Hi,
I have SMRTanalysis and PBJelly package installed. I was able to run the PBJelly with test data provided with software. However, when I was running it for a bacterial genome which is (~10 MB in size and ~350 scaffolds with ~3000 gaps) and used pacbio long reads for correction. I got memory correction error as:
Command:
Error:
Any suggestions to resolve this? I know PBJelly is not best describe to handle the memory but any suggestion regarding memory/parameter optimization will be helpful.
Thanks
I have SMRTanalysis and PBJelly package installed. I was able to run the PBJelly with test data provided with software. However, when I was running it for a bacterial genome which is (~10 MB in size and ~350 scaffolds with ~3000 gaps) and used pacbio long reads for correction. I got memory correction error as:
Command:
Code:
nohup Jelly.py assembly Protocol.xml -x "--nproc=8" &
Code:
======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fe21cf7cb96] make-consensus[0x40ce91] make-consensus[0x427e89] make-consensus[0x409d1c] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fe21cf1f76d] make-consensus[0x406439] ======= Memory map: ======== 00400000-0047c000 r-xp 00000000 08:21 113928 /data2/smart/smrtanalysis-1.4.0/analysis/bin/make-consensus 0067b000-0067d000 r--p 0007b000 08:21 113928 /data2/smart/smrtanalysis-1.4.0/analysis/bin/make-consensus 0067d000-0067e000 rw-p 0007d000 08:21 113928 /data2/smart/smrtanalysis-1.4.0/analysis/bin/make-consensus 0067e000-0067f000 rw-p 00000000 00:00 0 01b28000-01b8e000 rw-p 00000000 00:00 0 [heap] 7fe21cce8000-7fe21ccfd000 r-xp 00000000 08:01 933932 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fe21ccfd000-7fe21cefc000 ---p 00015000 08:01 933932 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fe21cefc000-7fe21cefd000 r--p 00014000 08:01 933932 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fe21cefd000-7fe21cefe000 rw-p 00015000 08:01 933932 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fe21cefe000-7fe21d0b3000 r-xp 00000000 08:01 933906 /lib/x86_64-linux-gnu/libc-2.15.so 7fe21d0b3000-7fe21d2b2000 ---p 001b5000 08:01 933906 /lib/x86_64-linux-gnu/libc-2.15.so 7fe21d2b2000-7fe21d2b6000 r--p 001b4000 08:01 933906 /lib/x86_64-linux-gnu/libc-2.15.so 7fe21d2b6000-7fe21d2b8000 rw-p 001b8000 08:01 933906 /lib/x86_64-linux-gnu/libc-2.15.so 7fe21d2b8000-7fe21d2bd000 rw-p 00000000 00:00 0 7fe21d2bd000-7fe21d3b8000 r-xp 00000000 08:01 933918 /lib/x86_64-linux-gnu/libm-2.15.so 7fe21d3b8000-7fe21d5b7000 ---p 000fb000 08:01 933918 /lib/x86_64-linux-gnu/libm-2.15.so 7fe21d5b7000-7fe21d5b8000 r--p 000fa000 08:01 933918 /lib/x86_64-linux-gnu/libm-2.15.so 7fe21d5b8000-7fe21d5b9000 rw-p 000fb000 08:01 933918 /lib/x86_64-linux-gnu/libm-2.15.so 7fe21d5b9000-7fe21d69b000 r-xp 00000000 08:01 748647 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 7fe21d69b000-7fe21d89a000 ---p 000e2000 08:01 748647 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 7fe21d89a000-7fe21d8a2000 r--p 000e1000 08:01 748647 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 7fe21d8a2000-7fe21d8a4000 rw-p 000e9000 08:01 748647 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 7fe21d8a4000-7fe21d8ba000 rw-p 00000000 00:00 0 7fe21d8c0000-7fe21d8d8000 r-xp 00000000 08:21 119775 /data2/smart/smrtanalysis-1.4.0/common/lib/libz.so.1 7fe21d8d8000-7fe21dad7000 ---p 00018000 08:21 119775 /data2/smart/smrtanalysis-1.4.0/common/lib/libz.so.1 7fe21dad7000-7fe21dad8000 r--p 00017000 08:21 119775 /data2/smart/smrtanalysis-1.4.0/common/lib/libz.so.1 7fe21dad8000-7fe21dad9000 rw-p 00018000 08:21 119775 /data2/smart/smrtanalysis-1.4.0/common/lib/libz.so.1 7fe21dad9000-7fe21dafb000 r-xp 00000000 08:01 933924 /lib/x86_64-linux-gnu/ld-2.15.so 7fe21dcf4000-7fe21dcfb000 rw-p 00000000 00:00 0 7fe21dcfb000-7fe21dcfc000 r--p 00022000 08:01 933924 /lib/x86_64-linux-gnu/ld-2.15.so 7fe21dcfc000-7fe21dcfe000 rw-p 00023000 08:01 933924 /lib/x86_64-linux-gnu/ld-2.15.so 7fffcf60a000-7fffcf62c000 rw-p 00000000 00:00 0 [stack] 7fffcf78b000-7fffcf78c000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] *** glibc detected *** make-consensus: free(): invalid next size (fast): 0x0000000000a0e5f0 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f166a931b96] make-consensus[0x43e287] make-consensus[0x43a1fc] make-consensus[0x409cb1] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f166a8d476d] make-consensus[0x406439] ======= Memory map: ========
Thanks
Comment