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breakdancer's Introduction
# Genome
Genome analysis software from The Genome Institute at Washington University
School of Medicine, funded by the National Human Genome Research Institute.
## Testing
Running tests currently depends on many TGI resources so testing cannot be
performed outside TGI at this time. Within TGI you can run tests by doing,
genome-test-env test-tracker prove --lsf --git
This chains the `genome-test-env` and `test-tracker` commands together. See
`test-tracker prove --help` for its usage. For example, you may need to pass a
value to the `--git` option if your branch is not setup to track
`origin/master`.
breakdancer's People
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davz kortschak yangjr downsea flysickdog timknut tjyaul ding-lab monkollek yeung678 gatoravi mmesbahu b1234561 sahirmohit dna-language rmarduga hy714335634 cbrueffer jhwarlock ascatanach rezajf xuwei684 senaj zhouanbo scalavision juzheng87 whhyh1314 anandksrao gokalpcelik babita004 uwb-linux linhxxx xiaohuaniu0032 fengzhuo17 stephenda krol33 ruth-moraa victorycto felipeluz97 khurrammaqboolbreakdancer's Issues
install instructions incorrect
I tried following the instructions found in INSTALL.md. There seems to be an error. Specifically, this part:
$ mkdir build
$ cd build
cmake expects CMakeLists.txt, so if you cd into an empty directory, it will not run. Copying CMakeLists.txt to build resulted in other errors later on. However, running cmake from breakdancer (top-level) directory worked.
Unfortunately, running make later in the next step failed with this error:
/bin/sh: ./bootstrap.sh: No such file or directory
Problem in installing breakdancer
Hi,
I have downloaded the .zip file of breakdancer and transferred it to linux server, as my server is not able to get it directly through git clone command. After unzipping it i have tried to intall it, as per the instruction but its not working for me.
my server details is "Linux webserver 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux"
none of the commands are helping me to insatll the software, sudo cmake is asking for password, but if I am giving root password it is not working with my user name.
Need help
Discrepancies between BreakdancerMax default parameter run and -t option run
Hi,
On the same library, I ran both BreakdancerMax with default parameters and BreakdancerMax with the -t option that only detects the transchromosomal rearrangements. However, the number of transchromosomal events found by the default parameters run is larger than the one with the -t option. Just to give an example, I've selected all the transchromosomal events starting on Chromosome 10 in both cases, highlighting the events found in the default parameters run only:
The default parameters run:
chr10 59493617 4+1- chr11 69284 3+4- CTX -317 47 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 36165895 0+4- chr11 11760642 0+4- CTX -317 99 4 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|4
chr10 99351219 0+5- chr11 13840459 6+4- CTX -317 99 5 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|5
chr10 44101892 0+2- chr11 50274486 0+2- CTX -317 78 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 67549127 7+0- chr12 56711722 6+0- CTX -317 99 6 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|6
chr10 90749478 0+2- chr14 53749751 2+0- CTX -317 73 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 94915497 3+0- chr15 8201602 0+2- CTX -317 49 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 22939846 7+4- chr15 44759776 4+7- CTX -317 99 11 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|11
chr10 63926843 0+3- chr19 31445334 2+1- CTX -317 56 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 89306396 1+1- chr1 155416168 0+3- CTX -317 54 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 88527610 3+0- chr20 10169565 0+3- CTX -317 70 3 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|3
chr10 11923555 3+2- chr20 59786793 3+0- CTX -317 87 3 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|3
chr10 11923555 0+2- chr20 59786969 0+2- CTX -317 65 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 24165906 0+6- chr21 33437827 6+0- CTX -317 99 6 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|6
chr10 27713482 5+0- chr25 13773396 0+4- CTX -317 95 4 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|4
chr10 40453018 2+4- chr2 101878154 0+5- CTX -317 99 4 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|4
chr10 93900761 0+2- chr2 118704332 2+0- CTX -317 63 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 33835019 2+0- chr5 33578170 0+2- CTX -317 71 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 94554066 0+5- chr7 41573162 8+0- CTX -317 99 5 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|5
chr10 77541591 4+0- chr7 98752725 0+4- CTX -317 99 4 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|4
chr10 9620113 0+7- chr7 109241573 0+7- CTX -317 99 7 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|7
chr10 76824090 0+2- chr8 67941664 3+1- CTX -317 56 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 42282393 8+0- chr8 75868300 8+0- CTX -317 99 8 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|8
chr10 44759787 3+0- chrX 3998339 2+3- CTX -317 67 3 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|3
chr10 44760025 0+3- chrX 3998339 2+0- CTX -317 48 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 87463628 4+0- chrX 36867371 0+2- CTX -317 54 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
The -t option run:
chr10 36165839 0+3- chr11 11760701 0+3- CTX -317 97 3 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|3
chr10 59493617 4+1- chr11 69284 0+2- CTX -317 62 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 99351219 0+5- chr11 13840459 5+0- CTX -317 99 5 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|5
chr10 44101892 0+2- chr11 50274486 0+2- CTX -317 78 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 67549069 4+0- chr12 56711777 5+0- CTX -317 99 4 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|4
chr10 90749478 0+2- chr14 53749751 2+0- CTX -317 73 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 22939660 6+0- chr15 44759844 0+6- CTX -317 99 6 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|6
chr10 22939846 0+2- chr15 44760053 2+0- CTX -317 73 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 11923555 3+2- chr20 59786793 3+0- CTX -317 87 3 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|3
chr10 11923555 0+2- chr20 59786969 0+2- CTX -317 65 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 24165906 0+5- chr21 33437912 5+0- CTX -317 99 5 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|5
chr10 27713476 4+0- chr25 13773396 0+3- CTX -317 79 3 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|3
chr10 40453018 2+4- chr2 101878221 0+4- CTX -317 99 4 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|4
chr10 93900761 0+2- chr2 118704332 2+0- CTX -317 63 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 33835019 2+0- chr5 33578170 0+2- CTX -317 71 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 94554066 0+5- chr7 41573162 5+0- CTX -317 99 5 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|5
chr10 9620113 0+6- chr7 109241640 0+6- CTX -317 99 6 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|6
chr10 42282393 8+0- chr8 75868300 8+0- CTX -317 99 8 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|8
chr10 76824090 0+2- chr8 67941772 2+0- CTX -317 72 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 44759787 2+0- chrX 3998339 0+3- CTX -317 68 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 44759958 0+2- chrX 3998502 2+0- CTX -317 68 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
chr10 87463628 4+0- chrX 36867371 0+2- CTX -317 64 2 /users/idarolti/Cattle_sperm/picard2/SRR1262834_sorted_picard.bam|2
Do you know why this difference exists? If I am interested in looking at transchromosomal events only, which run should I use? Also, I have noticed that the confidence score/number of reads supporting and the start and end positions also change between the two runs. Why would that be?
Thank you!
Problems with breakdancer outputs
Hi,
I am trying to use results come from breakdancer and found multiple problems associated with the output vcf (converted using a python script by https://github.com/ALLBio/allbiotc2/blob/master/breakdancer/breakdancer2vcf.py).
1. Start and End Coordinates are not always correct
2. SVLEN is not correct as other tools does, meaning "END-STAR=SVTLEN"
3. Whats your definition of SVTYPE=INS? I found start and end has big difference ? Which should not be as per my understanding from different tool representation such as Delly.
"START and END should have only "1" nucleotide difference. OR some other tool such as WHAMG represents STAR and END same".
## WHAMG represents STAR and END same
**chr1 1442939** . T <INS> . . SVTYPE=INS;**END=1442939**;
## Delly represents STAR and start+1=END
**chr11 58325539** INS00059630 G GCACACACATGTACACA . PASS PRECISE;SVTYPE=INS;SVMETHOD=EMBL.DELLYv0.7.8;CHR2=chr11;**END=58325540**;PE=0;MAPQ=60;CT=NtoN;CIPOS=-10,10;CIEND=-10,10;INSLEN=16
but BREAKDancer output has some different way of representation which i really don't understand.
**chr1 24662379** . . . . PASS PROGRAM=breakdancer;SVTYPE=INS;SVLEN=-3686;**SVEND=24721723**
## Original output from breakdancer
chr 1 24662379 59+59- chr 1 24721723 59+59- INS -3686 99 37 /projects/grs-lab/RupeshWork/ResultsMP/180920-110831_JGBF_LeJ_GT17-02246-MP_AGTCAA_S51_L008/mapped_bowtie2/JGBF_LeJ_GT17-02246-MP_AGTCAA_S51_L008_realigned.bam|37 -nan NA
Can you please advice to overcome these problems? As while using SURVIVOR merge its not working due to conflict of END within the breakdancer vcf.
breakdancer to vcf
Dear devs,
Is there a script to convert native breakdancer output to vcf format?
Best wishes,
Fengyuan
bam2cfg error
root@xiaodoudou-ZHAOYANG-E52-80:/home/xiaodoudou# perl /home/xiaodoudou/breakdancer-1.4.5/perl/bam2cfg.pl /home/xiaodoudou/WGS/zdyl2.bam
[Mon Dec 10 15:19:53 2018 /home/xiaodoudou/breakdancer-1.4.5/perl/bam2cfg.pl] Processing bam: /home/xiaodoudou/WGS/zdyl2.bam
Can't exec "samtools": no such file or directory at /home/xiaodoudou/breakdancer-1.4.5/perl/bam2cfg.pl line 66.
unable to open /home/xiaodoudou/WGS/zdyl2.bam
i don't know what's wrong and how to solve this problem,please give me some suggestions
How can make breakdancer provide genotype information of an SV?
BreakDancer-1.1.2 Cpp runtime: taking too long ...
Hi,
I'm running BreakDancerMax (BreakDancer-1.1.2 Cpp) on 67 samples (67 bamfiles; 29 Autosomes each). Its running for 36 days (860 hrs, still running) on a linux cluster (1 core with 256 GB RAM) and finished around one third of the chromosomes .....
could you suggest how can I speed up the process?
However, BreakDancerMax took ~24 days and ~28 days on a sample of 18 and 27 animals (29 Autosomes) respectively.
I'll really appreciate your help
....Regards,
Mesbah
Output bed file positions
Hello!
Before i tell my problem, i must say that i realy appreciate your tool! I use it for a few days and now it's time to filter output data, so i wanted to manipulate bed file which was generated with -g option. I noticed that start position is always GREATER than end position:
track name=chr1_901835_DEL_260 description="BreakDancer chr1 901835 DEL 260" useScore=0
chr1 902045 901961 MG00HS05:416:C35D4ACXX:1:1305:3595:49116|fz7445-lib 600 1 902045 901961 255,0,0
chr1 901738 901636 MG00HS05:416:C35D4ACXX:1:1305:3595:49116|fz7445-lib 600 0 901738 901636 0,0,255
Can you explain, why?
I tried to load this file as a custom track in UCSC genome browser and got error (start > end). In documentation you mentioned that this bed file can be used in GBrowse (i don't want lo install it!) - does it mean that your bed files compatible only with that browser?
Second, can you explain why size field sometimes takes negative value? I think that size means nothing or CTX, but what about other sv types?
Thank you!
Error during make
Hello, I am trying to build breakdancer version 1.4.5 on ubuntu 16.0.4 and I am getting error during make step - log is attached.
I tried to update cmake and gcc but I am still getting same error.
The previous step cmake .. worked without errors. How can I make it work?
breakdancer_error.txt
Thanks
linking error: BamConfigEntry.cpp:(.text+0x1686): undefined reference to boost::re_detail::perl_matcher
I have a problem to compile BreakDancer. The error occurs when linking breakdancer-max. The error is as follows. Any idea how to fix this?
[ 71%] Linking CXX executable ../../../../bin/breakdancer-max
../../lib/io/libio.a(BamConfigEntry.cpp.o): In function `BamConfigEntry::translate_token(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
BamConfigEntry.cpp:(.text+0x1686): undefined reference to `boost::re_detail::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
../../lib/io/libio.a(BamConfigEntry.cpp.o): In function `boost::re_detail::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
BamConfigEntry.cpp:(.text._ZN5boost9re_detail12perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost9re_detail12perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x33d): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
../../lib/io/libio.a(BamConfigEntry.cpp.o): In function `boost::re_detail::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
BamConfigEntry.cpp:(.text._ZN5boost9re_detail12perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv[_ZN5boost9re_detail12perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv]+0x14c): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `void boost::archive::basic_xml_oarchive<boost::archive::xml_oarchive>::save_override<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const>(boost::serialization::nvp<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const> const&, int) [clone .isra.321] [clone .constprop.895]':
ConfigLoader.cpp:(.text+0xd5): undefined reference to `boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::save(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `void boost::archive::basic_xml_iarchive<boost::archive::xml_iarchive>::load_override<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(boost::serialization::nvp<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > const&, int) [clone .isra.159] [clone .constprop.913]':
ConfigLoader.cpp:(.text._ZN5boost7archive18basic_xml_iarchiveINS0_12xml_iarchiveEE13load_overrideINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKNS_13serialization3nvpIT_EEi.isra.159.constprop.913[_ZN7Options9serializeIN5boost7archive12xml_iarchiveEEEvRT_j]+0x1c): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `boost::archive::detail::iserializer<boost::archive::xml_iarchive, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const':
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveESt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_EE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveESt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_EE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x22): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveESt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_EE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveESt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_EE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x4c): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `boost::archive::detail::iserializer<boost::archive::xml_iarchive, boost::array<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, 11ul> >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const':
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveENS_5arrayINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEELm11EEEE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveENS_5arrayINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEELm11EEEE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x7e): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `boost::archive::detail::oserializer<boost::archive::xml_oarchive, boost::array<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, 11ul> >::save_object_data(boost::archive::detail::basic_oarchive&, void const*) const':
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11oserializerINS0_12xml_oarchiveENS_5arrayINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEELm11EEEE16save_object_dataERNS1_14basic_oarchiveEPKv[_ZNK5boost7archive6detail11oserializerINS0_12xml_oarchiveENS_5arrayINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEELm11EEEE16save_object_dataERNS1_14basic_oarchiveEPKv]+0xa5): undefined reference to `boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::save(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `boost::archive::detail::oserializer<boost::archive::xml_oarchive, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >::save_object_data(boost::archive::detail::basic_oarchive&, void const*) const':
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11oserializerINS0_12xml_oarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16save_object_dataERNS1_14basic_oarchiveEPKv[_ZNK5boost7archive6detail11oserializerINS0_12xml_oarchiveESt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EEE16save_object_dataERNS1_14basic_oarchiveEPKv]+0xc2): undefined reference to `boost::archive::xml_oarchive_impl<boost::archive::xml_oarchive>::save(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `boost::archive::detail::iserializer<boost::archive::xml_iarchive, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int> >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const':
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveESt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjEE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveESt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjEE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x29): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `boost::archive::detail::iserializer<boost::archive::xml_iarchive, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned long> >::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const':
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveESt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmEE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveESt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmEE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x29): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `boost::archive::detail::iserializer<boost::archive::xml_iarchive, LibraryConfig>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const':
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveE13LibraryConfigE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveE13LibraryConfigE16load_object_dataERNS1_14basic_iarchiveEPvj]+0xb2): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
ConfigLoader.cpp:(.text._ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveE13LibraryConfigE16load_object_dataERNS1_14basic_iarchiveEPvj[_ZNK5boost7archive6detail11iserializerINS0_12xml_iarchiveE13LibraryConfigE16load_object_dataERNS1_14basic_iarchiveEPvj]+0x117): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
../../lib/io/libio.a(ConfigLoader.cpp.o): In function `void Options::serialize<boost::archive::xml_iarchive>(boost::archive::xml_iarchive&, unsigned int)':
ConfigLoader.cpp:(.text._ZN7Options9serializeIN5boost7archive12xml_iarchiveEEEvRT_j[_ZN7Options9serializeIN5boost7archive12xml_iarchiveEEEvRT_j]+0x1e5): undefined reference to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'
../../lib/io/libio.a(ConfigLoader.cpp.o):ConfigLoader.cpp:(.text._ZN7Options9serializeIN5boost7archive12xml_iarchiveEEEvRT_j[_ZN7Options9serializeIN5boost7archive12xml_iarchiveEEEvRT_j]+0x2d8): more undefined references to `boost::archive::xml_iarchive_impl<boost::archive::xml_iarchive>::load(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' follow
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `int boost::re_detail::global_toi<int, boost::icu_regex_traits>(int const*&, int const*, int, boost::icu_regex_traits const&) [clone .isra.35]':
icu.cpp:(.text+0x6d): undefined reference to `u_digit_50'
icu.cpp:(.text+0x96): undefined reference to `u_digit_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::icu_regex_traits::lookup_classname(int const*, int const*) const':
icu.cpp:(.text+0x695): undefined reference to `u_tolower_50'
icu.cpp:(.text+0x69f): undefined reference to `u_isspace_50'
icu.cpp:(.text+0x6c0): undefined reference to `u_tolower_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::icu_regex_traits::isctype(int, unsigned long) const':
icu.cpp:(.text+0x888): undefined reference to `u_charType_50'
icu.cpp:(.text+0x90c): undefined reference to `u_isblank_50'
icu.cpp:(.text+0x924): undefined reference to `u_isspace_50'
icu.cpp:(.text+0x9a1): undefined reference to `u_digit_50'
icu.cpp:(.text+0x9df): undefined reference to `u_isspace_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::icu_regex_traits::lookup_collatename(int const*, int const*) const':
icu.cpp:(.text+0x17f6): undefined reference to `u_charFromName_50'
icu.cpp:(.text+0x1822): undefined reference to `u_charFromName_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::re_detail::perl_matcher<int const*, std::allocator<boost::sub_match<int const*> >, boost::icu_regex_traits>::match_literal()':
icu.cpp:(.text._ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE13match_literalEv[_ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE13match_literalEv]+0x66): undefined reference to `u_tolower_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::re_detail::perl_matcher<int const*, std::allocator<boost::sub_match<int const*> >, boost::icu_regex_traits>::unwind_short_set_repeat(bool)':
icu.cpp:(.text._ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE23unwind_short_set_repeatEb[_ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE23unwind_short_set_repeatEb]+0x10b): undefined reference to `u_tolower_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::re_detail::perl_matcher<int const*, std::allocator<boost::sub_match<int const*> >, boost::icu_regex_traits>::unwind_char_repeat(bool)':
icu.cpp:(.text._ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE18unwind_char_repeatEb[_ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE18unwind_char_repeatEb]+0xfb): undefined reference to `u_tolower_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::re_detail::perl_matcher<int const*, std::allocator<boost::sub_match<int const*> >, boost::icu_regex_traits>::match_set()':
icu.cpp:(.text._ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE9match_setEv[_ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE9match_setEv]+0x63): undefined reference to `u_tolower_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::re_detail::perl_matcher<int const*, std::allocator<boost::sub_match<int const*> >, boost::icu_regex_traits>::match_combining()':
icu.cpp:(.text._ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE15match_combiningEv[_ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE15match_combiningEv]+0x61): undefined reference to `u_tolower_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o):icu.cpp:(.text._ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE15match_combiningEv[_ZN5boost9re_detail12perl_matcherIPKiSaINS_9sub_matchIS3_EEENS_16icu_regex_traitsEE15match_combiningEv]+0x81): more undefined references to `u_tolower_50' follow
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `void boost::checked_delete<boost::re_detail::icu_regex_traits_implementation>(boost::re_detail::icu_regex_traits_implementation*)':
icu.cpp:(.text._ZN5boost14checked_deleteINS_9re_detail31icu_regex_traits_implementationEEEvPT_[_ZN5boost14checked_deleteINS_9re_detail31icu_regex_traits_implementationEEEvPT_]+0x36): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost14checked_deleteINS_9re_detail31icu_regex_traits_implementationEEEvPT_[_ZN5boost14checked_deleteINS_9re_detail31icu_regex_traits_implementationEEEvPT_]+0x70): undefined reference to `icu_50::Locale::~Locale()'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::detail::sp_counted_impl_p<boost::re_detail::icu_regex_traits_implementation>::dispose()':
icu.cpp:(.text._ZN5boost6detail17sp_counted_impl_pINS_9re_detail31icu_regex_traits_implementationEE7disposeEv[_ZN5boost6detail17sp_counted_impl_pINS_9re_detail31icu_regex_traits_implementationEE7disposeEv]+0x37): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost6detail17sp_counted_impl_pINS_9re_detail31icu_regex_traits_implementationEE7disposeEv[_ZN5boost6detail17sp_counted_impl_pINS_9re_detail31icu_regex_traits_implementationEE7disposeEv]+0x75): undefined reference to `icu_50::Locale::~Locale()'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::basic_regex<int, boost::icu_regex_traits>::imbue(icu_50::Locale)':
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x54): undefined reference to `icu_50::Locale::Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x71): undefined reference to `icu_50::Locale::Locale(icu_50::Locale const&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0xa1): undefined reference to `icu_50::Collator::createInstance(icu_50::Locale const&, UErrorCode&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0xf5): undefined reference to `icu_50::Collator::createInstance(icu_50::Locale const&, UErrorCode&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x187): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x287): undefined reference to `icu_50::Locale::Locale(icu_50::Locale const&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x29d): undefined reference to `icu_50::Locale::Locale(icu_50::Locale const&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x2ad): undefined reference to `icu_50::Locale::Locale(icu_50::Locale const&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x2ca): undefined reference to `icu_50::Locale::Locale(icu_50::Locale const&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x2fa): undefined reference to `icu_50::Collator::createInstance(icu_50::Locale const&, UErrorCode&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x34e): undefined reference to `icu_50::Collator::createInstance(icu_50::Locale const&, UErrorCode&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x43d): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x447): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x6f0): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x703): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x710): undefined reference to `icu_50::Locale::~Locale()'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o):icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE5imbueEN6icu_506LocaleE]+0x71a): more undefined references to `icu_50::Locale::~Locale()' follow
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::re_detail::basic_regex_creator<int, boost::icu_regex_traits>::create_startmap(boost::re_detail::re_syntax_base*, unsigned char*, unsigned int*, unsigned char)':
icu.cpp:(.text._ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE15create_startmapEPNS0_14re_syntax_baseEPhPjh[_ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE15create_startmapEPNS0_14re_syntax_baseEPhPjh]+0x5bc): undefined reference to `u_tolower_50'
icu.cpp:(.text._ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE15create_startmapEPNS0_14re_syntax_baseEPhPjh[_ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE15create_startmapEPNS0_14re_syntax_baseEPhPjh]+0x5d3): undefined reference to `u_tolower_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::re_detail::basic_regex_creator<int, boost::icu_regex_traits>::create_startmaps(boost::re_detail::re_syntax_base*)':
icu.cpp:(.text._ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE16create_startmapsEPNS0_14re_syntax_baseE[_ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE16create_startmapsEPNS0_14re_syntax_baseE]+0xff4): undefined reference to `u_tolower_50'
icu.cpp:(.text._ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE16create_startmapsEPNS0_14re_syntax_baseE[_ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE16create_startmapsEPNS0_14re_syntax_baseE]+0x1035): undefined reference to `u_tolower_50'
icu.cpp:(.text._ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE16create_startmapsEPNS0_14re_syntax_baseE[_ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE16create_startmapsEPNS0_14re_syntax_baseE]+0x1065): undefined reference to `u_tolower_50'
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o):icu.cpp:(.text._ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE16create_startmapsEPNS0_14re_syntax_baseE[_ZN5boost9re_detail19basic_regex_creatorIiNS_16icu_regex_traitsEE16create_startmapsEPNS0_14re_syntax_baseE]+0x1084): more undefined references to `u_tolower_50' follow
../../../../vendor/boost/boost/lib/libboost_regex.a(icu.o): In function `boost::basic_regex<int, boost::icu_regex_traits>::do_assign(int const*, int const*, unsigned int)':
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j]+0x4c7): undefined reference to `icu_50::Locale::Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j]+0x4e4): undefined reference to `icu_50::Locale::Locale(icu_50::Locale const&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j]+0x514): undefined reference to `icu_50::Collator::createInstance(icu_50::Locale const&, UErrorCode&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j]+0x568): undefined reference to `icu_50::Collator::createInstance(icu_50::Locale const&, UErrorCode&)'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j]+0x605): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j]+0x84e): undefined reference to `icu_50::Locale::~Locale()'
icu.cpp:(.text._ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j[_ZN5boost11basic_regexIiNS_16icu_regex_traitsEE9do_assignEPKiS4_j]+0x863): undefined reference to `icu_50::Locale::~Locale()'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/breakdancer-max] Error 1
make[1]: *** [build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir/all] Error 2
make: *** [all] Error 2
Update: I can compile it on my Mac (with Clang), so it's probably a compiler or OS issue. I tried different versions of gcc, and clang, but none of them work. So it's probably he OS issue. The command uname -r gives me 3.10.0-514.26.2.el7.x86_64. I guess that it's redhat.
I'm trying to compile it in an OpenAFS environment. Should this be the trouble?
multiple bam SV detection
Hello,
I have a problem with breakdancer. I try to call structural variants from several bams at the same time but it doesn't work.
First I create the config file :
~/Soft/breakdancer/breakdancer/perl/bam2cfg.pl bam1.bam bam2.bam ... last_bam.bam > config_file.cfg
(the first two lines of my config file :
readgroup:group01 platform:illumina map:bam1.bam readlen:142.77 lib:lib1 num:9999 lower:17.79 upper:991.23 mean:486.76 std:121.61 SWnormality:-21.57 exe:samtools view
readgroup:group12 platform:illumina map:bam2.bam readlen:143.80 lib:lib1 num:9997 lower:57.39 upper:935.82 mean:458.82 std:109.60 SWnormality:-28.19 exe:samtools view
)
and then I use breakdancer-max :
~/Soft/breakdancer/breakdancer/build/bin/breakdancer-max config_file.cfg
(I get this kinds of warnings: "WARNING: at line 2, library lib1 overwritten!", one for each line of the config file)
The problem is that in my ouput, only the structural variants of the last bam of the config list is present.
For example, one line of the output :
chr_1 147015 467+6- chr_1 150331 4+300- DEL 3448 99 257 last_bam.bam|257 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 30.16
And it is the same for each line.
Would you have any idea why I have this kind of results, should I use different parameters or maybe I made a mistake creating the config file?
Thank you in advance for your help.
How to manually prepare a configuration file
Hi, I'm analyzing a dataset with BreakdancerMax using a manual configuration file. I've filled in all the required fields, but Breakdancer claims that there are no BAMs in the configuration file. My config file is as follows (I'm analyzing one BAM at a time):
map:/mnt/data/input/gs/simons_bams/bams/LP6005442-DNA_H01.srt.aln.bam mean:578.123519011319 std:145.554308908044 readlen:338.305181282826 sample:LP6005442-DNA_H01.srt.aln.bam exe:samtools view platform:illumina readgroup:LP6005442-DNA_H01
Drastic differences between identical breakdancer runs
We (unintentionally) ran breakdancer twice on several sample tumor-normal pair using the same breakdancer version. The first run was 6 months ago and the second run was one month ago. We noticed that the results differ drastically despite the fact that the config files generated by bam2cfg are identical (except the paths to the bam files). Whereas run 1 has several dozen somatic events, run 2 has no somatic events. In the header parameters we noticed differences in for example seqcov and phycov. How are these values determined? How can we explain these drastic differences? I’ve highlighted similarities between run1 and 2 in yellow and differences in cyan.
Run 1:
Software: 1.4.5 (commit 251f983)
Command: /scratch/genomic_med/vapor/flowr_bdancer/breakdancer_nautilus/breakdancer/bin/breakdancer-max -o 10 -h 1d77eb0d-c0a9-4681-9227-b3738cbf265c__0a2475da-42bb-4adb-b86c-5492511e09f1/conf.file
Library Statistics:
/scratch/bcb/fpbarthel/TCGA/WGS/GBM/0a2475da-42bb-4adb-b86c-5492511e09f1/G26378.TCGA-02-2483-10A-01D-1494-08.1.bam mean:311.71 std:90.79 uppercutoff:572.48 lowercutoff:0 readlen:101 library:Sage-127186 reflen:135464726 seqcov:31.5374 phycov:48.6659 1:7262 2:27082 4:1178829 8:6890 32:338595
/scratch/bcb/fpbarthel/TCGA/WGS/GBM/0a2475da-42bb-4adb-b86c-5492511e09f1/G26378.TCGA-02-2483-10A-01D-1494-08.1.bam mean:335.15 std:109.83 uppercutoff:642.46 lowercutoff:0 readlen:101 library:Sage-127238 reflen:135464726 seqcov:24.7833 phycov:41.1194 1:2470 2:14956 4:525772 8:2352 32:123892
/scratch/bcb/fpbarthel/TCGA/WGS/GBM/1d77eb0d-c0a9-4681-9227-b3738cbf265c/G26378.TCGA-02-2483-01A-01D-1494-08.1.bam mean:310.45 std:122.05 uppercutoff:745.32 lowercutoff:0 readlen:101 library:Sage-127239 reflen:135464726 seqcov:9.45366 phycov:14.5291 1:3438 2:4854 4:238007 8:3072 32:152646
Run 2:
Software: 1.4.5 (commit 251f983)
Command: breakdancer-max -o 10 -h /scratch/bcb/fpbarthel/WGS_GBM_TP_NB_1_of_3/breakdancer/bd-02-2483.cfg
Library Statistics:
/scratch/bcb/fpbarthel/WGS_GBM_TP_NB_1_of_3/TCGA-02-2483-10/G26378.TCGA-02-2483-10A-01D-1494-08.1.bam mean:311.71 std:90.79 uppercutoff:572.48 lowercutoff:0 readlen:101 library:Sage-127186 reflen:135464726 seqcov:11.0158 phycov:16.9987 1:990 2:7492 4:204802 8:1000 32:46965
/scratch/bcb/fpbarthel/WGS_GBM_TP_NB_1_of_3/TCGA-02-2483-10/G26378.TCGA-02-2483-10A-01D-1494-08.1.bam mean:335.15 std:109.83 uppercutoff:642.46 lowercutoff:0 readlen:101 library:Sage-127238 reflen:135464726 seqcov:24.7833 phycov:41.1194 1:2470 2:14956 4:525772 8:2352 32:123892
/scratch/bcb/fpbarthel/WGS_GBM_TP_NB_1_of_3/TCGA-02-2483-01/G26378.TCGA-02-2483-01A-01D-1494-08.1.bam mean:310.45 std:122.05 uppercutoff:745.32 lowercutoff:0 readlen:101 library:Sage-127239 reflen:135464726 seqcov:29.9752 phycov:46.0684 1:9710 2:13554 4:1212034 8:8962 32:444276
bam2cfg should provide feedback to the user about potential BAM problems
These should (minimally) include:
- A lack of normal readpairs in the BAM files (instead of simply producing no output)
- Readgroup collisions across BAM files.
- Library name collisions across BAM files.
In each case it should suggest a solution.
error in building "samtools-lib-build"
Hi, I have followed the INSTALL document on , but got some errors in building the samtools-lib-build in the make step.
First, I thought cmake returned no error.
[zuoxy@login01 build]$ cmake .. -DCMAKE_INSTALL_PREFIX=/share/apps/work/breakdancer/local
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Score floating point type: double
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
No CMAKE_BUILD_TYPE specified, defaulting to release
-- Performing Test CXX11_FLAG0
-- Performing Test CXX11_FLAG0 - Failed
-- Performing Test CXX11_FLAG1
-- Performing Test CXX11_FLAG1 - Success
-- C++11 support enabled via -std=c++0x
-- Performing Test CXX11_STDLIB_FLAG0
-- Performing Test CXX11_STDLIB_FLAG0 - Success
-- Sufficient C++11 library support found with flag ' '
-- Found ZLIB: /usr/local/lib/libz.so (found version "1.2.8")
-- Configuring done
-- Generating done
-- Build files have been written to: /share/apps/work/breakdancer/build
But the make failed:
[zuoxy@login01 build]$ make
Scanning dependencies of target boost-libs
[ 1%] Creating directories for 'boost-libs'
[ 3%] Performing download step (verify and extract) for 'boost-libs'
-- verifying file...
file='/share/apps/work/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
src='/share/apps/work/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
dst='/share/apps/work/breakdancer/build/vendor/boost/boost-src'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 4%] No patch step for 'boost-libs'
[ 6%] No update step for 'boost-libs'
[ 7%] Performing configure step for 'boost-libs'
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Detecting Python version... 2.7
Detecting Python root... /share/apps/python/2.7.10
Unicode/ICU support for Boost.Regex?... /usr
Generating Boost.Build configuration in project-config.jam...
Bootstrapping is done. To build, run:
./b2
To adjust configuration, edit 'project-config.jam'.
Further information:
- Command line help:
./b2 --help
- Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html
- Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html
[ 9%] Performing build step for 'boost-libs'
[ 10%] No install step for 'boost-libs'
[ 12%] Completed 'boost-libs'
[ 12%] Built target boost-libs
Scanning dependencies of target samtools-lib
[ 14%] Creating directories for 'samtools-lib'
[ 15%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
file='/share/apps/work/breakdancer/vendor/samtools-0.1.19.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
src='/share/apps/work/breakdancer/vendor/samtools-0.1.19.tar.gz'
dst='/share/apps/work/breakdancer/build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 17%] No patch step for 'samtools-lib'
[ 18%] No update step for 'samtools-lib'
[ 20%] Performing configure step for 'samtools-lib'
Building samtools, build log at /share/apps/work/breakdancer/build/vendor/samtools/build.log
[ 21%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Error 2
make: *** [all] Error 2
Thanks for any comments~~
Bests,
Hiuyu
Documentation should include information on what the flags mean out of bam2cfg
See: https://www.biostars.org/p/150224/
0 - Marked as duplicate or a single-ended read
1 - The aligner doesn't report the read as properly paired and both the read and its mate are mapped to the plus strand (e.g. --> -->)
2 - The aligner doesn't report the read as properly paired, but the orientation is as expected (e.g. --> <--)
4 - The aligner doesn't report the read as properly paired and the larger coordinate read is not on the negative strand (e.g. <-- -->)
8 - The aligner doesn't report the read as properly paired and both the read and its mate are mapped to the minus strand (e.g. <-- <--)
18 - The aligner reports the read as properly paired and the leftmost read is on the plus strand (e.g. --> <--)
20 - The aligner reports the read as properly paired and the leftmost read is on the minus strand (e.g. <-- -->)
64 - read's mate is unmapped
192 - read is unmapped
problems with bam2cfg
Hi, I'm facing problems to generate the cfgfile with bam2cfg option from breakdancer.
First I thought it was just the RG header that was wrong in my bam file, but now I already fixed it and still, it is not generating. Before it was creating an empty cfgfile, as I saw in other issues, but now it's not creating a cfg file at all.
Does anybody know if this bam2cfg is still working? Because I don't see many pieces of information about it.
And when I launch the command, it finishes saying to me that the job was successfully completed (?)
Here follows my command line and my output file:
#!/usr/bin/env
module add /breakdancer/1.4.5
bam2cfg.pl -g -h sample.sorted.bam > sample.cfg
OUTPUT:
SBD_KRB5CCNAME_VAL=
LSF_VERSION=27
LOGNAME=adibatti
LSB_UNIXGROUP_INT=cig_reym
LSB_BATCH_NEW_SESSION=y
HOSTTYPE=X86_64
LSB_BATCH_JID=992776
LSB_JOBRES_PID=25148
LSB_JOBID=992776
LSB_JOBINDEX=0
LSB_JOBFILENAME=/home/adibatti/.lsbatch/1534151815.992776
LSB_CHKFILENAME=/home/adibatti/.lsbatch/1534151815.992776
LSB_TRAPSIGS=trap # 15 10 12 2
LSB_HOSTS=cpt133 cpt133
LSB_MCPU_HOSTS=cpt133 2
LSB_QUEUE=normal
LSB_JOBNAME=cfgfile
LSFUSER=adibatti
USER=adibatti
LSB_JOB_EXECUSER=adibatti
LSB_EXIT_PRE_ABORT=99
LS_EXEC_T=START
BSUB_BLOCK_EXEC_HOST=
PATH=/bin:/usr/bin/:/usr/mbin:/local/bin:/usr/local:/usr/ucb
LS_JOBPID=25148
LS_SUBCWD=/scratch/cluster/monthly/adibatti/WGS
LSB_SUB_HOST=frt
LSB_SUB_USER=adibatti
LSB_SUB_RES_REQ= rusage[mem=1000] span[hosts=1]
LSB_MAX_NUM_PROCESSORS=2
LSB_EXEC_HOSTTYPE=X86_64
LSF_ENVDIR=/mnt/common/lsf/conf
LSF_EGO_ENVDIR=/mnt/common/lsf/conf/ego/prdclst/kernel
LSF_SERVERDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/etc
LSF_BINDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/bin
LSF_LOGDIR=/mnt/common/lsf/log
LSF_LIBDIR=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
LD_LIBRARY_PATH=/mnt/common/lsf/9.1/linux2.6-glibc2.3-x86_64/lib
LSB_JOBEXIT_STAT=0
LSB_EXEC_CLUSTER=prdclst
LSB_EEXEC_REAL_UID=
LSB_EEXEC_REAL_GID=
LSB_EFFECTIVE_RSRCREQ=select[ (((type == any)&&(tmp>1024)))] order[r1m:ut] rusage[mem=1000.00] span[hosts=1] same[model]
LSB_DJOB_NUMPROC=2
LSF_LIC_FEATURES_NEEDED=543682721
LSF_CGROUP_TOPDIR_KEY=prdclst
LSF_JOB_TIMESTAMP_VALUE=1534151816
PWD=/scratch/cluster/monthly/adibatti/WGS
HOME=/home/adibatti
LSF_JOB_TMPDIR=/tmp/992776.tmpdir
LSB_DJOB_HOSTFILE=/home/adibatti/.lsbatch/1534151815.992776.hostfile
SHELL=/bin/env
Thank you!
Sourceforge page hosting old versions?
Hi all,
I didn't know about this much-improved version of Breakdancer because most Google hits lead to [http://breakdancer.sourceforge.net/], which hosts a version from 5 years ago. The credits seem to indicate it belongs to the same institution as improved version in this repository -- is it possible to update that SourceForge page and make the situation clearer for others?
Empty .cfg
I am using paired end Illumina sequencing data that has been mapped using bwa. I have tried sorting and indexing the bam files with both Samtools and Picard but repeatedly get an empty .cfg file. There is no specific error just:
[Wed Mar 21 11:26:14 2018 /lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl] Processing bam: EMS9.Equuscab2_nucl_picard_sorted.bam
[Wed Mar 21 11:26:14 2018 /lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl] Closing BAM file
[Wed Mar 21 11:26:14 2018 /lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl] Send TERM signal for 7142
[Wed Mar 21 11:26:16 2018 /lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl] samtools pid process 7142 is still there...
[Wed Mar 21 11:26:16 2018 lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl] invoking kill -9 on 7142 ...
[Wed Mar 21 11:26:16 2018 /lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl] Closing samtools process : 7142
Has anyone come up with a solution to this that doesn't involve manually making a config file for every genome?
Thanks.
No error messages when a job doesn't finish properly
Hello Author,
It might be only a cluster here. When I ran a job using 1 CPU, the result file doesn't show the full result because no lists appear on ChrY. Compared to a run with 4 CPUs, I saw a list on ChrY in a different pair of tumor and blood.
Should you include the error message in case of insufficient memory? It is difficult to distinguish between complete and incomplete jobs at a glance.
James
How to get the orientation of INV and translocations?
One of my downstream analyses requires to know the orientation of the breakpoints. For example, for INV, it needs to know whether it is head-to-head ("++") or tail-to-tail ("--"). And there can 4 possibilities for ITX/CTX: +-, ++, -+, and --. Can I get this information from BreakDancer results? There are columns named "Orientation1" and "Orientation2" which the manual says are the number of reads mapped on + and - strands. Is it something that can be used to infer the SV orientation described above?
Different chromosomes labeled as ITX
A few ITX in the breakdancer outputs have different chromosomes, e.g.
10 52455306 1+2- 11 52784873 13+12- ITX -173 44 6 1 0 1 0 1 00 0 2 1 0
Should I remove them or rename them as CTX?
Thanks,
Questions about the mechanism of breakdancer-max
Hi all,
I use breakdancer-max to run chr20 of sample NA12878. After I read the paper, I was confused about one sentence, which said "The algorithm searches for genomic regions that anchor substantially more anomalous read pairs(ARPs) than expected on average." And before search, each read pair is assigned a type defined in the paper. Thus, we can say all aligned read pairs are labeled.
My question is, how to define the genomic regions that are used for search? Is it like sliding window based brute force search (obviously not a brute force, just to make my question clear) or something else more efficient? And we can see there is an option -s specifies the minimum length of the region when we call breakdancer-max.
Thanks all and looking forward to discuss.
Compiling breakdancer: ` undefined reference to `std::__detail::_List_node_base::_M_hook`
Hi,
I tried to compile breakdancer, But I recevied the following C++ error: std::__detail::_List_node_base::_M_hook
here is my trace:
rm -rf breakdancer
git clone --recursive https://github.com/genome/breakdancer.git
Initialized empty Git repository in /commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/.git/
remote: Counting objects: 4480, done.
remote: Total 4480 (delta 0), reused 0 (delta 0), pack-reused 4480
Receiving objects: 100% (4480/4480), 10.49 MiB | 2.35 MiB/s, done.
Resolving deltas: 100% (2120/2120), done.
(cd breakdancer && mkdir build && cd build && cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv && make deps && make)
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
Score floating point type: double
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXX11_FLAG0
-- Performing Test CXX11_FLAG0 - Failed
-- Performing Test CXX11_FLAG1
-- Performing Test CXX11_FLAG1 - Success
-- C++11 support enabled via -std=c++0x
-- Performing Test CXX11_STDLIB_FLAG0
-- Performing Test CXX11_STDLIB_FLAG0 - Success
-- Sufficient C++11 library support found with flag ' '
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Configuring done
-- Generating done
-- Build files have been written to: /commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build
make[1]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make[2]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make[3]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make[4]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
Scanning dependencies of target boost-libs
make[4]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make[4]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
[ 6%] Creating directories for 'boost-libs'
[ 12%] Performing download step (verify and extract) for 'boost-libs'
-- verifying file...
file='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
src='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
dst='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build/vendor/boost/boost-src'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 18%] No patch step for 'boost-libs'
[ 25%] No update step for 'boost-libs'
[ 31%] Performing configure step for 'boost-libs'
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Detecting Python version... 2.6
Detecting Python root... /usr
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...
Bootstrapping is done. To build, run:
./b2
To adjust configuration, edit 'project-config.jam'.
Further information:
- Command line help:
./b2 --help
- Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html
- Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html
[ 37%] Performing build step for 'boost-libs'
[ 43%] No install step for 'boost-libs'
[ 50%] Completed 'boost-libs'
make[4]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
[ 50%] Built target boost-libs
make[4]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
Scanning dependencies of target samtools-lib
make[4]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make[4]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
[ 56%] Creating directories for 'samtools-lib'
[ 62%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
file='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/vendor/samtools-0.1.19.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
src='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/vendor/samtools-0.1.19.tar.gz'
dst='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 68%] No patch step for 'samtools-lib'
[ 75%] No update step for 'samtools-lib'
[ 81%] Performing configure step for 'samtools-lib'
Building samtools, build log at /commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build/vendor/samtools/build.log
[ 87%] Performing build step for 'samtools-lib'
[ 93%] No install step for 'samtools-lib'
[100%] Completed 'samtools-lib'
make[4]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
[100%] Built target samtools-lib
make[4]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
Scanning dependencies of target deps
make[4]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
[100%] Built target deps
make[3]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make[2]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
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[ 14%] Built target boost-libs
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[ 28%] Built target samtools-lib
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[ 28%] Built target deps
make[3]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
Scanning dependencies of target gtest160
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[ 29%] Creating directories for 'gtest160'
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-- verifying file...
file='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build-common/vendor/gtest-1.6.0.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
src='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build-common/vendor/gtest-1.6.0.tar.gz'
dst='/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build/vendor/src/gtest160'
-- extracting... [tar xfz]
-- extracting... [analysis]
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-- The CXX compiler identification is GNU 4.8.2
-- The C compiler identification is GNU 4.8.2
-- Check for working CXX compiler: /cm/shared/apps/gcc/4.8.2/bin/c++
-- Check for working CXX compiler: /cm/shared/apps/gcc/4.8.2/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working C compiler: /cm/shared/apps/gcc/4.8.2/bin/gcc
-- Check for working C compiler: /cm/shared/apps/gcc/4.8.2/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Found PythonInterp: /usr/bin/python (found version "2.6.6")
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build/vendor/gtest160-build
[ 38%] Performing build step for 'gtest160'
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Scanning dependencies of target gtest
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[ 50%] Building CXX object CMakeFiles/gtest.dir/src/gtest-all.cc.o
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[ 50%] Built target gtest
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Scanning dependencies of target gtest_main
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[100%] Building CXX object CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
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Scanning dependencies of target breakdancer
make[3]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
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[ 43%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BedWriter.cpp.o
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[ 49%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/SvBuilder.cpp.o
Linking CXX static library libbreakdancer.a
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Scanning dependencies of target io
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make[3]: Entering directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
Scanning dependencies of target breakdancer-max
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[ 73%] Building CXX object build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir/BreakDancerMax.cpp.o
Linking CXX executable ../../../../bin/breakdancer-max
../../../../vendor/boost/boost/lib/libboost_serialization.a(shared_ptr_helper.o): In function `boost::archive::detail::shared_ptr_helper::append(boost_132::shared_ptr<void const> const&)':
shared_ptr_helper.cpp:(.text+0x6d): undefined reference to `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o): In function `boost::exception_detail::error_info_injector<std::invalid_argument>::~error_info_injector()':
instances.cpp:(.text._ZN5boost16exception_detail19error_info_injectorISt16invalid_argumentED2Ev[_ZN5boost16exception_detail19error_info_injectorISt16invalid_argumentED5Ev]+0x33): undefined reference to `std::invalid_argument::~invalid_argument()'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o): In function `boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >::~clone_impl()':
instances.cpp:(.text._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorISt16invalid_argumentEEED1Ev[boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >::~clone_impl()]+0x3a): undefined reference to `std::invalid_argument::~invalid_argument()'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o): In function `boost::exception_detail::error_info_injector<std::invalid_argument>::~error_info_injector()':
instances.cpp:(.text._ZN5boost16exception_detail19error_info_injectorISt16invalid_argumentED0Ev[boost::exception_detail::error_info_injector<std::invalid_argument>::~error_info_injector()]+0x32): undefined reference to `std::invalid_argument::~invalid_argument()'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o): In function `boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >::~clone_impl()':
instances.cpp:(.text._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorISt16invalid_argumentEEED0Ev[boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >::~clone_impl()]+0x3a): undefined reference to `std::invalid_argument::~invalid_argument()'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o): In function `boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >::rethrow() const':
instances.cpp:(.text._ZNK5boost16exception_detail10clone_implINS0_19error_info_injectorISt16invalid_argumentEEE7rethrowEv[boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >::rethrow() const]+0xbd): undefined reference to `std::invalid_argument::~invalid_argument()'
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o):instances.cpp:(.text._ZNK5boost16exception_detail10clone_implINS0_19error_info_injectorISt16invalid_argumentEEE5cloneEv[boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<std::invalid_argument> >::clone() const]+0x179): more undefined references to `std::invalid_argument::~invalid_argument()' follow
../../../../vendor/boost/boost/lib/libboost_regex.a(instances.o): In function `boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long)':
instances.cpp:(.text._ZN5boost12object_cacheINS_9re_detail21cpp_regex_traits_baseIcEENS1_31cpp_regex_traits_implementationIcEEE6do_getERKS3_m[boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long)]+0xda): undefined reference to `std::__detail::_List_node_base::_M_transfer(std::__detail::_List_node_base*, std::__detail::_List_node_base*)'
instances.cpp:(.text._ZN5boost12object_cacheINS_9re_detail21cpp_regex_traits_baseIcEENS1_31cpp_regex_traits_implementationIcEEE6do_getERKS3_m[boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long)]+0x105): undefined reference to `std::__detail::_List_node_base::_M_transfer(std::__detail::_List_node_base*, std::__detail::_List_node_base*)'
instances.cpp:(.text._ZN5boost12object_cacheINS_9re_detail21cpp_regex_traits_baseIcEENS1_31cpp_regex_traits_implementationIcEEE6do_getERKS3_m[boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long)]+0x332): undefined reference to `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)'
instances.cpp:(.text._ZN5boost12object_cacheINS_9re_detail21cpp_regex_traits_baseIcEENS1_31cpp_regex_traits_implementationIcEEE6do_getERKS3_m[boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>, boost::re_detail::cpp_regex_traits_implementation<char> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned long)]+0x682): undefined reference to `std::__detail::_List_node_base::_M_unhook()'
collect2: ld returned 1 exit status
make[3]: *** [bin/breakdancer-max] Error 1
make[3]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make[2]: *** [build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir/all] Error 2
make[2]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/commun/data/users/lindenb/notebook/2016/20160321.wgs_snv/breakdancer/build'
make: *** [all] Error 2
what have I done wrong, please ?
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