Question: *** buffer overflow detected ***: blastclust terminated?? Is there another way to create a non-redundant set of proteins?
0
gravatar for jamie.pike
5 months ago by
jamie.pike60
jamie.pike60 wrote:

I am trying to create a non-redundant set of proteins using blastclust, but I keep getting a buffer overflow error. Is anyone aware of a way to stop this, or can perhaps recommend an alternative program for creating non-redundant protein sets? There are currently 54 proteins in the FASTA.

blastclust version 2.2.26

My command:

blastclust -i input.fsa_aa -p T -L 1 -b T -S 100 -o output_non-redundant.Blastclust

Error message:

Aug 13, 2020  2:29 PM Start clustering of 54 queries
*** buffer overflow detected ***: blastclust terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777f5)[0x7fe5286db7f5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7fe52877d21c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117220)[0x7fe52877b220]
/lib/x86_64-linux-gnu/libc.so.6(+0x116789)[0x7fe52877a789]
/lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0x80)[0x7fe5286df6c0]
/lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x139b)[0x7fe5286b251b]
/lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7fe52877a814]
/lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7fe52877a76d]
blastclust(Nlm_Main+0x117c)[0x55f804f95a8c]
/usr/lib/x86_64-linux-gnu/libncbi.so.6(main+0x1c)[0x7fe528c60e5c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fe528684840]
blastclust(+0x3129)[0x55f804f93129]
======= Memory map: ========
55f804f90000-55f804f99000 r-xp 00000000 fc:00 28580580                   /usr/bin/blastclust
55f805198000-55f805199000 r--p 00008000 fc:00 28580580                   /usr/bin/blastclust
55f805199000-55f80519a000 rw-p 00009000 fc:00 28580580                   /usr/bin/blastclust
55f80660c000-55f80697e000 rw-p 00000000 00:00 0                          [heap]
7fe5276f1000-7fe527707000 r-xp 00000000 fc:00 46662157                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe527707000-7fe527906000 ---p 00016000 fc:00 46662157                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe527906000-7fe527907000 rw-p 00015000 fc:00 46662157                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fe527907000-7fe527912000 r-xp 00000000 fc:00 46661920                   /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fe527912000-7fe527b11000 ---p 0000b000 fc:00 46661920                   /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fe527b11000-7fe527b12000 r--p 0000a000 fc:00 46661920                   /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fe527b12000-7fe527b13000 rw-p 0000b000 fc:00 46661920                   /lib/x86_64-linux-gnu/libnss_files-2.23.so
7fe527b13000-7fe527b19000 rw-p 00000000 00:00 0 
7fe527b19000-7fe527b24000 r-xp 00000000 fc:00 46661925                   /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fe527b24000-7fe527d23000 ---p 0000b000 fc:00 46661925                   /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fe527d23000-7fe527d24000 r--p 0000a000 fc:00 46661925                   /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fe527d24000-7fe527d25000 rw-p 0000b000 fc:00 46661925                   /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7fe527d25000-7fe527d3b000 r-xp 00000000 fc:00 46661910                   /lib/x86_64-linux-gnu/libnsl-2.23.so
7fe527d3b000-7fe527f3a000 ---p 00016000 fc:00 46661910                   /lib/x86_64-linux-gnu/libnsl-2.23.so
7fe527f3a000-7fe527f3b000 r--p 00015000 fc:00 46661910                   /lib/x86_64-linux-gnu/libnsl-2.23.so
7fe527f3b000-7fe527f3c000 rw-p 00016000 fc:00 46661910                   /lib/x86_64-linux-gnu/libnsl-2.23.so
7fe527f3c000-7fe527f3e000 rw-p 00000000 00:00 0 
7fe527f3e000-7fe527f46000 r-xp 00000000 fc:00 46661923                   /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fe527f46000-7fe528145000 ---p 00008000 fc:00 46661923                   /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fe528145000-7fe528146000 r--p 00007000 fc:00 46661923                   /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fe528146000-7fe528147000 rw-p 00008000 fc:00 46661923                   /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7fe528147000-7fe52824f000 r-xp 00000000 fc:00 46661911                   /lib/x86_64-linux-gnu/libm-2.23.so
7fe52824f000-7fe52844e000 ---p 00108000 fc:00 46661911                   /lib/x86_64-linux-gnu/libm-2.23.so
7fe52844e000-7fe52844f000 r--p 00107000 fc:00 46661911                   /lib/x86_64-linux-gnu/libm-2.23.so
7fe52844f000-7fe528450000 rw-p 00108000 fc:00 46661911                   /lib/x86_64-linux-gnu/libm-2.23.so
7fe528450000-7fe528463000 r-xp 00000000 fc:00 28580547                   /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20120620
7fe528463000-7fe528662000 ---p 00013000 fc:00 28580547                   /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20120620
7fe528662000-7fe528663000 r--p 00012000 fc:00 28580547                   /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20120620
7fe528663000-7fe528664000 rw-p 00013000 fc:00 28580547                   /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20120620
7fe528664000-7fe528824000 r-xp 00000000 fc:00 46661907                   /lib/x86_64-linux-gnu/libc-2.23.so
7fe528824000-7fe528a24000 ---p 001c0000 fc:00 46661907                   /lib/x86_64-linux-gnu/libc-2.23.so
7fe528a24000-7fe528a28000 r--p 001c0000 fc:00 46661907                   /lib/x86_64-linux-gnu/libc-2.23.so
7fe528a28000-7fe528a2a000 rw-p 001c4000 fc:00 46661907                   /lib/x86_64-linux-gnu/libc-2.23.so
7fe528a2a000-7fe528a2e000 rw-p 00000000 00:00 0 
7fe528a2e000-7fe528a46000 r-xp 00000000 fc:00 46661908                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fe528a46000-7fe528c45000 ---p 00018000 fc:00 46661908                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fe528c45000-7fe528c46000 r--p 00017000 fc:00 46661908                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fe528c46000-7fe528c47000 rw-p 00018000 fc:00 46661908                   /lib/x86_64-linux-gnu/libpthread-2.23.so
7fe528c47000-7fe528c4b000 rw-p 00000000 00:00 0 
7fe528c4b000-7fe528ced000 r-xp 00000000 fc:00 28580560                   /usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20120620
7fe528ced000-7fe528eed000 ---p 000a2000 fc:00 28580560                   /usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20120620
7fe528eed000-7fe528ef0000 r--p 000a2000 fc:00 28580560                   /usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20120620
7fe528ef0000-7fe528ef1000 rw-p 000a5000 fc:00 28580560                   /usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20120620
7fe528ef1000-7fe528f04000 rw-p 00000000 00:00 0 
7fe528f04000-7fe52951f000 r-xp 00000000 fc:00 28580558                   /usr/lib/x86_64-linux-gnu/libncbiobj.so.6.1.20120620
7fe52951f000-7fe52971e000 ---p 0061b000 fc:00 28580558                   /usr/lib/x86_64-linux-gnu/libncbiobj.so.6.1.20120620
7fe52971e000-7fe529758000 r--p 0061a000 fc:00 28580558                   /usr/lib/x86_64-linux-gnu/libncbiobj.so.6.1.20120620
7fe529758000-7fe529820000 rw-p 00654000 fc:00 28580558                   /usr/lib/x86_64-linux-gnu/libncbiobj.so.6.1.20120620
7fe529820000-7fe529827000 rw-p 00000000 00:00 0 
7fe529827000-7fe529985000 r-xp 00000000 fc:00 28580555                   /usr/lib/x86_64-linux-gnu/libncbitool.so.6.1.20120620
7fe529985000-7fe529b84000 ---p 0015e000 fc:00 28580555                   /usr/lib/x86_64-linux-gnu/libncbitool.so.6.1.20120620
7fe529b84000-7fe529b87000 r--p 0015d000 fc:00 28580555                   /usr/lib/x86_64-linux-gnu/libncbitool.so.6.1.20120620
7fe529b87000-7fe529b9f000 rw-p 00160000 fc:00 28580555                   /usr/lib/x86_64-linux-gnu/libncbitool.so.6.1.20120620
7fe529b9f000-7fe529ba1000 rw-p 00000000 00:00 0 
7fe529ba1000-7fe529bc7000 r-xp 00000000 fc:00 46661918                   /lib/x86_64-linux-gnu/ld-2.23.so
7fe529da3000-7fe529da9000 rw-p 00000000 00:00 0 
7fe529dc5000-7fe529dc6000 rw-p 00000000 00:00 0 
7fe529dc6000-7fe529dc7000 r--p 00025000 fc:00 46661918                   /lib/x86_64-linux-gnu/ld-2.23.so
7fe529dc7000-7fe529dc8000 rw-p 00026000 fc:00 46661918                   /lib/x86_64-linux-gnu/ld-2.23.so
7fe529dc8000-7fe529dc9000 rw-p 00000000 00:00 0 
7ffe675f0000-7ffe67611000 rw-p 00000000 00:00 0                          [stack]
7ffe6772b000-7ffe6772d000 r--p 00000000 00:00 0                          [vvar]
7ffe6772d000-7ffe6772f000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

Top seven predicted proteins in the input FASTA:

>GCA_007994515.1_UK0001_genomic.fna_Candidate_Sequence_g5.t1
MRLLSLPSTLLLAANAAAYDTLLHFGPTAQVETRSIDQIYKAALKKGGVVTAWFGGDEKN
QEDAVKKAFETAFPGMKLNLTVDLSKYLDGNIDQQLANNNVYVDTVALQTTQDFPRWKDE
GALLYYAPAGFDKIYSGLKDIDAAFYGYTGIAWQLIWNANKLKGKEAPAEYSDFLAPEYK
GKLALTYPNDDDSILFLFDQILNKYGETWFTKLLQQKPRWVRGAATPQTLVRDPKTPYAA
TFTSAMGLTTGAGSLNATYPKKSNFISWAQHTAILKDAPHPEGAKLLQNFLLSKDFQKTN
GFWPVRIDVAPPAGFPQFINQLNTDPHNFMKFMSDPERVERLRFWFEKRLGTAQGLSPLD
DDL
>GCA_007994515.1_UK0001_genomic.fna_Candidate_Sequence_g6.t1
MLAELSVAFTLAAFALASPPIDKLCPSQSGIPAKPNPTLPSNGGASELPEPSQGAALKHI
ALGFGIQNYTCADTDTTPTSVGALAVLYDVTHLYPGQGHSSLTQAEWASVPGEVLNTLNV
PLNLNENGIGASPIKPFPKKQDLKVRSLSKKISYLGHHYFNSVGVPTFDLDKACQLLIAK
KIDGIKAPGSSPSGPDGTGAVDWLFLGDAGGSHGISFVYRVLTASGASHGCKTKGVDSTS
YAAMYWFYN
>GCA_007994515.1_UK0001_genomic.fna_Candidate_Sequence_g7.t1
MKLSAVAAMAFATFHIAEAQNKNIQVGCYAVDSRQDGLLPKLLLNSDARAKADPDLRFGF
WDGGNKICCDGPRNCARYWAFTYNHPYNWASKTSTGTIDGQNVKFVCVGYQMGQCTIN
>GCA_007994515.1_UK0001_genomic.fna_Candidate_Sequence_g8.t1
MKLSAVAAMAFATFHIAEAQNKNIQVGCYAVDSRQDGLLPKLLLNSDARAKADPDLRFGF
WDGGNKICCDGPRNCARYWAFTYNHPYNWASKTSTGTIDGQNVKFVCVGYQMGQCTIN
>GCA_007994515.1_UK0001_genomic.fna_Candidate_Sequence_g9.t1
MKLSAVAAMAFATFHIAEAQNKNIQVGCYAVDSRQDGLLPKLLLNSDARAKADPDLRFGF
WDGGNKICCDGPRNCARYWAFTYNHPYNWASKTSTGTIDGQNVKFVCVGYQMGQCTIN
>GCA_007994515.1_UK0001_genomic.fna_Candidate_Sequence_g11.t1
MKLSAVAAMAFATFHIAEAQNKNIQVGCYAVDSRQDGLLPKLLLNSDARAKADPDLRFGF
WDGGNKICCDGPRNCARYWAFTYNHPYNWASKTSTGTIDGQNV
ADD COMMENTlink written 5 months ago by jamie.pike60
3
gravatar for GenoMax
5 months ago by
GenoMax94k
United States
GenoMax94k wrote:

You can try CD-HIT instead.

ADD COMMENTlink written 5 months ago by GenoMax94k

Works perfectly, thank you

ADD REPLYlink written 5 months ago by jamie.pike60
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