000a5000 08:01 2505475 /opt/cnvnator-0.3.2/lib/root/libGpad.so 7f594edab000-7f594edad000 rw-p 000ae000 08:01 2505475 /opt/cnvnator-0.3.2/lib/root/libGpad.so 7f594edad000-7f594edae000 rw-p 00000000 00:00 0 7f594edae000-7f594eede000 r-xp 00000000 08:01 2505452 /opt/cnvnator-0.3.2/lib/root/libGraf.so 7f594eede000-7f594f0de000 ---p 00130000 08:01 2505452 /opt/cnvnator-0.3.2/lib/root/libGraf.so 7f594f0de000-7f594f0eb000 r--p 00130000 08:01 2505452 /opt/cnvnator-0.3.2/lib/root/libGraf.so 7f594f0eb000-7f594f0ef000 rw-p 0013d000 08:01 2505452 /opt/cnvnator-0.3.2/lib/root/libGraf.so 7f594f0ef000-7f594f0fd000 rw-p 00000000 00:00 0 7f594f0fd000-7f594f450000 r-xp 00000000 08:01 2505419 /opt/cnvnator-0.3.2/lib/root/libHist.so 7f594f450000-7f594f64f000 ---p 00353000 08:01 2505419 /opt/cnvnator-0.3.2/lib/root/libHist.so 7f594f64f000-7f594f676000 r--p 00352000 08:01 2505419 /opt/cnvnator-0.3.2/lib/root/libHist.so 7f594f676000-7f594f67a000 rw-p 00379000 08:01 2505419 /opt/cnvnator-0.3.2/lib/root/libHist.so 7f594f67a000-7f594f685000 rw-p 00000000 00:00 0 7f594f685000-7f594f924000 r-xp 00000000 08:01 2505513 /opt/cnvnator-0.3.2/lib/root/libRIO.so 7f594f924000-7f594fb23000 ---p 0029f000 08:01 2505513 /opt/cnvnator-0.3.2/lib/root/libRIO.so 7f594fb23000-7f594fb2e000 r--p 0029e000 08:01 2505513 /opt/cnvnator-0.3.2/lib/root/libRIO.so 7f594fb2e000-7f594fb31000 rw-p 002a9000 08:01 2505513 /opt/cnvnator-0.3.2/lib/root/libRIO.so 7f594fb31000-7f594fb34000 rw-p 00000000 00:00 0 7f594fb34000-7f594feab000 r-xp 00000000 08:01 2505517 /opt/cnvnator-0.3.2/lib/root/libCore.so 7f594feab000-7f59500aa000 ---p 00377000 08:01 2505517 /opt/cnvnator-0.3.2/lib/root/libCore.so 7f59500aa000-7f59500d1000 r--p 00376000 08:01 2505517 /opt/cnvnator-0.3.2/lib/root/libCore.so 7f59500d1000-7f59500da000 rw-p 0039d000 08:01 2505517 /opt/cnvnator-0.3.2/lib/root/libCore.so 7f59500da000-7f595010f000 rw-p 00000000 00:00 0 7f595010f000-7f59501b0000 r-xp 00000000 08:01 2505405 /opt/cnvnator-0.3.2/lib/libyeppp.so 7f59501b0000-7f59503af000 ---p 000a1000 08:01 2505405 /opt/cnvnator-0.3.2/lib/libyeppp.so 7f59503af000-7f59503b0000 r--p 000a0000 08:01 2505405 /opt/cnvnator-0.3.2/lib/libyeppp.so 7f59503b0000-7f59503b2000 rw-p 000a1000 08:01 2505405 /opt/cnvnator-0.3.2/lib/libyeppp.so 7f59503b2000-7f59503cb000 r-xp 00000000 08:01 6558135 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f59503cb000-7f59505ca000 ---p 00019000 08:01 6558135 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f59505ca000-7f59505cb000 r--p 00018000 08:01 6558135 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f59505cb000-7f59505cc000 rw-p 00019000 08:01 6558135 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f59505cc000-7f59505f2000 r-xp 00000000 08:01 6585623 /lib/x86_64-linux-gnu/ld-2.23.so 7f59505f3000-7f5950674000 rw-p 00000000 00:00 0 7f59506bc000-7f59507da000 rw-p 00000000 00:00 0 7f59507f0000-7f59507f1000 rw-p 00000000 00:00 0 7f59507f1000-7f59507f2000 r--p 00025000 08:01 6585623 /lib/x86_64-linux-gnu/ld-2.23.so 7f59507f2000-7f59507f3000 rw-p 00026000 08:01 6585623 /lib/x86_64-linux-gnu/ld-2.23.so 7f59507f3000-7f59507f4000 rw-p 00000000 00:00 0 7ffc3382a000-7ffc33f9d000 rw-p 00000000 00:00 0 [stack] 7ffc33fb1000-7ffc33fb4000 r--p 00000000 00:00 0 [vvar] 7ffc33fb4000-7ffc33fb6000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] /usr/local/bin/cnvnator: line 8: 25195 Aborted (core dumped) ${BASE}/bin/cnvnator-0.3.2 $@

Please help with this error

abyzov commented 6 years ago

Hi, function to parse SAM was implemented before using BAM was not common. I would advise to parse BAM.

The error looks like some problem with compilation. Does ROOT start without problems?

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745