Hi,
When running Cufflinks 2.0.1 it generates the error:
*** glibc detected *** cufflinks: double free or corruption (!prev): 0x000000003f909d00 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3abc47245f]
/lib64/libc.so.6(cfree+0x4b)[0x3abc4728bb]
cufflinks[0x416f0c]
cufflinks[0x416daf]
cufflinks[0x416fdc]
cufflinks[0x41703c]
cufflinks[0x416daf]
cufflinks[0x40d05b]
cufflinks[0x4210fc]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3abc41d994]
cufflinks(sin+0xc1)[0x405bd9]
======= Memory map: ========
00400000-00601000 r-xp 00000000 cfc:dd64c 311077305 /cufflinks-2.0.1.Linux_x86_64/cufflinks
00801000-00805000 rwxp 00201000 cfc:dd64c 311077305 /cufflinks-2.0.1.Linux_x86_64/cufflinks
00805000-00825000 rwxp 00805000 00:00 0
15704000-409b7000 rwxp 15704000 00:00 0 [heap]
409b7000-409b8000 ---p 409b7000 00:00 0
409b8000-40bb8000 rwxp 409b8000 00:00 0
41157000-41158000 ---p 41157000 00:00 0
41158000-41358000 rwxp 41158000 00:00 0
41743000-41744000 ---p 41743000 00:00 0
41744000-41944000 rwxp 41744000 00:00 0
41944000-41945000 ---p 41944000 00:00 0
41945000-41b45000 rwxp 41945000 00:00 0
41b45000-41b46000 ---p 41b45000 00:00 0
41b46000-41d46000 rwxp 41b46000 00:00 0
41d5f000-41d60000 ---p 41d5f000 00:00 0
41d60000-41f60000 rwxp 41d60000 00:00 0
41f60000-41f61000 ---p 41f60000 00:00 0
41f61000-42161000 rwxp 41f61000 00:00 0
42161000-42162000 ---p 42161000 00:00 0
42162000-42362000 rwxp 42162000 00:00 0
42362000-42363000 ---p 42362000 00:00 0
42363000-42563000 rwxp 42363000 00:00 0
3abc000000-3abc01c000 r-xp 00000000 00:13 23758096 /lib64/ld-2.5.so
3abc21c000-3abc21d000 r-xp 0001c000 00:13 23758096 /lib64/ld-2.5.so
3abc21d000-3abc21e000 rwxp 0001d000 00:13 23758096 /lib64/ld-2.5.so
3abc400000-3abc54e000 r-xp 00000000 00:13 23758095 /lib64/libc-2.5.so
3abc54e000-3abc74e000 ---p 0014e000 00:13 23758095 /lib64/libc-2.5.so
3abc74e000-3abc752000 r-xp 0014e000 00:13 23758095 /lib64/libc-2.5.so
3abc752000-3abc753000 rwxp 00152000 00:13 23758095 /lib64/libc-2.5.so
3abc753000-3abc758000 rwxp 3abc753000 00:00 0
3abcc00000-3abcc16000 r-xp 00000000 00:13 23758108 /lib64/libpthread-2.5.so
3abcc16000-3abce15000 ---p 00016000 00:13 23758108 /lib64/libpthread-2.5.so
3abce15000-3abce16000 r-xp 00015000 00:13 23758108 /lib64/libpthread-2.5.so
3abce16000-3abce17000 rwxp 00016000 00:13 23758108 /lib64/libpthread-2.5.so
3abce17000-3abce1b000 rwxp 3abce17000 00:00 0
3abd000000-3abd082000 r-xp 00000000 00:13 23758249 /lib64/libm-2.5.so
3abd082000-3abd281000 ---p 00082000 00:13 23758249 /lib64/libm-2.5.so
3abd281000-3abd282000 r-xp 00081000 00:13 23758249 /lib64/libm-2.5.so
3abd282000-3abd283000 rwxp 00082000 00:13 23758249 /lib64/libm-2.5.so
3abdc00000-3abdc14000 r-xp 00000000 00:13 23665721 /usr/lib64/libz.so.1.2.3
3abdc14000-3abde13000 ---p 00014000 00:13 23665721 /usr/lib64/libz.so.1.2.3
3abde13000-3abde14000 rwxp 00013000 00:13 23665721 /usr/lib64/libz.so.1.2.3
3abe400000-3abe40d000 r-xp 00000000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
3abe40d000-3abe60d000 ---p 0000d000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
3abe60d000-3abe60e000 rwxp 0000d000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
2aaaaaaab000-2aaaabc0e000 rwxp 2aaaaaaab000 00:00 0
2aaaac000000-2aaaafe62000 rwxp 2aaaac000000 00:00 0
2aaaafe62000-2aaab0000000 ---p 2aaaafe62000 00:00 0
2aaab0000000-2aaab3c72000 rwxp 2aaab0000000 00:00 0
2aaab3c72000-2aaab4000000 ---p 2aaab3c72000 00:00 0
2aaab4000000-2aaab7ffd000 rwxp 2aaab4000000 00:00 0
2aaab7ffd000-2aaab8000000 ---p 2aaab7ffd000 00:00 0
2aaab8000000-2aaabbd75000 rwxp 2aaab8000000 00:00 0
2aaabbd75000-2aaabc000000 ---p 2aaabbd75000 00:00 0
2aaabc000000-2aaabf8d8000 rwxp 2aaabc000000 00:00 0
2aaabf8d8000-2aaac0000000 ---p 2aaabf8d8000 00:00 0
2aaac0000000-2aaac2e3d000 rwxp 2aaac0000000 00:00 0
2aaac2e3d000-2aaac4000000 ---p 2aaac2e3d000 00:00 0
2aaac4000000-2aaac7d6f000 rwxp 2aaac4000000 00:00 0
2aaac7d6f000-2aaac8000000 ---p 2aaac7d6f000 00:00 0
2aaac8600000-2aaac9421000 rwxp 2aaac8600000 00:00 0
2aaacc000000-2aaacfee4000 rwxp 2aaacc000000 00:00 0
2aaacfee4000-2aaad0000000 ---p 2aaacfee4000 00:00 0
2aaad0000000-2aaad3ffb000 rwxp 2aaad0000000 00:00 0
2aaad3ffb000-2aaad4000000 ---p 2aaad3ffb000 00:00 0
2aaad4000000-2aaad6d63000 rwxp 2aaad4000000 00:00 0
2b608771c000-2b608771d000 rwxp 2b608771c000 00:00 0
2b608772a000-2b608792d000 rwxp 2b608772a000 00:00 0
7fff7fffa000-7fff80010000 rw-p 7ffffffe8000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
It seems to be creating all the necessary output files and they seem to be ok.
The command I used was:
cufflinks -o cuff_MB -p 8 -G mygenome.gtf -b newTHref.fa -u -N --no-update-check --compatible-hits-norm ./MB_C/accepted_hits.bam
What is this error doing?
Thanks
When running Cufflinks 2.0.1 it generates the error:
*** glibc detected *** cufflinks: double free or corruption (!prev): 0x000000003f909d00 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3abc47245f]
/lib64/libc.so.6(cfree+0x4b)[0x3abc4728bb]
cufflinks[0x416f0c]
cufflinks[0x416daf]
cufflinks[0x416fdc]
cufflinks[0x41703c]
cufflinks[0x416daf]
cufflinks[0x40d05b]
cufflinks[0x4210fc]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3abc41d994]
cufflinks(sin+0xc1)[0x405bd9]
======= Memory map: ========
00400000-00601000 r-xp 00000000 cfc:dd64c 311077305 /cufflinks-2.0.1.Linux_x86_64/cufflinks
00801000-00805000 rwxp 00201000 cfc:dd64c 311077305 /cufflinks-2.0.1.Linux_x86_64/cufflinks
00805000-00825000 rwxp 00805000 00:00 0
15704000-409b7000 rwxp 15704000 00:00 0 [heap]
409b7000-409b8000 ---p 409b7000 00:00 0
409b8000-40bb8000 rwxp 409b8000 00:00 0
41157000-41158000 ---p 41157000 00:00 0
41158000-41358000 rwxp 41158000 00:00 0
41743000-41744000 ---p 41743000 00:00 0
41744000-41944000 rwxp 41744000 00:00 0
41944000-41945000 ---p 41944000 00:00 0
41945000-41b45000 rwxp 41945000 00:00 0
41b45000-41b46000 ---p 41b45000 00:00 0
41b46000-41d46000 rwxp 41b46000 00:00 0
41d5f000-41d60000 ---p 41d5f000 00:00 0
41d60000-41f60000 rwxp 41d60000 00:00 0
41f60000-41f61000 ---p 41f60000 00:00 0
41f61000-42161000 rwxp 41f61000 00:00 0
42161000-42162000 ---p 42161000 00:00 0
42162000-42362000 rwxp 42162000 00:00 0
42362000-42363000 ---p 42362000 00:00 0
42363000-42563000 rwxp 42363000 00:00 0
3abc000000-3abc01c000 r-xp 00000000 00:13 23758096 /lib64/ld-2.5.so
3abc21c000-3abc21d000 r-xp 0001c000 00:13 23758096 /lib64/ld-2.5.so
3abc21d000-3abc21e000 rwxp 0001d000 00:13 23758096 /lib64/ld-2.5.so
3abc400000-3abc54e000 r-xp 00000000 00:13 23758095 /lib64/libc-2.5.so
3abc54e000-3abc74e000 ---p 0014e000 00:13 23758095 /lib64/libc-2.5.so
3abc74e000-3abc752000 r-xp 0014e000 00:13 23758095 /lib64/libc-2.5.so
3abc752000-3abc753000 rwxp 00152000 00:13 23758095 /lib64/libc-2.5.so
3abc753000-3abc758000 rwxp 3abc753000 00:00 0
3abcc00000-3abcc16000 r-xp 00000000 00:13 23758108 /lib64/libpthread-2.5.so
3abcc16000-3abce15000 ---p 00016000 00:13 23758108 /lib64/libpthread-2.5.so
3abce15000-3abce16000 r-xp 00015000 00:13 23758108 /lib64/libpthread-2.5.so
3abce16000-3abce17000 rwxp 00016000 00:13 23758108 /lib64/libpthread-2.5.so
3abce17000-3abce1b000 rwxp 3abce17000 00:00 0
3abd000000-3abd082000 r-xp 00000000 00:13 23758249 /lib64/libm-2.5.so
3abd082000-3abd281000 ---p 00082000 00:13 23758249 /lib64/libm-2.5.so
3abd281000-3abd282000 r-xp 00081000 00:13 23758249 /lib64/libm-2.5.so
3abd282000-3abd283000 rwxp 00082000 00:13 23758249 /lib64/libm-2.5.so
3abdc00000-3abdc14000 r-xp 00000000 00:13 23665721 /usr/lib64/libz.so.1.2.3
3abdc14000-3abde13000 ---p 00014000 00:13 23665721 /usr/lib64/libz.so.1.2.3
3abde13000-3abde14000 rwxp 00013000 00:13 23665721 /usr/lib64/libz.so.1.2.3
3abe400000-3abe40d000 r-xp 00000000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
3abe40d000-3abe60d000 ---p 0000d000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
3abe60d000-3abe60e000 rwxp 0000d000 00:13 23758022 /lib64/libgcc_s-4.1.2-20080825.so.1
2aaaaaaab000-2aaaabc0e000 rwxp 2aaaaaaab000 00:00 0
2aaaac000000-2aaaafe62000 rwxp 2aaaac000000 00:00 0
2aaaafe62000-2aaab0000000 ---p 2aaaafe62000 00:00 0
2aaab0000000-2aaab3c72000 rwxp 2aaab0000000 00:00 0
2aaab3c72000-2aaab4000000 ---p 2aaab3c72000 00:00 0
2aaab4000000-2aaab7ffd000 rwxp 2aaab4000000 00:00 0
2aaab7ffd000-2aaab8000000 ---p 2aaab7ffd000 00:00 0
2aaab8000000-2aaabbd75000 rwxp 2aaab8000000 00:00 0
2aaabbd75000-2aaabc000000 ---p 2aaabbd75000 00:00 0
2aaabc000000-2aaabf8d8000 rwxp 2aaabc000000 00:00 0
2aaabf8d8000-2aaac0000000 ---p 2aaabf8d8000 00:00 0
2aaac0000000-2aaac2e3d000 rwxp 2aaac0000000 00:00 0
2aaac2e3d000-2aaac4000000 ---p 2aaac2e3d000 00:00 0
2aaac4000000-2aaac7d6f000 rwxp 2aaac4000000 00:00 0
2aaac7d6f000-2aaac8000000 ---p 2aaac7d6f000 00:00 0
2aaac8600000-2aaac9421000 rwxp 2aaac8600000 00:00 0
2aaacc000000-2aaacfee4000 rwxp 2aaacc000000 00:00 0
2aaacfee4000-2aaad0000000 ---p 2aaacfee4000 00:00 0
2aaad0000000-2aaad3ffb000 rwxp 2aaad0000000 00:00 0
2aaad3ffb000-2aaad4000000 ---p 2aaad3ffb000 00:00 0
2aaad4000000-2aaad6d63000 rwxp 2aaad4000000 00:00 0
2b608771c000-2b608771d000 rwxp 2b608771c000 00:00 0
2b608772a000-2b608792d000 rwxp 2b608772a000 00:00 0
7fff7fffa000-7fff80010000 rw-p 7ffffffe8000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
It seems to be creating all the necessary output files and they seem to be ok.
The command I used was:
cufflinks -o cuff_MB -p 8 -G mygenome.gtf -b newTHref.fa -u -N --no-update-check --compatible-hits-norm ./MB_C/accepted_hits.bam
What is this error doing?
Thanks
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