gpertea
commented
4 years ago Could you please verify if you have been running v2.0.6 when you experienced these crashes -- instead of v2.0.5 that was the first patched release that worked for CentOS 6 as per #251 ? Unfortunately that v2.0.5 release was affected by a regression bug that caused this kind of crashes (not matter the value of the -p option). Do you have v2.0.6 installed there? (stringtie --version should show the version).
asmitagpta
Hi,
This is in connection to https://github.com/gpertea/stringtie/issues/251 'error while installing StringTie' on CentOS release 6.9 (Final).
Thanks a lot for incorporating the update. I managed to install the program successfully.
However, I seem to encounter a new problem while running this version since some time now. The program runs fine when I don't provide any reference GTF file for assembly generating an output GTF. However, I would like to run it in a guided mode with a reference Ensemble GTF. When this file is provided with -G option, the program always crashes with a similar kind of error -
glibc detected /apps/stringtie/stringtie: malloc(): memory corruption (fast): 0x00000000036a3501 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3fd8875dee] /lib64/libc.so.6[0x3fd887a4b8] /lib64/libc.so.6(__libc_malloc+0x5c)[0x3fd887aaac] /apps/stringtie/stringtie[0x404570] /apps/stringtie/stringtie[0x428c49] /apps/stringtie/stringtie[0x4836af] /apps/stringtie/stringtie[0x44d832] /apps/stringtie/stringtie[0x490b89] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3fd881ed1d] /apps/stringtie/stringtie[0x402c49] ======= Memory map: ======== 00400000-004be000 r-xp 00000000 08:02 18877471 /apps/stringtie/stringtie 006bd000-006bf000 rw-p 000bd000 08:02 18877471 /apps/stringtie/stringtie 006bf000-006c7000 rw-p 00000000 00:00 0 00a38000-142ef000 rw-p 00000000 00:00 0 [heap] 3fd8400000-3fd8420000 r-xp 00000000 08:02 47972382 /lib64/ld-2.12.so 3fd8620000-3fd8621000 r--p 00020000 08:02 47972382 /lib64/ld-2.12.so 3fd8621000-3fd8622000 rw-p 00021000 08:02 47972382 /lib64/ld-2.12.so 3fd8622000-3fd8623000 rw-p 00000000 00:00 0 3fd8800000-3fd898a000 r-xp 00000000 08:02 47972470 /lib64/libc-2.12.so 3fd898a000-3fd8b8a000 ---p 0018a000 08:02 47972470 /lib64/libc-2.12.so 3fd8b8a000-3fd8b8e000 r--p 0018a000 08:02 47972470 /lib64/libc-2.12.so 3fd8b8e000-3fd8b90000 rw-p 0018e000 08:02 47972470 /lib64/libc-2.12.so 3fd8b90000-3fd8b94000 rw-p 00000000 00:00 0 3fd8c00000-3fd8c17000 r-xp 00000000 08:02 47972915 /lib64/libpthread-2.12.so 3fd8c17000-3fd8e17000 ---p 00017000 08:02 47972915 /lib64/libpthread-2.12.so 3fd8e17000-3fd8e18000 r--p 00017000 08:02 47972915 /lib64/libpthread-2.12.so 3fd8e18000-3fd8e19000 rw-p 00018000 08:02 47972915 /lib64/libpthread-2.12.so 3fd8e19000-3fd8e1d000 rw-p 00000000 00:00 0 3fd9400000-3fd9483000 r-xp 00000000 08:02 47972491 /lib64/libm-2.12.so 3fd9483000-3fd9682000 ---p 00083000 08:02 47972491 /lib64/libm-2.12.so 3fd9682000-3fd9683000 r--p 00082000 08:02 47972491 /lib64/libm-2.12.so 3fd9683000-3fd9684000 rw-p 00083000 08:02 47972491 /lib64/libm-2.12.so 3fd9800000-3fd9815000 r-xp 00000000 08:02 47972521 /lib64/libz.so.1.2.3 3fd9815000-3fd9a14000 ---p 00015000 08:02 47972521 /lib64/libz.so.1.2.3 3fd9a14000-3fd9a15000 r--p 00014000 08:02 47972521 /lib64/libz.so.1.2.3 3fd9a15000-3fd9a16000 rw-p 00015000 08:02 47972521 /lib64/libz.so.1.2.3 3fdf000000-3fdf016000 r-xp 00000000 08:02 47972428 /lib64/libgcc_s-4.4.7-20120601.so.1 3fdf016000-3fdf215000 ---p 00016000 08:02 47972428 /lib64/libgcc_s-4.4.7-20120601.so.1 3fdf215000-3fdf216000 rw-p 00015000 08:02 47972428 /lib64/libgcc_s-4.4.7-20120601.so.1 3fdf400000-3fdf4e8000 r-xp 00000000 08:02 27527830 /usr/lib64/libstdc++.so.6.0.13 3fdf4e8000-3fdf6e8000 ---p 000e8000 08:02 27527830 /usr/lib64/libstdc++.so.6.0.13 3fdf6e8000-3fdf6ef000 r--p 000e8000 08:02 27527830 /usr/lib64/libstdc++.so.6.0.13 3fdf6ef000-3fdf6f1000 rw-p 000ef000 08:02 27527830 /usr/lib64/libstdc++.so.6.0.13 3fdf6f1000-3fdf706000 rw-p 00000000 00:00 0 7f8368000000-7f8368021000 rw-p 00000000 00:00 0 7f8368021000-7f836c000000 ---p 00000000 00:00 0 7f836ffff000-7f8370000000 rw-p 00000000 00:00 0 7f8370000000-7f8373a4f000 rw-p 00000000 00:00 0 7f8373a4f000-7f8374000000 ---p 00000000 00:00 0 7f83750e5000-7f83750e6000 ---p 00000000 00:00 0 7f83750e6000-7f8375aec000 rw-p 00000000 00:00 0 7f8375b1c000-7f8375b1f000 rw-p 00000000 00:00 0 7ffeb636e000-7ffeb6383000 rw-p 00000000 00:00 0 [stack] 7ffeb63d7000-7ffeb63d8000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped)
I have tried running the program with multiple option with different -p values (1/2/4/6/8/32) with similar error message. I also played around with changing default values for -f, -a, -j and met similar fate.
Since I am interested in finding novel isoforms, I would like to run the program with a reference GTF. Can you please suggest if I'm going wrong somewhere or if it's the build issue?
Thanks a ton for the update again!