I'm trying to do an open modification search with SpectraST's tierwise scoring functionality as follows:
> spectrast -sLdata/processed/human_yeast_targetdecoy.splib -sR -sM300 -s_OMT -sExls -s_XMR250 -s_RNP50 -s_NOB -s_BIN4 -s_RLI101 data/external/iPRG2012.mgf This is the same iPRG2012 dataset as used in the OMT paper, with as spectral library the concatenated NIST human & yeast ion trap spectral library with added decoys. The search crashes with an invalid pointer error, see the log in the attachment. If I run the search with the exact same parameters and files but *without OMT scoring* it works without any problems. So it seems some invalid pointer operation is happening in the OMT scoring functionality. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
$ spectrast -sLdata/processed/human_yeast_targetdecoy.splib -sR -sM300 -s_OMT -sExls -s_XMR250 -s_RNP50 -s_NOB -s_BIN4 -s_RLI101 data/external/iPRG2012.mgf SpectraST started at Mon Mar 12 15:29:10 2018. Library File loaded: "data/processed/human_yeast_targetdecoy.splib". Searching "data/external/iPRG2012.mgf" (1 of 1)...to be setModByType: 115 to be setModByType: 53 to be setModByType: 129 to be setModByType: 129 to be setModByType: 153 *** glibc detected *** spectrast: munmap_chunk(): invalid pointer: 0x000000030976a120 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3942e75dee] spectrast[0x468ae1] spectrast[0x4ca263] spectrast[0x4cbc8b] spectrast[0x47e18e] spectrast[0x507878] spectrast[0x4a43e0] spectrast[0x4a2913] spectrast[0x49c83a] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3942e1ed1d] spectrast[0x40b889] ======= Memory map: ======== 00400000-0064a000 r-xp 00000000 00:3e 1346982025 /net/gs/vol3/software/modules-sw/tpp/5.1.0/Linux/RHEL6/x86_64/bin/spectrast 0084a000-0084e000 rw-p 0024a000 00:3e 1346982025 /net/gs/vol3/software/modules-sw/tpp/5.1.0/Linux/RHEL6/x86_64/bin/spectrast 0084e000-00853000 rw-p 00000000 00:00 0 02662000-36192a000 rw-p 00000000 00:00 0 [heap] 3942a00000-3942a20000 r-xp 00000000 fd:00 17752245 /lib64/ld-2.12.so 3942c20000-3942c21000 r--p 00020000 fd:00 17752245 /lib64/ld-2.12.so 3942c21000-3942c22000 rw-p 00021000 fd:00 17752245 /lib64/ld-2.12.so 3942c22000-3942c23000 rw-p 00000000 00:00 0 3942e00000-3942f8a000 r-xp 00000000 fd:00 17752304 /lib64/libc-2.12.so 3942f8a000-394318a000 ---p 0018a000 fd:00 17752304 /lib64/libc-2.12.so 394318a000-394318e000 r--p 0018a000 fd:00 17752304 /lib64/libc-2.12.so 394318e000-3943190000 rw-p 0018e000 fd:00 17752304 /lib64/libc-2.12.so 3943190000-3943194000 rw-p 00000000 00:00 0 3943200000-3943283000 r-xp 00000000 fd:00 17752358 /lib64/libm-2.12.so 3943283000-3943482000 ---p 00083000 fd:00 17752358 /lib64/libm-2.12.so 3943482000-3943483000 r--p 00082000 fd:00 17752358 /lib64/libm-2.12.so 3943483000-3943484000 rw-p 00083000 fd:00 17752358 /lib64/libm-2.12.so 3943a00000-3943a17000 r-xp 00000000 fd:00 17752306 /lib64/libpthread-2.12.so 3943a17000-3943c17000 ---p 00017000 fd:00 17752306 /lib64/libpthread-2.12.so 3943c17000-3943c18000 r--p 00017000 fd:00 17752306 /lib64/libpthread-2.12.so 3943c18000-3943c19000 rw-p 00018000 fd:00 17752306 /lib64/libpthread-2.12.so 3943c19000-3943c1d000 rw-p 00000000 00:00 0 3943e00000-3943e15000 r-xp 00000000 fd:00 17752315 /lib64/libz.so.1.2.3 3943e15000-3944014000 ---p 00015000 fd:00 17752315 /lib64/libz.so.1.2.3 3944014000-3944015000 r--p 00014000 fd:00 17752315 /lib64/libz.so.1.2.3 3944015000-3944016000 rw-p 00015000 fd:00 17752315 /lib64/libz.so.1.2.3 3944200000-3944207000 r-xp 00000000 fd:00 17752327 /lib64/librt-2.12.so 3944207000-3944406000 ---p 00007000 fd:00 17752327 /lib64/librt-2.12.so 3944406000-3944407000 r--p 00006000 fd:00 17752327 /lib64/librt-2.12.so 3944407000-3944408000 rw-p 00007000 fd:00 17752327 /lib64/librt-2.12.so 2b3ad9bdf000-2b3ad9bf1000 rw-p 00000000 00:00 0 2b3ad9bfc000-2b3ad9bfd000 rw-p 00000000 00:00 0 2b3ad9bfd000-2b3ad9cef000 r-xp 00000000 00:3e 1170911685 /net/gs/vol3/software/modules-sw/gcc/4.9.1/Linux/RHEL6/x86_64/lib64/libstdc++.so.6.0.20 2b3ad9cef000-2b3ad9eee000 ---p 000f2000 00:3e 1170911685 /net/gs/vol3/software/modules-sw/gcc/4.9.1/Linux/RHEL6/x86_64/lib64/libstdc++.so.6.0.20 2b3ad9eee000-2b3ad9ef7000 r--p 000f1000 00:3e 1170911685 /net/gs/vol3/software/modules-sw/gcc/4.9.1/Linux/RHEL6/x86_64/lib64/libstdc++.so.6.0.20 2b3ad9ef7000-2b3ad9ef9000 rw-p 000fa000 00:3e 1170911685 /net/gs/vol3/software/modules-sw/gcc/4.9.1/Linux/RHEL6/x86_64/lib64/libstdc++.so.6.0.20 2b3ad9ef9000-2b3ad9f0f000 rw-p 00000000 00:00 0 2b3ad9f0f000-2b3ad9f25000 r-xp 00000000 00:3e 3673224794 /net/gs/vol3/software/modules-sw/gcc/4.9.1/Linux/RHEL6/x86_64/lib64/libgcc_s.so.1 2b3ad9f25000-2b3ada124000 ---p 00016000 00:3e 3673224794 /net/gs/vol3/software/modules-sw/gcc/4.9.1/Linux/RHEL6/x86_64/lib64/libgcc_s.so.1 2b3ada124000-2b3ada125000 rw-p 00015000 00:3e 3673224794 /net/gs/vol3/software/modules-sw/gcc/4.9.1/Linux/RHEL6/x86_64/lib64/libgcc_s.so.1 2b3ada125000-2b3ada12b000 rw-p 00000000 00:00 0 7fff6cf38000-7fff6cf4e000 rw-p 00000000 00:00 0 [stack] 7fff6cfeb000-7fff6cfec000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
