Error with classify.seqs

mothur bugs
1

Hi,
I’m encountering an error I’ve never seen before with the classify.seqs command. I ran the command last week using a different data set and had no issues? I’m calling the command on its own, not in a batch file, and have tried using 8, 4 and 1 processors, all giving the same error message:

*** glibc detected *** mothur: free(): invalid next size (normal): 0x00000000239b10f0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3914e75e66]
/lib64/libc.so.6[0x3914e789b3]
/usr/local/gcc/4.9.0/lib64/libstdc++.so.6(_ZNSs6assignERKSs+0x84)[0x7ffb13d0abe4]
mothur[0x4e188e]
mothur[0x4e401c]
mothur[0x65aae1]
mothur[0x108bae6]
mothur[0x10d9afa]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3914e1ed5d]
mothur[0x4100b1]
======= Memory map: ========
00400000-013f7000 r-xp 00000000 00:14 339095 /usr/local/mothur/1.35.1/mothur
015f7000-015f9000 rw-p 00ff7000 00:14 339095 /usr/local/mothur/1.35.1/mothur
015f9000-015fd000 rw-p 00000000 00:00 0
01d19000-239d2000 rw-p 00000000 00:00 0 [heap]
312ea00000-312ea22000 r-xp 00000000 08:02 524291 /lib64/libncurses.so.5.7
312ea22000-312ec21000 —p 00022000 08:02 524291 /lib64/libncurses.so.5.7
312ec21000-312ec22000 rw-p 00021000 08:02 524291 /lib64/libncurses.so.5.7
3914600000-3914620000 r-xp 00000000 08:02 524702 /lib64/ld-2.12.so
391481f000-3914820000 r–p 0001f000 08:02 524702 /lib64/ld-2.12.so
3914820000-3914821000 rw-p 00020000 08:02 524702 /lib64/ld-2.12.so
3914821000-3914822000 rw-p 00000000 00:00 0
3914a00000-3914a02000 r-xp 00000000 08:02 524710 /lib64/libdl-2.12.so
3914a02000-3914c02000 —p 00002000 08:02 524710 /lib64/libdl-2.12.so
3914c02000-3914c03000 r–p 00002000 08:02 524710 /lib64/libdl-2.12.so
3914c03000-3914c04000 rw-p 00003000 08:02 524710 /lib64/libdl-2.12.so
3914e00000-3914f8a000 r-xp 00000000 08:02 524703 /lib64/libc-2.12.so
3914f8a000-391518a000 —p 0018a000 08:02 524703 /lib64/libc-2.12.so
391518a000-391518e000 r–p 0018a000 08:02 524703 /lib64/libc-2.12.so
391518e000-391518f000 rw-p 0018e000 08:02 524703 /lib64/libc-2.12.so
391518f000-3915194000 rw-p 00000000 00:00 0
3915200000-3915217000 r-xp 00000000 08:02 524708 /lib64/libpthread-2.12.so
3915217000-3915417000 —p 00017000 08:02 524708 /lib64/libpthread-2.12.so
3915417000-3915418000 r–p 00017000 08:02 524708 /lib64/libpthread-2.12.so
3915418000-3915419000 rw-p 00018000 08:02 524708 /lib64/libpthread-2.12.so
3915419000-391541d000 rw-p 00000000 00:00 0
3915600000-391563a000 r-xp 00000000 08:02 524742 /lib64/libreadline.so.6.0
391563a000-391583a000 —p 0003a000 08:02 524742 /lib64/libreadline.so.6.0
391583a000-3915842000 rw-p 0003a000 08:02 524742 /lib64/libreadline.so.6.0
3915842000-3915843000 rw-p 00000000 00:00 0
3915a00000-3915a83000 r-xp 00000000 08:02 524704 /lib64/libm-2.12.so
3915a83000-3915c82000 —p 00083000 08:02 524704 /lib64/libm-2.12.so
3915c82000-3915c83000 r–p 00082000 08:02 524704 /lib64/libm-2.12.so
3915c83000-3915c84000 rw-p 00083000 08:02 524704 /lib64/libm-2.12.so
3916e00000-3916e1d000 r-xp 00000000 08:02 524501 /lib64/libtinfo.so.5.7
3916e1d000-391701d000 —p 0001d000 08:02 524501 /lib64/libtinfo.so.5.7
391701d000-3917021000 rw-p 0001d000 08:02 524501 /lib64/libtinfo.so.5.7
3917e00000-3917e02000 r-xp 00000000 08:02 524532 /lib64/libutil-2.12.so
3917e02000-3918001000 —p 00002000 08:02 524532 /lib64/libutil-2.12.so
3918001000-3918002000 r–p 00001000 08:02 524532 /lib64/libutil-2.12.so
3918002000-3918003000 rw-p 00002000 08:02 524532 /lib64/libutil-2.12.so
7ffb0616f000-7ffb0c000000 r–p 00000000 08:02 1051514 /usr/lib/locale/locale-archive
7ffb0c000000-7ffb0c021000 rw-p 00000000 00:00 0
7ffb0c021000-7ffb10000000 —p 00000000 00:00 0
7ffb11a8e000-7ffb11a9e000 rw-p 00000000 00:00 0
7ffb11a9e000-7ffb11a9f000 —p 00000000 00:00 0
7ffb11a9f000-7ffb1249f000 rw-p 00000000 00:00 0
7ffb1249f000-7ffb12b1d000 r–s 00000000 08:02 788097 /var/lib/sss/mc/passwd
7ffb12b1d000-7ffb12b24000 r-xp 00000000 08:02 524510 /lib64/libnss_sss.so.2
7ffb12b24000-7ffb12d24000 —p 00007000 08:02 524510 /lib64/libnss_sss.so.2
7ffb12d24000-7ffb12d25000 rw-p 00007000 08:02 524510 /lib64/libnss_sss.so.2
7ffb12d25000-7ffb12d31000 r-xp 00000000 08:02 524319 /lib64/libnss_files-2.12.so
7ffb12d31000-7ffb12f31000 —p 0000c000 08:02 524319 /lib64/libnss_files-2.12.so
7ffb12f31000-7ffb12f32000 r–p 0000c000 08:02 524319 /lib64/libnss_files-2.12.so
7ffb12f32000-7ffb12f33000 rw-p 0000d000 08:02 524319 /lib64/libnss_files-2.12.so
7ffb12f33000-7ffb12f38000 rw-p 00000000 00:00 0
7ffb12f38000-7ffb12f3f000 r-xp 00000000 08:02 524715 /lib64/librt-2.12.so
7ffb12f3f000-7ffb1313e000 —p 00007000 08:02 524715 /lib64/librt-2.12.so
7ffb1313e000-7ffb1313f000 r–p 00006000 08:02 524715 /lib64/librt-2.12.so
7ffb1313f000-7ffb13140000 rw-p 00007000 08:02 524715 /lib64/librt-2.12.so
7ffb13140000-7ffb13222000 r-xp 00000000 00:14 275179 /usr/local/openmpi/1.8.4-gcc/lib/libopen-pal.so.6.2.1
7ffb13222000-7ffb13422000 —p 000e2000 00:14 275179 /usr/local/openmpi/1.8.4-gcc/lib/libopen-pal.so.6.2.1
7ffb13422000-7ffb1342b000 rw-p 000e2000 00:14 275179 /usr/local/openmpi/1.8.4-gcc/lib/libopen-pal.so.6.2.1
7ffb1342b000-7ffb13432000 rw-p 00000000 00:00 0
7ffb13432000-7ffb13467000 r-xp 00000000 00:14 3062 /usr/local/torque/2.5.13/lib/libtorque.so.2.0.0
7ffb13467000-7ffb13666000 —p 00035000 00:14 3062 /usr/local/torque/2.5.13/lib/libtorque.so.2.0.0
7ffb13666000-7ffb13669000 rw-p 00034000 00:14 3062 /usr/local/torque/2.5.13/lib/libtorque.so.2.0.0
7ffb13669000-7ffb1373d000 rw-p 00000000 00:00 0
7ffb1373d000-7ffb13822000 r-xp 00000000 00:14 275223 /usr/local/openmpi/1.8.4-gcc/lib/libopen-rte.so.7.0.5
7ffb13822000-7ffb13a21000 —p 000e5000 00:14 275223 /usr/local/openmpi/1.8.4-gcc/lib/libopen-rte.so.7.0.5
7ffb13a21000-7ffb13a2c000 rw-p 000e4000 00:14 275223 /usr/local/openmpi/1.8.4-gcc/lib/libopen-rte.so.7.0.5
7ffb13a2c000-7ffb13a30000 rw-p 00000000 00:00 0
7ffb13a30000-7ffb13a46000 r-xp 00000000 00:14 125236 /usr/local/gcc/4.9.0/lib64/libgcc_s.so.1
7ffb13a46000-7ffb13c45000 —p 00016000 00:14 125236 /usr/local/gcc/4.9.0/lib64/libgcc_s.so.1
7ffb13c45000-7ffb13c46000 rw-p 00015000 00:14 125236 /usr/local/gcc/4.9.0/lib64/libgcc_s.so.1
7ffb13c46000-7ffb13d38000 r-xp 00000000 00:14 125964 /usr/local/gcc/4.9.0/lib64/libstdc++.so.6.0.20
7ffb13d38000-7ffb13f38000 —p 000f2000 00:14 125964 /usr/local/gcc/4.9.0/lib64/libstdc++.so.6.0.20
7ffb13f38000-7ffb13f41000 r–p 000f2000 00:14 125964 /usr/local/gcc/4.9.0/lib64/libstdc++.so.6.0.20
7ffb13f41000-7ffb13f43000 rw-p 000fb000 00:14 125964 /usr/local/gcc/4.9.0/lib64/libstdc++.so.6.0.20
7ffb13f43000-7ffb13f59000 rw-p 00000000 00:00 0
7ffb13f59000-7ffb1418d000 r-xp 00000000 00:14 275307 /usr/local/openmpi/1.8.4-gcc/lib/libmpi.so.1.6.0
7ffb1418d000-7ffb1438d000 —p 00234000 00:14 275307 /usr/local/openmpi/1.8.4-gcc/lib/libmpi.so.1.6.0
7ffb1438d000-7ffb143ae000 rw-p 00234000 00:14 275307 /usr/local/openmpi/1.8.4-gcc/lib/libmpi.so.1.6.0
7ffb143ae000-7ffb14442000 rw-p 00000000 00:00 0
7ffb14442000-7ffb1445a000 r-xp 00000000 00:14 275690 /usr/local/openmpi/1.8.4-gcc/lib/libmpi_cxx.so.1.1.3
7ffb1445a000-7ffb14659000 —p 00018000 00:14 275690 /usr/local/openmpi/1.8.4-gcc/lib/libmpi_cxx.so.1.1.3
7ffb14659000-7ffb1465c000 rw-p 00017000 00:14 275690 /usr/local/openmpi/1.8.4-gcc/lib/libmpi_cxx.so.1.1.3
7ffb1465c000-7ffb1465d000 rw-p 00000000 00:00 0
7ffb1465f000-7ffb14660000 rw-p 00000000 00:00 0
7ffb14660000-7ffb14667000 r–s 00000000 08:02 1051772 /usr/lib64/gconv/gconv-modules.cache
7ffb14667000-7ffb14668000 rw-p 00000000 00:00 0
7fff16d17000-7fff16d2c000 rw-p 00000000 00:00 0 [stack]
7fff16dbb000-7fff16dbc000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
[hpc-compute4:47265] *** Process received signal ***
[hpc-compute4:47265] Signal: Aborted (6)
[hpc-compute4:47265] Signal code: (-6)
[hpc-compute4:47265] [ 0] /lib64/libpthread.so.0[0x391520f710]
[hpc-compute4:47265] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x3914e32625]
[hpc-compute4:47265] [ 2] /lib64/libc.so.6(abort+0x175)[0x3914e33e05]
[hpc-compute4:47265] [ 3] /lib64/libc.so.6[0x3914e70537]
[hpc-compute4:47265] [ 4] /lib64/libc.so.6[0x3914e75e66]
[hpc-compute4:47265] [ 5] /lib64/libc.so.6[0x3914e789b3]
[hpc-compute4:47265] [ 6] /usr/local/gcc/4.9.0/lib64/libstdc++.so.6(_ZNSs6assignERKSs+0x84)[0x7ffb13d0abe4]
[hpc-compute4:47265] [ 7] mothur[0x4e188e]
[hpc-compute4:47265] [ 8] mothur[0x4e401c]
[hpc-compute4:47265] [ 9] mothur[0x65aae1]
[hpc-compute4:47265] [10] mothur[0x108bae6]
[hpc-compute4:47265] [11] mothur[0x10d9afa]
[hpc-compute4:47265] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3914e1ed5d]
[hpc-compute4:47265] [13] mothur[0x4100b1]
[hpc-compute4:47265] *** End of error message ***

The command:
classify.seqs(fasta=ND_final.trim.unique.good.filter.unique.precluster.pick.fasta, count=ND_final.trim.unique.good.filter.unique.precluster.count_table, reference=trainset14_032015.pds.fasta, taxonomy=trainset14_032015.pds.tax, cutoff=80, processors=1)

Any ideas what is going on?

2

Are you using our mpi enabled version? We are removing the mpi source from our next version. Have you tried our current version compiled without the readline options? https://github.com/mothur/mothur/releases/tag/v1.36.1

3

I am having a very similar issue. I’ve tried using the pre-compiled versions of mothur 1.36.0, 1.36.1 regular, and 1.36.1with No Read Line, and all of them crash mothur with an “Illegal operation” error. The log files are not helpful, as they do not record the error message or even the command I typed. I tried using multiple processors as well as just using a single processor, and it made no difference. I have not tried compiling mothur on my own yet.

4

Just to add one more data point, my institute still has 1.33.3 (I believe, it’s an older version from 2014) installed so I tried the exact same classify.seqs command with that, with the same data files, and it worked just fine.