classify.seqs - Reading template probabilities...glibc detec

mothur bugs
1

Hi,

when using mothur with classify.seqs we get Reading template probabilities… *** glibc detected *** mothur: free(): invalid next size (normal): 0x00000000217a9c80 ***
See message below!

Infos:
uname -a
Linux rose 2.6.32-62-server #125-Ubuntu SMP Mon Jun 9 16:20:45 UTC 2014 x86_64 GNU/Linux
24G RAM, 24x CPUs

What can we do about this?

thanks a lot
Cs-Tech Team

##################
mothur

mothur v.1.33.3
Last updated: 4/4/2014

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type ‘help()’ for information on the commands that are available

Type ‘quit()’ to exit program

mothur > set.dir(input=/mnt/fastq/MetaGlacier/mothurKurz2)

Mothur’s directories:
inputDir=/mnt/fastq/MetaGlacier/mothurKurz2/

mothur > classify.seqs(fasta=warum.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=warum.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)


Using 1 processors. Reading template taxonomy... DONE. Reading template probabilities... *** glibc detected *** mothur: free(): invalid next size (normal): 0x00000000217a9c80 *** ======= Backtrace: ========= /lib/libc.so.6(+0x78bf6)[0x7fd348f52bf6] /lib/libc.so.6(cfree+0x73)[0x7fd348f591d3] /usr/lib/libstdc++.so.6(_ZNSs6assignERKSs+0x85)[0x7fd3497a41f5] mothur[0x44f64c] mothur[0x456983] mothur[0x5d9cff] mothur[0x775d12] mothur[0xa8c414] /lib/libc.so.6(__libc_start_main+0xfd)[0x7fd348ef8c8d] mothur[0x406789] ======= Memory map: ======== 00400000-01345000 r-xp 00000000 fb:01 284870 /usr/local/bin/mothur 01545000-01546000 r--p 00f45000 fb:01 284870 /usr/local/bin/mothur 01546000-01547000 rw-p 00f46000 fb:01 284870 /usr/local/bin/mothur 01547000-01549000 rw-p 00000000 00:00 0 02ba7000-217c8000 rw-p 00000000 00:00 0 [heap] 7fd344000000-7fd344021000 rw-p 00000000 00:00 0 7fd344021000-7fd348000000 ---p 00000000 00:00 0 7fd3484d5000-7fd348cd6000 rw-p 00000000 00:00 0 7fd348cd6000-7fd348cd8000 r-xp 00000000 fb:01 523390 /lib/libdl-2.11.1.so 7fd348cd8000-7fd348ed8000 ---p 00002000 fb:01 523390 /lib/libdl-2.11.1.so 7fd348ed8000-7fd348ed9000 r--p 00002000 fb:01 523390 /lib/libdl-2.11.1.so 7fd348ed9000-7fd348eda000 rw-p 00003000 fb:01 523390 /lib/libdl-2.11.1.so 7fd348eda000-7fd349058000 r-xp 00000000 fb:01 523630 /lib/libc-2.11.1.so 7fd349058000-7fd349257000 ---p 0017e000 fb:01 523630 /lib/libc-2.11.1.so 7fd349257000-7fd34925b000 r--p 0017d000 fb:01 523630 /lib/libc-2.11.1.so 7fd34925b000-7fd34925c000 rw-p 00181000 fb:01 523630 /lib/libc-2.11.1.so 7fd34925c000-7fd349261000 rw-p 00000000 00:00 0 7fd349261000-7fd349277000 r-xp 00000000 fb:01 523336 /lib/libgcc_s.so.1 7fd349277000-7fd349476000 ---p 00016000 fb:01 523336 /lib/libgcc_s.so.1 7fd349476000-7fd349477000 r--p 00015000 fb:01 523336 /lib/libgcc_s.so.1 7fd349477000-7fd349478000 rw-p 00016000 fb:01 523336 /lib/libgcc_s.so.1 7fd349478000-7fd3494fa000 r-xp 00000000 fb:01 523828 /lib/libm-2.11.1.so 7fd3494fa000-7fd3496f9000 ---p 00082000 fb:01 523828 /lib/libm-2.11.1.so 7fd3496f9000-7fd3496fa000 r--p 00081000 fb:01 523828 /lib/libm-2.11.1.so 7fd3496fa000-7fd3496fb000 rw-p 00082000 fb:01 523828 /lib/libm-2.11.1.so 7fd3496fb000-7fd3497f1000 r-xp 00000000 fb:01 262402 /usr/lib/libstdc++.so.6.0.13 7fd3497f1000-7fd3499f1000 ---p 000f6000 fb:01 262402 /usr/lib/libstdc++.so.6.0.13 7fd3499f1000-7fd3499f8000 r--p 000f6000 fb:01 262402 /usr/lib/libstdc++.so.6.0.13 7fd3499f8000-7fd3499fa000 rw-p 000fd000 fb:01 262402 /usr/lib/libstdc++.so.6.0.13 7fd3499fa000-7fd349a0f000 rw-p 00000000 00:00 0 7fd349a0f000-7fd349a16000 r-xp 00000000 fb:01 523320 /lib/librt-2.11.1.so 7fd349a16000-7fd349c15000 ---p 00007000 fb:01 523320 /lib/librt-2.11.1.so 7fd349c15000-7fd349c16000 r--p 00006000 fb:01 523320 /lib/librt-2.11.1.so 7fd349c16000-7fd349c17000 rw-p 00007000 fb:01 523320 /lib/librt-2.11.1.so 7fd349c17000-7fd349c2f000 r-xp 00000000 fb:01 523359 /lib/libpthread-2.11.1.so 7fd349c2f000-7fd349e2e000 ---p 00018000 fb:01 523359 /lib/libpthread-2.11.1.so 7fd349e2e000-7fd349e2f000 r--p 00017000 fb:01 523359 /lib/libpthread-2.11.1.so 7fd349e2f000-7fd349e30000 rw-p 00018000 fb:01 523359 /lib/libpthread-2.11.1.so 7fd349e30000-7fd349e34000 rw-p 00000000 00:00 0 7fd349e34000-7fd349fbb000 r-xp 00000000 fb:01 266718 /usr/lib/libmpich.so.1.2 7fd349fbb000-7fd34a1ba000 ---p 00187000 fb:01 266718 /usr/lib/libmpich.so.1.2 7fd34a1ba000-7fd34a1c5000 r--p 00186000 fb:01 266718 /usr/lib/libmpich.so.1.2 7fd34a1c5000-7fd34a1c7000 rw-p 00191000 fb:01 266718 /usr/lib/libmpich.so.1.2 7fd34a1c7000-7fd34a1ff000 rw-p 00000000 00:00 0 7fd34a1ff000-7fd34a220000 r-xp 00000000 fb:01 266722 /usr/lib/libmpichcxx.so.1.2 7fd34a220000-7fd34a420000 ---p 00021000 fb:01 266722 /usr/lib/libmpichcxx.so.1.2 7fd34a420000-7fd34a422000 r--p 00021000 fb:01 266722 /usr/lib/libmpichcxx.so.1.2 7fd34a422000-7fd34a423000 rw-p 00023000 fb:01 266722 /usr/lib/libmpichcxx.so.1.2 7fd34a423000-7fd34a461000 r-xp 00000000 fb:01 523357 /lib/libncurses.so.5.7 7fd34a461000-7fd34a661000 ---p 0003e000 fb:01 523357 /lib/libncurses.so.5.7 7fd34a661000-7fd34a665000 r--p 0003e000 fb:01 523357 /lib/libncurses.so.5.7 7fd34a665000-7fd34a666000 rw-p 00042000 fb:01 523357 /lib/libncurses.so.5.7 7fd34a666000-7fd34a69f000 r-xp 00000000 fb:01 523641 /lib/libreadline.so.6.1 7fd34a69f000-7fd34a89e000 ---p 00039000 fb:01 523641 /lib/libreadline.so.6.1 7fd34a89e000-7fd34a8a0000 r--p 00038000 fb:01 523641 /lib/libreadline.so.6.1 7fd34a8a0000-7fd34a8a6000 rw-p 0003a000 fb:01 523641 /lib/libreadline.so.6.1 7fd34a8a6000-7fd34a8a7000 rw-p 00000000 00:00 0 7fd34a8a7000-7fd34a8c7000 r-xp 00000000 fb:01 523391 /lib/ld-2.11.1.so 7fd34aa23000-7fd34aa67000 rw-p 00000000 00:00 0 7fd34aa67000-7fd34aaa6000 r--p 00000000 fb:01 19512 /usr/lib/locale/en_GB.utf8/LC_CTYPE 7fd34aaa6000-7fd34aaad000 rw-p 00000000 00:00 0 7fd34aabd000-7fd34aac4000 r--s 00000000 fb:01 264811 /usr/lib/gconv/gconv-modules.cache 7fd34aac4000-7fd34aac6000 rw-p 00000000 00:00 0 7fd34aac6000-7fd34aac7000 r--p 0001f000 fb:01 523391 /lib/ld-2.11.1.so 7fd34aac7000-7fd34aac8000 rw-p 00020000 fb:01 523391 /lib/ld-2.11.1.so 7fd34aac8000-7fd34aac9000 rw-p 00000000 00:00 0 7fff4c7e3000-7fff4c7f8000 rw-p 00000000 00:00 0 [stack] 7fff4c7ff000-7fff4c800000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted ##################
2

can you try deleting all of the files that begin with trainset except for trainset9_032012.pds.fasta and trainset9_032012.pds.tax and then try again? Sometimes things get corrupted and then this happens.

pat

3

great that worked! although encountered another problem;

mothur > cluster.split(fasta=warum.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=warum.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table, taxonomy=warum.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.15)

Using 1 processors.
Using splitmethod fasta.
Splitting the file…
[ERROR]: Bacteria(100);unclassified;unclassified;unclassified;unclassified;unclassified; is already in your taxonomy file, names must be unique.
[ERROR]: Bacteria(100);unclassified;unclassified;unclassified;unclassified;unclassified; is already in your taxonomy file, names must be unique.
[ERROR]: Bacteria(100);unclassified;unclassified;unclassified;unclassified;unclassified; is already in your taxonomy file, names must be unique.

thanks very much

konrad

4

Have you worked with these files outside of mothur? And can you confirm that you’re using the trainset files that we provide from the wiki? This type of error generally happens when you have a space in a sequence name or a taxonomy file.