tong2200
commented
5 years ago I also caught the error from buildPosMap when I ran MaSuRCA-3.2.8. The error message caught by strace is:
write(11, "3069480\t7180044060193\t0\t150\tf\n71"..., 4096) = 4096
read(3, "GAATAGATATGGCAGGTTTCAGGACACTGA\nT"..., 4096) = 4096
read(3, "llllllllllllllllllllll\nlllllllll"..., 4096) = 4096
read(3, "\n{CCO\nacc:(7180044060323,1342148"..., 4096) = 4096
write(10, "\t0\t150\tf\naa197810158\t71800440602"..., 4096) = 4096
write(21, "044060096\t150\n7180044060097\t150\n"..., 4096) = 4096
read(3, "GTCTCCGCACTGGTCCTCTTCCACG\nTCCTCT"..., 4096) = 4096
read(3, "\ndln:0\ndel:\n}\n{MPS\ntyp:R\nmid:ba6"..., 4096) = 4096
read(3, "``\n```\n.\nfor:0\nnpc:2\nnou:"..., 4096) = 4096 read(3, "os:0,150\ndln:0\ndel:\n}\n{UPS\ntyp:s"..., 4096) = 4096 read(3, "el:\n}\n}\n{CCO\nacc:(7180044060359,"..., 4096) = 4096 read(3, "````````````````````````\n"..., 4096) = 4096
read(3, "50\ndln:0\ndel:\n}\n{MPS\ntyp:R\nmid:a"..., 4096) = 4096
write(10, "44060323\t0\t150\tf\naa197889886\t718"..., 4096) = 4096
read(3, "ATACAGAATGGTGTCGTCTGTGTAGAGGTAGA"..., 4096) = 4096
--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_ACCERR, si_addr=0x7f7eed33e1f0} ---
+++ killed by SIGSEGV (core dumped) +++
% time seconds usecs/call calls errors syscall
57.57 58.434596 9 6836159 write 33.08 33.579053 2 15915194 read 7.73 7.840929 270377 29 open 1.57 1.590790 79540 20 munmap 0.04 0.045191 284 159 mremap 0.00 0.001822 83 22 fstat 0.00 0.000880 10 84 mmap 0.00 0.000186 5 36 brk 0.00 0.000156 10 16 mprotect 0.00 0.000066 8 8 close 0.00 0.000047 47 1 execve 0.00 0.000038 38 1 1 access 0.00 0.000012 6 2 rt_sigaction 0.00 0.000006 6 1 rt_sigprocmask 0.00 0.000005 5 1 getrlimit 0.00 0.000005 5 1 set_tid_address 0.00 0.000004 4 1 arch_prctl 0.00 0.000004 4 1 set_robust_list
100.00 101.493790 22751736 1 total
strace command line:
strace -C -d -v -o strace.log ~/MaSuRCA-3.2.8/CA/Linux-amd64/bin/buildPosMap -i genome.asm -o genome
machadodj
Hi,
I am getting the below segmentation fault from buildPosMap. I am running MaSuRCA 3.2.6. The assembler continues despite this issue and appears to complete correctly so I assume it is not a critical problem.
Thanks.
----------------------------------------END Tue Sep 18 01:31:50 2018 (1201 seconds) ERROR: Failed with signal SEGV (11)
runCA failed.
Stack trace:
at /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/bin/../CA8/Linux-amd64/bin/runCA line 1613. main::caFailure("buildPosMap failed", "/30days/uqtstep3/POLARELLA_GLACIALIS/CCMP1383/GENOME_ASSEMBLI"...) called at /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/bin/../CA8/Linux-amd64/bin/runCA line 5905 main::terminate() called at /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/bin/../CA8/Linux-amd64/bin/runCA line 6532
Last few lines of the relevant log file (/30days/uqtstep3/POLARELLA_GLACIALIS/CCMP1383/GENOME_ASSEMBLIES/MaSuRCA/ASSEMBLY/CA.mr.41.15.17.0.029/9-terminator/buildPosMap.err):
Failed with 'Segmentation fault'
Backtrace (mangled):
/gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap[0x407185] /lib64/libpthread.so.0[0x3fbe40f7e0] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap[0x403fa3] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap[0x406008] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3fbd81ed1d] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap[0x401ef9]
Backtrace (demangled):
[0] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap() [0x407185] [1] /lib64/libpthread.so.0() [0x3fbe40f7e0] [2] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap() [0x403fa3] [3] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap() [0x406008] [4] /lib64/libc.so.6::(null) + 0xfd [0x3fbd81ed1d] [5] /gpfs1/scratch/30days/uqtstep3/PROGRAMS/MaSuRCA-3.2.6/CA8/Linux-amd64/bin/buildPosMap() [0x401ef9]
GDB:
Failure message:
buildPosMap failed