mothur

dist.shared bug


#1

I get a funny error (see below), when running dist.shared. When I switch back to 1.36 dist.shared works on the file. Happy to share the input file for you to sort it out/replicate error if interested. I am running a fully patched Ubuntu 16.04.2 LTS and mothur 1.39.5. Looks like something with glibc


mothur > dist.shared(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.shared, calc=jclass-braycurtis, subsample=T, label=0,processors=4)

Using 4 processors.
0
*** Error in `/home/f/Mothur1.39.5/mothur/mothur’: free(): invalid next size (normal): 0x0000000001ebcbf0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f5eb40ac7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f5eb40b537a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f5eb40b953c]
/home/f/Mothur1.39.5/mothur/mothur[0x1159d43]
/home/f/Mothur1.39.5/mothur/mothur[0x11986ec]
/home/f/Mothur1.39.5/mothur/mothur[0x508f3e]
/home/f/Mothur1.39.5/mothur/mothur[0xbd8e08]
/home/f/Mothur1.39.5/mothur/mothur[0xbdc3f9]
/home/f/Mothur1.39.5/mothur/mothur[0x44f479]
/home/f/Mothur1.39.5/mothur/mothur[0x409b69]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f5eb4055830]
/home/f/Mothur1.39.5/mothur/mothur[0x40f4f1]
======= Memory map: ========
00400000-01446000 r-xp 00000000 08:07 10500236 /home/f/Mothur1.39.5/mothur/mothur
01645000-01648000 rw-p 01045000 08:07 10500236 /home/f/Mothur1.39.5/mothur/mothur
01648000-0164a000 rw-p 00000000 00:00 0
01c06000-02b58000 rw-p 00000000 00:00 0 [heap]
7f5eac000000-7f5eac021000 rw-p 00000000 00:00 0
7f5eac021000-7f5eb0000000 —p 00000000 00:00 0
7f5eb12e9000-7f5eb2003000 rw-p 00000000 00:00 0
7f5eb2084000-7f5eb39b6000 rw-p 00000000 00:00 0
7f5eb39b6000-7f5eb3e0c000 r–p 00000000 08:07 1093070 /usr/lib/locale/locale-archive
7f5eb3e0c000-7f5eb3e31000 r-xp 00000000 08:07 4457353 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f5eb3e31000-7f5eb4030000 —p 00025000 08:07 4457353 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f5eb4030000-7f5eb4034000 r–p 00024000 08:07 4457353 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f5eb4034000-7f5eb4035000 rw-p 00028000 08:07 4457353 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f5eb4035000-7f5eb41f5000 r-xp 00000000 08:07 4456685 /lib/x86_64-linux-gnu/libc-2.23.so
7f5eb41f5000-7f5eb43f5000 —p 001c0000 08:07 4456685 /lib/x86_64-linux-gnu/libc-2.23.so
7f5eb43f5000-7f5eb43f9000 r–p 001c0000 08:07 4456685 /lib/x86_64-linux-gnu/libc-2.23.so
7f5eb43f9000-7f5eb43fb000 rw-p 001c4000 08:07 4456685 /lib/x86_64-linux-gnu/libc-2.23.so
7f5eb43fb000-7f5eb43ff000 rw-p 00000000 00:00 0
7f5eb43ff000-7f5eb4415000 r-xp 00000000 08:07 4457952 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f5eb4415000-7f5eb4614000 —p 00016000 08:07 4457952 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f5eb4614000-7f5eb4615000 rw-p 00015000 08:07 4457952 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f5eb4615000-7f5eb471d000 r-xp 00000000 08:07 4456544 /lib/x86_64-linux-gnu/libm-2.23.so
7f5eb471d000-7f5eb491c000 —p 00108000 08:07 4456544 /lib/x86_64-linux-gnu/libm-2.23.so
7f5eb491c000-7f5eb491d000 r–p 00107000 08:07 4456544 /lib/x86_64-linux-gnu/libm-2.23.so
7f5eb491d000-7f5eb491e000 rw-p 00108000 08:07 4456544 /lib/x86_64-linux-gnu/libm-2.23.so
7f5eb491e000-7f5eb4a90000 r-xp 00000000 08:07 1054353 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f5eb4a90000-7f5eb4c90000 —p 00172000 08:07 1054353 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f5eb4c90000-7f5eb4c9a000 r–p 00172000 08:07 1054353 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f5eb4c9a000-7f5eb4c9c000 rw-p 0017c000 08:07 1054353 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f5eb4c9c000-7f5eb4ca0000 rw-p 00000000 00:00 0
7f5eb4ca0000-7f5eb4cdd000 r-xp 00000000 08:07 4460794 /lib/x86_64-linux-gnu/libreadline.so.6.3
7f5eb4cdd000-7f5eb4edd000 —p 0003d000 08:07 4460794 /lib/x86_64-linux-gnu/libreadline.so.6.3
7f5eb4edd000-7f5eb4edf000 r–p 0003d000 08:07 4460794 /lib/x86_64-linux-gnu/libreadline.so.6.3
7f5eb4edf000-7f5eb4ee5000 rw-p 0003f000 08:07 4460794 /lib/x86_64-linux-gnu/libreadline.so.6.3
7f5eb4ee5000-7f5eb4ee6000 rw-p 00000000 00:00 0
7f5eb4ee6000-7f5eb4f0c000 r-xp 00000000 08:07 4456478 /lib/x86_64-linux-gnu/ld-2.23.so
7f5eb4f5e000-7f5eb4fdf000 rw-p 00000000 00:00 0
7f5eb5020000-7f5eb5061000 rw-p 00000000 00:00 0
7f5eb509a000-7f5eb50e0000 rw-p 00000000 00:00 0
7f5eb5101000-7f5eb5102000 rw-p 00000000 00:00 0
7f5eb5102000-7f5eb5109000 r–s 00000000 08:07 1344197 /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f5eb5109000-7f5eb510b000 rw-p 00000000 00:00 0
7f5eb510b000-7f5eb510c000 r–p 00025000 08:07 4456478 /lib/x86_64-linux-gnu/ld-2.23.so
7f5eb510c000-7f5eb510d000 rw-p 00026000 08:07 4456478 /lib/x86_64-linux-gnu/ld-2.23.so
7f5eb510d000-7f5eb510e000 rw-p 00000000 00:00 0
7ffce963f000-7ffce9660000 rw-p 00000000 00:00 0 [stack]
7ffce9669000-7ffce966b000 r–p 00000000 00:00 0 [vvar]
7ffce966b000-7ffce966d000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)


#2

Thanks for letting us know. This bug will be fixed in the next release coming soon. You can track the progress here, https://github.com/mothur/mothur/issues/357 and https://github.com/mothur/mothur/issues/347.