Hello,
I start running several augustus v3.2.2 processes (testing different parameters) providing an additional hintsfile from several sources. After ~4 days running, all of them stop with the same problem (std error log file didn't capture this, as i was running in screen i can only see the information below). Did this ever happened to someone ?
My linux server version is Ubuntu 12.04 LTS and kernel version 3.11.0-26-generic.
Thanks,
Pedro Barbosa
7fcf9bcc6000-7fcf9bec5000 ---p 00016000 08:02 666911 /usr/local/lib/libz.so.1.2.8
7fcf9bec5000-7fcf9bec6000 r--p 00015000 08:02 666911 /usr/local/lib/libz.so.1.2.8
7fcf9bec6000-7fcf9bec7000 rw-p 00016000 08:02 666911 /usr/local/lib/libz.so.1.2.8
7fcf9bec8000-7fcf9bed7000 r-xp 00000000 08:02 2097157 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fcf9bed7000-7fcf9c0d6000 ---p 0000f000 08:02 2097157 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fcf9c0d6000-7fcf9c0d7000 r--p 0000e000 08:02 2097157 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fcf9c0d7000-7fcf9c0d8000 rw-p 0000f000 08:02 2097157 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fcf9c0d8000-7fcf9c0f0000 r-xp 00000000 08:02 2110523 /lib/x86_64-linux-gnu/libpthread-2.21.so
7fcf9c0f0000-7fcf9c2f0000 ---p 00018000 08:02 2110523 /lib/x86_64-linux-gnu/libpthread-2.21.so
7fcf9c2f0000-7fcf9c2f1000 r--p 00018000 08:02 2110523 /lib/x86_64-linux-gnu/libpthread-2.21.so
7fcf9c2f1000-7fcf9c2f2000 rw-p 00019000 08:02 2110523 /lib/x86_64-linux-gnu/libpthread-2.21.so
7fcf9c2f2000-7fcf9c2f6000 rw-p 00000000 00:00 0
7fcf9c2f8000-7fcf9c4b8000 r-xp 00000000 08:02 2110536 /lib/x86_64-linux-gnu/libc-2.21.so
7fcf9c4b8000-7fcf9c6b8000 ---p 001c0000 08:02 2110536 /lib/x86_64-linux-gnu/libc-2.21.so
7fcf9c6b8000-7fcf9c6bc000 r--p 001c0000 08:02 2110536 /lib/x86_64-linux-gnu/libc-2.21.so
7fcf9c6bc000-7fcf9c6be000 rw-p 001c4000 08:02 2110536 /lib/x86_64-linux-gnu/libc-2.21.so
7fcf9c6be000-7fcf9c6c2000 rw-p 00000000 00:00 0
7fcf9c6c8000-7fcf9c6de000 r-xp 00000000 08:02 2097561 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fcf9c6de000-7fcf9c8dd000 ---p 00016000 08:02 2097561 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fcf9c8dd000-7fcf9c8de000 r--p 00015000 08:02 2097561 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fcf9c8de000-7fcf9c8df000 rw-p 00016000 08:02 2097561 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fcf9c8e0000-7fcf9c9e7000 r-xp 00000000 08:02 2110531 /lib/x86_64-linux-gnu/libm-2.21.so
7fcf9c9e7000-7fcf9cbe6000 ---p 00107000 08:02 2110531 /lib/x86_64-linux-gnu/libm-2.21.so
7fcf9cbe6000-7fcf9cbe7000 r--p 00106000 08:02 2110531 /lib/x86_64-linux-gnu/libm-2.21.so
7fcf9cbe7000-7fcf9cbe8000 rw-p 00107000 08:02 2110531 /lib/x86_64-linux-gnu/libm-2.21.so
7fcf9cbe8000-7fcf9cd55000 r-xp 00000000 08:02 525573 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fcf9cd55000-7fcf9cf55000 ---p 0016d000 08:02 525573 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fcf9cf55000-7fcf9cf5f000 r--p 0016d000 08:02 525573 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fcf9cf5f000-7fcf9cf61000 rw-p 00177000 08:02 525573 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fcf9cf61000-7fcf9cf65000 rw-p 00000000 00:00 0
7fcf9cf68000-7fcf9cf7e000 r-xp 00000000 08:02 681944 /usr/local/lib/libboost_iostreams.so.1.58.0
7fcf9cf7e000-7fcf9d17e000 ---p 00016000 08:02 681944 /usr/local/lib/libboost_iostreams.so.1.58.0
7fcf9d17e000-7fcf9d17f000 r--p 00016000 08:02 681944 /usr/local/lib/libboost_iostreams.so.1.58.0
7fcf9d17f000-7fcf9d180000 rw-p 00017000 08:02 681944 /usr/local/lib/libboost_iostreams.so.1.58.0
7fcf9d180000-7fcf9d1a4000 r-xp 00000000 08:02 2110522 /lib/x86_64-linux-gnu/ld-2.21.so
7fcf9d37d000-7fcf9d380000 rw-p 00000000 00:00 0
7fcf9d3a1000-7fcf9d3a3000 rw-p 00000000 00:00 0
7fcf9d3a3000-7fcf9d3a4000 r--p 00023000 08:02 2110522 /lib/x86_64-linux-gnu/ld-2.21.so
7fcf9d3a4000-7fcf9d3a5000 rw-p 00024000 08:02 2110522 /lib/x86_64-linux-gnu/ld-2.21.so
7fcf9d3a5000-7fcf9d3a7000 rw-p 00000000 00:00 0
7fcf9d3a7000-7fcf9d3ac000 rw-p 00000000 00:00 0
7fffdab0a000-7fffdab2c000 rw-p 00000000 00:00 0 [stack]
7fffdac00000-7fffdac02000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
real 5111m47.010s
user 5040m4.028s
sys 69m17.702s
augustus - aborted (core dumped)
Moderator: bioinf
Re: augustus - aborted (core dumped)
Maybe it has happened, before.
The best thing in such cases is to try to narrow down the problem to a tiny example to give us something to work with. E.g. try to reproduce the error on a single scaffold with a small hints file and a particular extrinsic.cfg file, a particular species parameter set... pack these files, accompanied by the command that causes the crash, reproducibly, and we will try to track the problem.
The best thing in such cases is to try to narrow down the problem to a tiny example to give us something to work with. E.g. try to reproduce the error on a single scaffold with a small hints file and a particular extrinsic.cfg file, a particular species parameter set... pack these files, accompanied by the command that causes the crash, reproducibly, and we will try to track the problem.