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View Code? Open in Web Editor NEWThe LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
License: Other
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yuanbaowen521 jinfengchen ustcahwry cooketho eburgueno cyang-2014 abelew wyim-pgl pforai gregor-mendel-institute plantarum lijingjing1 flypythons dayedepps simonwaldherr guoshuai1314 samll-rookie tw7649116 guluzi xuzhichao830 sisyyuan stephanholgerd libcce wangzhennan14 zhaokai2014 antoniogps linguoliang heziqing gagnon-lab novapyth ziquanzhao moorezhulachesis's Issues
Configure error.
Dear LACHESIS,
Hello,
I tried compile recent version of LACHESIS-9b16824.
with ./configure , ./configure --without-samtools and ./configure --with-samtools=PATH.
I failed with "checking for sam_open in -lbam... no"
previous message "checking if samtools is wanted... no
checking sam.h usability... yes
checking sam.h presence... yes
checking for sam.h... yes"
The message show that samtools sam.h is fine. but I don't know why the LACHESIS can not find the libbam.a
I also copied libbam.a to /usr/local/lib/ and all the headers to /usr/local/include/bam
Of course samtools located in path.
Could you please check this error?
I think the autoconf has some problem.
Regards,
Won
How to get chromosome bins
Hi,
Running LACHESIS in the below way did not provide the expected chromosome numbers because I got 115 groups.
/usr/local/bin/Lachesis lachesis.ini
/LACHESIS/src/bin/CreateScaffoldedFasta.pl QMg_NbQ4P_RN.fasta lachesis
cat lachesis/REPORT.txt provided:
SPECIES = plant
OUTPUT_DIR = lachesis
DRAFT_ASSEMBLY_FASTA = QMg_NbQ4P_RN.fasta
SAM_DIR = /QRISdata/Q0231/lachesis
SAM_FILES = N_Ben_HiC2_rep1.bam N_Ben_HiC4_rep1.bam
RE_SITE_SEQ = GATC
USE_REFERENCE = 0
SIM_BIN_SIZE = 0
REF_ASSEMBLY_FASTA = test_case/hg19/Homo_sapiens_assembly19.fasta
BLAST_FILE_HEAD = test_case/draft_assembly/assembly
DO_CLUSTERING = 1
DO_ORDERING = 1
DO_REPORTING = 1
OVERWRITE_GLM = 0
OVERWRITE_CLMS = 0
CLUSTER_N = 19
CLUSTER_CONTIGS_WITH_CENS = -1
CLUSTER_MIN_RE_SITES = 25
CLUSTER_MAX_LINK_DENSITY = 2
CLUSTER_NONINFORMATIVE_RATIO = 3
CLUSTER_DRAW_HEATMAP = 1
CLUSTER_DRAW_DOTPLOT = 1
ORDER_MIN_N_RES_IN_TRUNK = 15
ORDER_MIN_N_RES_IN_SHREDS = 15
ORDER_DRAW_DOTPLOTS = 1
REPORT_EXCLUDED_GROUPS = -1
REPORT_QUALITY_FILTER = 1
REPORT_DRAW_HEATMAP = 1
ReportChart!
Info about input assembly:
DE NOVO ASSEMBLY, with no reference genome (less validation available)
Species: benth
N contigs: 1512 Total length: 2774612304 N50: 4284592
N clusters (derived): 115
N non-singleton clusters: 22
N orderings found: 115
############################
# #
# CLUSTERING METRICS #
# #
############################
Number of contigs in clusters: 1495 (98.88% of all contigs)
Length of contigs in clusters: 2773873324 (99.97% of all sequence length)
+----------+-----------+-------------+
| CLUSTER | NUMBER OF | LENGTH OF |
| NUMBER | CONTIGS | CONTIGS |
+----------+-----------+-------------+
| 0 | 114 | 285238080 |
| 1 | 97 | 232421157 |
| 2 | 117 | 197340285 |
| 3 | 84 | 187516710 |
| 4 | 80 | 179402476 |
| 5 | 89 | 165376221 |
| 6 | 65 | 157315626 |
| 7 | 80 | 151833938 |
| 8 | 80 | 148910574 |
| 9 | 79 | 140080377 |
| 10 | 88 | 137055451 |
| 11 | 65 | 135577112 |
| 12 | 60 | 133912412 |
| 13 | 70 | 117818930 |
| 14 | 65 | 116531146 |
| 15 | 63 | 102263122 |
| 16 | 28 | 93089711 |
| 17 | 48 | 87456991 |
| 18 | 15 | 964930 |
| 19 | 6 | 294111 |
| 20 | 7 | 283069 |
| 21 | 1 | 239832 |
| 22 | 1 | 145336 |
| 23 | 1 | 104136 |
| 24 | 1 | 101472 |
| 25 | 1 | 94178 |
| 26 | 1 | 77308 |
| 27 | 1 | 67648 |
| 28 | 1 | 67087 |
| 29 | 1 | 64664 |
| 30 | 1 | 59313 |
| 31 | 1 | 59081 |
| 32 | 1 | 57897 |
| 33 | 1 | 53810 |
| 34 | 1 | 50546 |
| 35 | 1 | 49583 |
| 36 | 2 | 48675 |
| 37 | 1 | 48060 |
| 38 | 1 | 44526 |
| 39 | 1 | 39160 |
| 40 | 1 | 37315 |
| 41 | 1 | 35095 |
| 42 | 1 | 32532 |
| 43 | 1 | 29921 |
| 44 | 1 | 28202 |
| 45 | 1 | 26998 |
| 46 | 1 | 26886 |
| 47 | 1 | 26813 |
| 48 | 1 | 26698 |
| 49 | 1 | 26687 |
| 50 | 1 | 26517 |
| 51 | 1 | 26501 |
| 52 | 1 | 26414 |
| 53 | 1 | 26363 |
| 54 | 1 | 26348 |
| 55 | 1 | 26272 |
| 56 | 1 | 26153 |
| 57 | 1 | 26101 |
| 58 | 1 | 26099 |
| 59 | 1 | 26012 |
| 60 | 1 | 25913 |
| 61 | 1 | 25836 |
| 62 | 1 | 25798 |
| 63 | 1 | 25728 |
| 64 | 1 | 25694 |
| 65 | 1 | 25584 |
| 66 | 1 | 25530 |
| 67 | 1 | 25343 |
| 68 | 1 | 25268 |
| 69 | 1 | 25212 |
| 70 | 1 | 25077 |
| 71 | 1 | 24936 |
| 72 | 1 | 24853 |
| 73 | 1 | 24700 |
| 74 | 1 | 24228 |
| 75 | 1 | 23985 |
| 76 | 1 | 23909 |
| 77 | 1 | 23321 |
| 79 | 1 | 23222 |
| 80 | 1 | 23141 |
| 81 | 1 | 23114 |
| 82 | 1 | 22951 |
| 83 | 1 | 22856 |
| 84 | 1 | 22373 |
| 85 | 1 | 22328 |
| 86 | 1 | 22169 |
| 87 | 1 | 20926 |
| 88 | 1 | 20183 |
| 89 | 1 | 19684 |
| 90 | 1 | 19675 |
| 91 | 1 | 19626 |
| 92 | 1 | 19153 |
| 93 | 1 | 18885 |
| 94 | 1 | 18838 |
| 95 | 1 | 18639 |
| 96 | 1 | 18249 |
| 97 | 1 | 18248 |
| 98 | 1 | 18233 |
| 99 | 1 | 18201 |
| 100 | 1 | 18200 |
| 101 | 1 | 18180 |
| 102 | 1 | 18142 |
| 103 | 1 | 17982 |
| 104 | 1 | 17787 |
| 105 | 1 | 17473 |
| 106 | 1 | 17401 |
| 107 | 1 | 17265 |
| 108 | 1 | 16586 |
| 109 | 1 | 16091 |
| 110 | 1 | 16056 |
| 111 | 1 | 15989 |
| 112 | 1 | 15859 |
| 113 | 1 | 15540 |
| 114 | 1 | 15213 |
+----------+-----------+-------------+
| TOTAL | 1495 | 2773873324 |
+----------+-----------+-------------+
############################
# #
# ORDERING METRICS #
# #
############################
Number of contigs in orderings: 0 (0% of all contigs in clusters, 0% of all contigs)
Length of contigs in orderings: 0 (0% of all length in clusters, 0% of all sequence length)
Number of contigs in trunks: 0 (-nan% of contigs in orderings)
Length of contigs in trunks: 0 (-nan% of length in orderings)
Fraction of contigs in orderings with high orientation quality: 0 (-nan%), with length 0 (-nan%)
Fraction of contigs in trunks with high orientation quality: 0 (-nan%), with length 0 (-nan%)
How am I able to the expected 19 chromosomes?
Thank you in advance,
Michal
blastalignment
Hi,
I have used a reference genome for assembling. For the Draft assembly fasta file is to big to mapping to the reference genome. So for some fasta sequence I only choose the first 1,000,000bp for mapping. I have used the parameter "blastn -outfmt 7". And the names of the blast result file are in right format.
When I run lachesis, it shows the following err massege:
Lachesis: TextFileParsers.cc:488: void ParseBlastAlignmentFiles(const std::vector<std::basic_string >&, const std::vector&, const std::vector<std::basic_string >&, const string&): Assertion `stop_on_Q <= query_lengths[query_ID]' failed.
/opt/gridview//pbs/dispatcher/mom_priv/jobs/714734.admin.SC: line 1: 30684
I don't know why it shows this. And how can I fix it.
looking forward for help
error
/public/msq/WHF4-1/script/PreprocessSAMs.pl MI.sam ../Mi_Wuhan.fasta
Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/WHF4-1/script/make_bed_around_RE_site.pl ../Mi_Wuhan.fasta GATC 500
Can't exec "/public/msq/WHF4-1/script/make_bed_around_RE_site.pl": Permission denied at /public/msq/WHF4-1/script/PreprocessSAMs.pl line 75.
Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /usr/local/bin/bedtools intersect -abam MI.bam -b ../Mi_Wuhan.fasta.near_GATC.500.bed > MI.REduced.bam
Error: Unable to open file ../Mi_Wuhan.fasta.near_GATC.500.bed. Exiting.
Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/miniconda2/bin/samtools view -F12 MI.REduced.bam -b -o MI.REduced.paired_only.bam
Thu Nov 1 08:56:13 2018: PreprocessSAMs.pl: /public/msq/miniconda2/bin/samtools flagstat MI.REduced.paired_only.bam > MI.REduced.paired_only.flagstat
heatmap.MWAH.R has hard coded RScript path
The heatmap.MWAH.R file distributed with the program has a hardcoded path to RScript (/net/gs/vol3/software/modules-sw/R/2.15.1/Linux/RHEL6/x86_64/bin/Rscript) rather than using a standard path so this fails on all external systems.
No link data
Dear authors,
I'm trying to scaffold a huge genome (~32Gbp). We produced about 2 billion valid Hi-C reads. LACHESIS runs through, and generates 14 clusters that totally make sense (judging by contig IDs, because I also have other linkage information available, therefore, I know which contigs might be on the same chromosome. Not all of them, though, but a few is enough for that kind of test). However, at the last stage LACHESIS does not generate any scaffolds and gives me the following error messages
TESTME: /projects/scaffolding/HiC/lachesis/scaffolds_run01/cached_data/group13.CLM
: ChromLinkMatrix::ReadFile <- /projects/scaffolding/HiC/lachesis/scaffolds_run01/cached_data/group13.CLM N contigs = 423
WARNING: ChromLinkMatrix::ReadFile: CLM file '/projects/scaffolding/HiC/lachesis/scaffolds_run01/cached_data/group13.CLM' has multiple contigs but no link data
Loading contig RE lengths for use in normalization <- /projects/scaffolding/HiC/lachesis/scaffolds_run01/cached_data/group13.CLM.RE_sites
MakeTrunkOrder!
MakeFullOrder!
I would be very thankful for any advice
With the test dataset it runs through beautifully and produces a meaningful result. Therefore, I suspect that either something is wrong with my dataset or the program just runs out of memory (huge genome!), but doesn't really report that.
At the end of the day, it manages to report 14 clusters. Therefore, I believe that the HiC data are at least not garbage. But why does it fail to find links? Are there any specific options I must set in the INI file? Does anyone have any experience with scaffolding large genomes?
Thank you!
Gaps
Hi，
LACHESIS is a so good software to do genome assembling. I have run it with no reference genome. In the group file, the gap_size_after_contig colum correspond to ".". When I converted the fasta file to agp file, it seems that the gap is 1000bp. Is my understanding rigtht or wrong? Looking forward for your help
potential pull request
Greetings,
Some time ago (September?) I was playing with Lachesis and made a fairly large number of trivial changes suggested by the clang tidy tool; I promptly forgot about them.
This morning, someone in the department asked for a little help using Lachesis and I found myself making a few new changes (notably changing the C style comments in the shell/R/perl scripts) so that the various scripts will work for him.
I do not wish to make a big pull request without first checking in. Thus, if you would consider it, perhaps take a peek at: https://github.com/abelew/LACHESIS/commits/master and note the commits made in September. If they are not too troublesome, I would be happy to send a pull request (which at least as of now does not conflict with anything).
Probably the best change there is a Makefile target which calls upon the clang-tidy tool.
I hope you have a good day,
atb
QuickDotplot fails if home directory doesn't have a bin subdir
There is a bug in QuickDotplot. The lines:
my $script_file = "$ENV{'HOME'}/bin/QuickDotplot.R";
write_R_script($script_file);
..cause a failure if the user running the program doesn't already have a directory called 'bin' in their home directory. I can hack this to work by either creating that dir or changing it to:
my $script_file = "$ENV{'HOME'}/QuickDotplot.R";
..but this is still buggy as if two instances of the program run at the same time then they'll fight for that filename and you'll get unwanted results. This should be fixed by generating a proper File::Temp based temporary file for the R script rather than having a hard coded name.
Error in grid.newpage() : could not open file 'out/HiC_heatmap.jpg'
when I run this software,I had miss this mistake,how to solve it ?
How many reads does it take to produce a Hi-C data set good enough for LACHESIS?
Hi,
I notice that in the manuscript, you sequenced 100 million reads for the scaffolding of human genome, which is extremely high and expensive. I wonder what's the lowest required depth (least amount of sequences reads needed) for it? Also I guess the amount of reads needed would decrease for genome with smaller size? For example if human genome (~3Gb) need 100 millions, a bony fish genome(~1.2Gb) would only need 40 millions, is it right? Just trying to lower the budget threshold for HI-C. :)
SAMtool issue during compile step
I am using samtools-1.2, it complains about hstlib and sam.h during SAMStepper.cc step
In file included from SAMStepper.cc:2:0:
SAMStepper.h:49:17: fatal error: sam.h: No such file or directory
#include "sam.h"
^
Lachesis failed at the step of LoadDenovoCLMSFromSAMs.
Hi, everyone!
Lachesis is a grate software to link, order scaffolds. After test the software with the demo, I failed to run the script with my data. It failed at the step of LoadDenovoCLMSFromSAMs. According to the script of "ChromLinkMatrix.cc", it said "an internal inconsistency in the SAM file. Maybe the file is truncated or it has an incorrect header". Considering it may be caused by sort problem, I had re-run the sort step with picard by sorting the file with reads name. However, it was still failed, so I had following question:
- What does "internal inconsistency and incorrect header" mean?
- What 'c2.tid == c1.mtid` was used to?
- According to the log, it said "Filling 24 clusters", but I had assigned "CLUSTER_N = 21", why?
Any suggestion would be grateful!
Error and log were list below:
\1. Error:
Lachesis: ChromLinkMatrix.cc:2221: void LoadDeNovoCLMsFromSAM(const string&, const string&, const ClusterVec&, std::vector<ChromLinkMatrix*>): Assertion `c2.tid == c1.mtid' failed
\2. Log:
Filling 24 clusters with Hi-C data from SAM file /myPath/preprocessSAMs/test.bam (dot = 1M alignments)
Compiling error
Hello, I am trying to installl LACHESIS in our linux server (centos6.2) with gcc4.9, boost1.61 and samtools v0.19.
I think I have installed all the dependency correctly, however, I still got error when compiling HMM.c.
Could you please help me solve this problem? Thanks so much!
Please see below for error details:
make[2]: Leaving directory /home/zhangxt/software/LACHESIS-master/include/gtools' make -C markov make[2]: Entering directory/home/zhangxt/software/LACHESIS-master/include/markov'
g++ -c TestMarkovModel.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c SymbolSet.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c WDAG.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c MarkovModel.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c MarkovChain.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
g++ -c HMM.cc -Wall -ansi -pedantic -g -O3 -std=c++11 -I/home/zhangxt/software/boost_1_61_0
HMM.cc: In member function 'bool HMM::AdjustProbsToBaumWelch(const WDAG&)':
HMM.cc:422:38: error: call of overloaded 'isnan(gnu_cxx::__alloc_traitsstd::allocator::value_type&)' is ambiguous
if ( isnan( new_trans_probs[S1][S2] ) )
^
HMM.cc:422:38: note: candidates are:
In file included from /home/zhangxt/include/features.h:358:0,
from /home/zhangxt/include/c++/4.9.0/x86_64-unknown-linux-gnu/bits/os_defines.h:39,
from /home/zhangxt/include/c++/4.9.0/x86_64-unknown-linux-gnu/bits/c++config.h:430,
from /home/zhangxt/include/c++/4.9.0/bits/stl_algobase.h:59,
from /home/zhangxt/include/c++/4.9.0/vector:60,
from MarkovModel.h:46,
from HMM.h:57,
from HMM.cc:18:
/home/zhangxt/include/bits/mathcalls.h:235:1: note: int isnan(double)
__MATHDECL_1 (int,isnan,, (Mdouble __value)) __attribute ((const));
^
In file included from WDAG.h:28:0,
from HMM.h:58,
from HMM.cc:18:
/home/zhangxt/include/c++/4.9.0/cmath:626:3: note: constexpr bool std::isnan(long double)
isnan(long double __x)
^
/home/zhangxt/include/c++/4.9.0/cmath:622:3: note: constexpr bool std::isnan(double)
isnan(double __x)
^
/home/zhangxt/include/c++/4.9.0/cmath:618:3: note: constexpr bool std::isnan(float)
isnan(float __x)
^
make[2]: *** [HMM.o] Error 1
make[2]: Leaving directory /home/zhangxt/software/LACHESIS-master/include/markov' make[1]: *** [libJmarkov.a] Error 2 make[1]: Leaving directory/home/zhangxt/software/LACHESIS-master/include'
make: *** [libs] Error 2
CreateScaffoldedFasta.pl error
mml@mml:/media/mml/6f60ef75-45fb-4532-9f2a-1a5d642a3093/3C_data/Ctrp_WT$ CreateScaffoldedFasta.pl PacBio_denovo.fasta out
Wed Apr 25 14:14:42 2018: CreateScaffoldedFasta.pl with input fasta = PacBio_denovo.fasta, OUTPUT_DIR = out
Wed Apr 25 14:14:42 2018: Found 7 ordering files ('group*.ordering' in out/main_results/).
Wed Apr 25 14:14:42 2018: Reading in sequences from assembly file PacBio_denovo.fasta
Wed Apr 25 14:14:42 2018: Found 141 contigs/scaffolds in assembly.
ERROR: Ordering file out/main_results/group0.ordering includes contig named 'tig00000015', not found in fasta file PacBio_denovo.fasta
Wed Apr 25 14:14:42 2018: Creating a scaffold from file out/main_results/group0.ordering...
But, PacBio_denovo.fasta does contain tig00000015.
Unable to figure out how to fix this.
Bhagya C T
build failure
Hi,
during installation, at make step I get the following error:
Making all in src/include/gtools
make[1]: Entering directory /usr/local/software/lachesis-rev98/src/include/gtools' ar crv libJgtools.a N50.o ChromInterval.o HumanGenome.o CopyNumberProfile.o FileParsers.o SAMStepper.o; mv libJgtools.a .. a - N50.o a - ChromInterval.o a - HumanGenome.o a - CopyNumberProfile.o a - FileParsers.o a - SAMStepper.o make[1]: Leaving directory /usr/local/software/lachesis-rev98/src/include/gtools'
Making all in src/include/markov
make[1]: Entering directory /usr/local/software/lachesis-rev98/src/include/markov' ar crv libJmarkov.a SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o; mv libJmarkov.a .. a - SymbolSet.o a - WDAG.o a - MarkovModel.o a - MarkovChain.o a - HMM.o make[1]: Leaving directory /usr/local/software/lachesis-rev98/src/include/markov'
Making all in src/include
make[1]: Entering directory /usr/local/software/lachesis-rev98/src/include' make[1]: Nothing to be done for all'.
make[1]: Leaving directory /usr/local/software/lachesis-rev98/src/include' Making all in src make[1]: Entering directory /usr/local/software/lachesis-rev98/src'
make all-am
make[2]: Entering directory /usr/local/software/lachesis-rev98/src' /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-Reporter.o -MD -MP -MF .deps/Lachesis-Reporter.Tpo -c -o Lachesis-Reporter.o test -f 'Reporter.cc' || echo './'Reporter.cc mv -f .deps/Lachesis-Reporter.Tpo .deps/Lachesis-Reporter.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-ChromLinkMatrix.o -MD -MP -MF .deps/Lachesis-ChromLinkMatrix.Tpo -c -o Lachesis-ChromLinkMatrix.o test -f 'ChromLinkMatrix.cc' || echo './'ChromLinkMatrix.cc mv -f .deps/Lachesis-ChromLinkMatrix.Tpo .deps/Lachesis-ChromLinkMatrix.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-GenomeLinkMatrix.o -MD -MP -MF .deps/Lachesis-GenomeLinkMatrix.Tpo -c -o Lachesis-GenomeLinkMatrix.o test -f 'GenomeLinkMatrix.cc' || echo './'GenomeLinkMatrix.cc mv -f .deps/Lachesis-GenomeLinkMatrix.Tpo .deps/Lachesis-GenomeLinkMatrix.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-TrueMapping.o -MD -MP -MF .deps/Lachesis-TrueMapping.Tpo -c -o Lachesis-TrueMapping.o test -f 'TrueMapping.cc' || echo './'TrueMapping.cc mv -f .deps/Lachesis-TrueMapping.Tpo .deps/Lachesis-TrueMapping.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-LinkSizeDistribution.o -MD -MP -MF .deps/Lachesis-LinkSizeDistribution.Tpo -c -o Lachesis-LinkSizeDistribution.o test -f 'LinkSizeDistribution.cc' || echo './'LinkSizeDistribution.cc mv -f .deps/Lachesis-LinkSizeDistribution.Tpo .deps/Lachesis-LinkSizeDistribution.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-ContigOrdering.o -MD -MP -MF .deps/Lachesis-ContigOrdering.Tpo -c -o Lachesis-ContigOrdering.o test -f 'ContigOrdering.cc' || echo './'ContigOrdering.cc mv -f .deps/Lachesis-ContigOrdering.Tpo .deps/Lachesis-ContigOrdering.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-ClusterVec.o -MD -MP -MF .deps/Lachesis-ClusterVec.Tpo -c -o Lachesis-ClusterVec.o test -f 'ClusterVec.cc' || echo './'ClusterVec.cc mv -f .deps/Lachesis-ClusterVec.Tpo .deps/Lachesis-ClusterVec.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-RunParams.o -MD -MP -MF .deps/Lachesis-RunParams.Tpo -c -o Lachesis-RunParams.o test -f 'RunParams.cc' || echo './'RunParams.cc mv -f .deps/Lachesis-RunParams.Tpo .deps/Lachesis-RunParams.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-TextFileParsers.o -MD -MP -MF .deps/Lachesis-TextFileParsers.Tpo -c -o Lachesis-TextFileParsers.o test -f 'TextFileParsers.cc' || echo './'TextFileParsers.cc mv -f .deps/Lachesis-TextFileParsers.Tpo .deps/Lachesis-TextFileParsers.Po /usr/local/gcc/4.8.3//gcc/bin/g++ -DHAVE_CONFIG_H -I. -I. -Iinclude -I/usr/local/gcc/4.8.3//boost/1.57.0/include -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include/bam -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -MT Lachesis-Lachesis.o -MD -MP -MF .deps/Lachesis-Lachesis.Tpo -c -o Lachesis-Lachesis.o test -f 'Lachesis.cc' || echo './'Lachesis.cc mv -f .deps/Lachesis-Lachesis.Tpo .deps/Lachesis-Lachesis.Po /bin/bash ../libtool --tag=CXX --mode=link /usr/local/gcc/4.8.3//gcc/bin/g++ -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -static -lz -lpthread -Linclude -lJtime -lJgtools -lJmarkov -L/usr/local/gcc/4.8.3//boost/1.57.0/lib -Wl,-R,/usr/local/gcc/4.8.3//boost/1.57.0/lib -L/usr/local/gcc/4.8.3//boost/1.57.0/lib -Wl,-R,/usr/local/gcc/4.8.3//boost/1.57.0/lib -L/usr/local/gcc/4.8.3//zlib/1.2.7/lib -L/usr/local/gcc/4.8.3//samtools/0.1.19/lib -L/usr/local/gcc/4.8.3//boost/1.57.0/lib -L/usr/local/gcc/4.8.3//samtools/0.1.19/lib -lz -lpthread -lm -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -lboost_system -lboost_program_options -lboost_filesystem -lbam -lz libtool: link: /usr/local/gcc/4.8.3//gcc/bin/g++ -fPIC -march=native -mtune=native -O2 -pipe -I/usr/local/gcc/4.8.3//zlib/1.2.7/include -I/usr/local/gcc/4.8.3//samtools/0.1.19/include -I/usr/local/gcc/4.8.3//boost/1.57.0/include -Wl,-R -Wl,/usr/local/gcc/4.8.3//boost/1.57.0/lib -Wl,-R -Wl,/usr/local/gcc/4.8.3//boost/1.57.0/lib -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -Linclude -lJtime -lJgtools -lJmarkov -L/usr/local/gcc/4.8.3//boost/1.57.0/lib -L/usr/local/gcc/4.8.3//zlib/1.2.7/lib -L/usr/local/gcc/4.8.3//samtools/0.1.19/lib -lpthread -lm -lboost_system -lboost_program_options -lboost_filesystem -lbam -lz Lachesis-Reporter.o: In function Reporter::Reporter(RunParams const&, ClusterVec const&, std::vector<ContigOrdering, std::allocator > const&, std::vector<ContigOrdering, std::allocator > const&)':
Reporter.cc:(.text+0x2d87): undefined reference to NTargetsInSAM(std::string const&)' Reporter.cc:(.text+0x2dfe): undefined reference to TargetLengths(std::string const&)'
Lachesis-Reporter.o: In function MakeWholeAssemblyHeatmap(RunParams const&, int, bool)': Reporter.cc:(.text+0x7245): undefined reference to TargetLengths(std::string const&)'
Lachesis-ChromLinkMatrix.o: In function LoadNonDeNovoCLMsFromSAM(std::string const&, std::vector<ChromLinkMatrix*, std::allocator<ChromLinkMatrix*> >)': ChromLinkMatrix.cc:(.text+0x670d): undefined reference to NTargetsInSAM(std::string const&)'
ChromLinkMatrix.cc:(.text+0x6827): undefined reference to SAMStepper::SAMStepper(std::string const&)' Lachesis-ChromLinkMatrix.o: In function ChromLinkMatrix::LoadFromSAMNonDeNovo(std::string const&, int)':
ChromLinkMatrix.cc:(.text+0x6c1b): undefined reference to NTargetsInSAM(std::string const&)' Lachesis-ChromLinkMatrix.o: In function LoadDeNovoCLMsFromSAM(std::string const&, std::string const&, ClusterVec const&, std::vector<ChromLinkMatrix*, std::allocator<ChromLinkMatrix*> >)':
ChromLinkMatrix.cc:(.text+0x6fe8): undefined reference to TargetLengths(std::string const&)' ChromLinkMatrix.cc:(.text+0x7568): undefined reference to SAMStepper::SAMStepper(std::string const&)'
Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::NonDeNovoTrueMapping() const': GenomeLinkMatrix.cc:(.text+0x1a37): undefined reference to HumanGenome_chroms()'
GenomeLinkMatrix.cc:(.text+0x1a3f): undefined reference to HumanGenome_chrom_lengths()' Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::BinsPerChromInHumanGenome() const':
GenomeLinkMatrix.cc:(.text+0x1bdc): undefined reference to HumanGenome_chroms()' GenomeLinkMatrix.cc:(.text+0x1bee): undefined reference to HumanGenome_chrom_lengths()'
Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::LoadFromSAM(std::string const&, std::vector<int, std::allocator<int> > const&)': GenomeLinkMatrix.cc:(.text+0x7a62): undefined reference to TargetLengths(std::string const&)'
GenomeLinkMatrix.cc:(.text+0x7ad1): undefined reference to SAMStepper::SAMStepper(std::string const&)' Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::GenomeLinkMatrix(std::string const&, std::vector<std::string, std::allocatorstd::string > const&, std::string const&)':
GenomeLinkMatrix.cc:(.text+0x8aba): undefined reference to NTargetsInSAM(std::string const&)' GenomeLinkMatrix.cc:(.text+0x8b4d): undefined reference to TargetLengths(std::string const&)'
Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::ReadFile(std::string const&)': GenomeLinkMatrix.cc:(.text+0xa07f): undefined reference to TargetLengths(std::string const&)'
Lachesis-TrueMapping.o: In function TrueMapping::PrintSeqLengthOnTargets(std::string const&, std::ostream&) const': TrueMapping.cc:(.text+0x19d): undefined reference to TargetLengths(std::string const&)'
Lachesis-TrueMapping.o: In function TrueMapping::TargetToHumanChromIDs() const': TrueMapping.cc:(.text+0x180c): undefined reference to HumanGenome_chroms()'
Lachesis-TrueMapping.o: In function TrueMapping::TrueMapping(std::string const&, int, std::vector<std::string, std::allocator<std::string> > const&, std::vector<std::string, std::allocator<std::string> > const&)': TrueMapping.cc:(.text+0x378e): undefined reference to HumanGenome_chroms()'
TrueMapping.cc:(.text+0x3868): undefined reference to HumanGenome_chrom_lengths()' TrueMapping.cc:(.text+0x39b7): undefined reference to HumanGenome_centromere_locs()'
Lachesis-TrueMapping.o: In function TrueMapping::ReadBlastAlignsFromFileSet(std::string const&, std::string const&, std::vector<std::string, std::allocator<std::string> > const&, std::string const&)': TrueMapping.cc:(.text+0x41e5): undefined reference to TargetLengths(std::string const&)'
TrueMapping.cc:(.text+0x41f2): undefined reference to TargetNames(std::string const&)' Lachesis-LinkSizeDistribution.o: In function LinkSizeDistribution::LinkSizeDistribution(std::vector<std::string, std::allocatorstd::string > const&)':
LinkSizeDistribution.cc:(.text+0x12b0): undefined reference to TargetLengths(std::string const&)' LinkSizeDistribution.cc:(.text+0x1686): undefined reference to SAMStepper::SAMStepper(std::string const&)'
Lachesis-RunParams.o: In function RunParams::VerifySAMFileHeaders() const': RunParams.cc:(.text+0x3e1): undefined reference to NTargetsInSAM(std::string const&)'
RunParams.cc:(.text+0x40a): undefined reference to NTargetsInSAM(std::string const&)' include/libJgtools.a(SAMStepper.o): In function open_SAM(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)':
/usr/include/c++/6/bits/basic_string.h:5086: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const' /usr/include/c++/6/bits/basic_string.h:5086: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::compare(char const*) const'
/usr/include/c++/6/bits/basic_string.h:5086: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const' include/libJgtools.a(SAMStepper.o): In function std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_check(unsigned long, char const*) const':
/usr/include/c++/6/bits/basic_string.h:262: undefined reference to std::__throw_out_of_range_fmt(char const*, ...)' include/libJgtools.a(SAMStepper.o): In function void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char*>(char*, char*, std::forward_iterator_tag)':
/usr/include/c++/6/bits/basic_string.tcc:219: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)' /usr/include/c++/6/bits/basic_string.tcc:219: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)'
/usr/include/c++/6/bits/basic_string.tcc:219: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)' /usr/include/c++/6/bits/basic_string.tcc:219: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)'
/usr/include/c++/6/bits/basic_string.tcc:219: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)' include/libJgtools.a(SAMStepper.o):/usr/include/c++/6/bits/basic_string.tcc:219: more undefined references to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)' follow
/usr/bin/ld: include/libJgtools.a(SAMStepper.o)(.text.startup+0x13): unresolvable AWAVAUI��ATUH��SH��XD�▒H�T$(E���� relocation against symbol `_ZNSt8ios_base4InitD1Ev@@GLIBCXX_3.4'
/usr/bin/ld: BFD (GNU Binutils for Ubuntu) 2.22 internal error, aborting at ../../bfd/reloc.c line 443 in bfd_get_reloc_size
/usr/bin/ld: Please report this bug.
collect2: error: ld returned 1 exit status
make[2]: *** [Lachesis] Error 1
make[2]: Leaving directory /usr/local/software/lachesis-rev98/src' make[1]: *** [all] Error 2 make[1]: Leaving directory /usr/local/software/lachesis-rev98/src'
make: *** [all-recursive] Error 1
It seems something wrong with libJgtools.a even if it didn't complain when making it. Please, any help is welcome!
Thanks,
Giuseppe
Building LACHESIS with Amazon Red Hat instance
When compiling, saw the error below. Fixed by adding #include to ChromLinkMatrix.cc. Afterwards was able to run ./Lachesis INIs/test_case.ini without segfault error seen on Ubuntu. These are the additions I made to the base instance:
sudo yum upgrade
sudo yum install gcc-c++
sudo yum install boost-devel.x86_64
sudo yum install zlib-devel
a - MarkovModel.o
a - MarkovChain.o
a - HMM.o
make[2]: Leaving directory /home/ec2-user/LACHESIS-master/include/markov' make[1]: Leaving directory/home/ec2-user/LACHESIS-master/include'
g++ -c Lachesis.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/home/ec2-user/samtools-0.1.19
g++ -c Reporter.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/home/ec2-user/samtools-0.1.19
g++ -c ChromLinkMatrix.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/home/ec2-user/samtools-0.1.19
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/hash_set:60,
from /usr/include/boost/graph/adjacency_list.hpp:25,
from ChromLinkMatrix.cc:22:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
ChromLinkMatrix.cc: In member function ‘ContigOrdering ChromLinkMatrix::MakeFullOrder(int, bool) const’:
ChromLinkMatrix.cc:970: error: ‘setprecision’ was not declared in this scope
make: *** [ChromLinkMatrix.o] Error 1
./configure checking samtools... failed
I configure by this code
./configure --with-samtools=/psd/biosoft/samtools_suit/samtools-0.1.19/ --with-boost=/psd/biosoft/boost_1_60_0_b1/
but I get the error messages ：
......................
checking if samtools is wanted... yes
checking sam.h usability... yes
checking sam.h presence... yes
checking for sam.h... yes
checking for sam_open in -lbam... no
checking samtools... failed
configure: error: either specify a valid samtools installation with --with-samtools=DIR or disable samtools usage with --without-samtools
also, I have tested other way and configure:
export LACHESIS_BOOST_DIR="/psd/biosoft/boost_1_60_0_b1/:$LACHESIS_BOOST_DIR"
export LACHESIS_SAMTOOLS_DIR="/psd/biosoft/samtools_suit/samtools-0.1.19/:$LACHESIS_SAMTOOLS_DIR"
but it didn't work, Samtools is well installed and available。
An configure error about boost
Hi,
When I install LACHESIS, there was an error.
checking for the Boost program_options library... (cached) yes
checking boost/regex.hpp usability... yes
checking boost/regex.hpp presence... yes
checking for boost/regex.hpp... yes
checking for the Boost regex library... no
configure: error: cannot find the flags to link with Boost regex
The version of gcc is 4.8 and the version of boost is 1.56. Can you help me so solve this? Thank you very much!
Wang
Determining the value of CLUSTER_N
For a genome with an unknown number of chromosomes (we have not karyotyped it yet), it there a good way to determine the number of chromosomes using Hi-C data? I tried to do some simple hierarchical clustering using the data points in heatmap.txt, but I cannot find obvious turning points... Does LACHESIS produce some results that can help one determine the number of chromosomes? Thanks!
unique mapping
I am curious how Lachesis will process the mapping files.
Will it only take unique reads?
I am scaffolding a genome with many repeat regions and I am worried about the mis-mapping.
Thanks!
Incorrect Reverse Complementation
Hi there,
At the very end of the CreateScaffoldedFasta.pl script, it appears that the "S" and "W" ambiguity codes are incorrectly reverse complemented.
S is complemented to W and visa-versa, when they should just reverse complement to themselves.
Thanks
LACHESIS segmentation fault in Ubuntu
When we compile LACHESIS on an Ubuntu system and run it on the provided test case, it crashes with a segmentation fault. The segfault occurs at the opening curly bracket of the function ChromLinkMatrix::ReadFile. Here's the stack trace provided by gdb:
Program received signal SIGSEGV, Segmentation fault.
ChromLinkMatrix::ReadFile (this=0x7ffffff83f60, CLM_file=...)
at ChromLinkMatrix.cc:280
280 {
===============
(gdb) i stack
#0 ChromLinkMatrix::ReadFile (this=0x7ffffff83f60, CLM_file=...) at ChromLinkMatrix.cc:280
#1 0x000000000040d980 in ChromLinkMatrix (CLM_file=..., this=0x7ffffff83f60) at ChromLinkMatrix.h:65
#2 LachesisOrdering (run_params=...) at Lachesis.cc:177
#3 0x0000000000407532 in main (argc=2, argv=0x7fffffffe698) at Lachesis.cc:281
If anyone with access to an Ubuntu build wants to help investigate this, please download and install LACHESIS (see README.txt for instructions) and then run it on the test case: Lachesis INIs/test_case.ini.
-- Josh
Segmentation fault while running lachesis on sample data
I built Lachesis with boost 1.54 and samtools 0.1.19 and the build was successful. After that, I ran Lachesis on the test data using test_case.ini. It is giving me an error. It is as follows:
Wed Jun 8 13:59:48 2016: prim_minimum_spanning_tree (iteration #0, previous trunk_size = 0)
terminate called after throwing an instance of 'boost::exception_detail::clone_implboost::exception_detail::error_info_injector<boost::negative_edge
what(): The graph may not contain an edge with negative weight.
Aborted (core dumped)
Any help about resolving this is appreciated. Thanks!
ChromLinkMatrix
Hi -
I got an error while running Lachesis. test_case runs fine. Message is the following :
Lachesis: ChromLinkMatrix.cc:2184: void LoadDeNovoCLMsFromSAM(const string&, const string&, const ClusterVec&, std::vector<ChromLinkMatrix*>): Assertion c1.tid == c2.mtid' failed.
Stage it happens is :
Filling 20 clusters with Hi-C data from SAM file ferdi/Linkage/HiC_mapping//HiC_S1.bam (dot = 1M alignments)
Thanks!
Ferdinand
checking for library containing deflate... no
Hi, I was tring to install LACHESIS on CentOS 6.9 with conda.
conda create -n LACHESIS python=2.7
conda install boost=1.57
export LACHESIS_BOOST_DIR=/home/shurh/miniconda3/envs/LACHESIS
export LACHESIS_SAMTOOLS_DIR=/data/software/rsem-1.2.9/sam
./configure --with-samtools=/data/software/rsem-1.2.9/sam --with-boost=/home/shurh/miniconda3/envs/LACHESISThen, I got a error about libz.
checking dependency style of gcc... gcc3
checking dependency style of g++... gcc3
checking whether to enable maintainer-specific portions of Makefiles... no
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for library containing deflate... no
configure: error: libz is required.
However, I have ready installed libz. How can I fix this?
Issue with boost library during compiling LACHESIS
I get another one with boost, I am using the latest one boost_1_59_0, do I need to switch to an older one too? Which version specifically?
g++ -Wall -ansi -pedantic -g -O3 TestMarkovModel.o SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o -o TestMarkovModel -lz -L/path/to/boost/boost_1_59_0/stage/lib -lboost_system -lboost_filesystem -lboost_regex
/usr/bin/ld: cannot find -lboost_system
/usr/bin/ld: cannot find -lboost_filesystem
/usr/bin/ld: cannot find -lboost_regex
collect2: error: ld returned 1 exit status
Makefile:40: recipe for target 'TestMarkovModel' failed
make[2]: *** [TestMarkovModel] Error 1
make[2]: Leaving directory 'path/to/LACHESIS/include/markov'
Makefile:47: recipe for target 'libJmarkov.a' failed
make[1]: *** [libJmarkov.a] Error 2
make[1]: Leaving directory '/path/to/LACHESIS/include'
Makefile:41: recipe for target 'libs' failed
make: *** [libs] Error 2
LACHESIS on Chicago data
Hi,
Do you think your LACHESIS pipeline could be applicable to Chicago ((Cell-free Hi-C for
Assembly and Genome Organization) data?
I imagine that the data produced by the Chicago methods should look very similiar to Hi-C data although maybe missing the very large insert reads compared to normal Hi-C.
Thank you,
Michel
Boost lib connect error? any one have solve it?
Making all in src/include/gtools
make[1]: Entering directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src/include/gtools' ar crv libJgtools.a N50.o ChromInterval.o HumanGenome.o CopyNumberProfile.o FileParsers.o SAMStepper.o; mv libJgtools.a .. a - N50.o a - ChromInterval.o a - HumanGenome.o a - CopyNumberProfile.o a - FileParsers.o a - SAMStepper.o make[1]: Leaving directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src/include/gtools'
Making all in src/include/markov
make[1]: Entering directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src/include/markov' ar crv libJmarkov.a SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o; mv libJmarkov.a .. a - SymbolSet.o a - WDAG.o a - MarkovModel.o a - MarkovChain.o a - HMM.o make[1]: Leaving directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src/include/markov'
Making all in src/include
make[1]: Entering directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src/include' make[1]: Nothing to be done for all'.
make[1]: Leaving directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src/include' Making all in src make[1]: Entering directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src'
make all-am
make[2]: Entering directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src' /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -static -lz -lpthread -Linclude -lJtime -lJgtools -lJmarkov -L/public1/home/stu_yanhanso libtool: link: g++ -g -O2 -Wl,-R -Wl,/public1/home/stu_yanhansong/software/boost_1_61_0//lib -Wl,-R -Wl,/public1/home/stu_yanhansong/software/boo make[2]: Leaving directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src'
make[1]: Leaving directory /public1/home/stu_yanhansong/software/Hi-C/LACHESIS-master/src' Lachesis-ChromLinkMatrix.o: In function AssertFilesExist(std::vector<std::string, std::allocatorstd::string > const&)':
/public1/home/stu_yanhansong/software/boost_1_61_0//include/boost/filesystem/operations.hpp:455: undefined reference to boost::filesystem::detai l::status(boost::filesystem::path const&, boost::system::error_code*)'Lachesis-ChromLinkMatrix.o: In function LoadNonDeNovoCLMsFromSAM(std::string const&, std::vector<ChromLinkMatrix*, std::allocator<ChromLinkMatri
x*> >)':/public1/home/stu_yanhansong/software/boost_1_61_0//include/boost/filesystem/operations.hpp:455: undefined reference to boost::filesystem::detai l::status(boost::filesystem::path const&, boost::system::error_code*)'Lachesis-ChromLinkMatrix.o: In function ChromLinkMatrix::ReadFile(std::string const&)':
/public1/home/stu_yanhansong/software/boost_1_61_0//include/boost/filesystem/operations.hpp:455: undefined reference to boost::filesystem::detai l::status(boost::filesystem::path const&, boost::system::error_code*)'Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::LoadFromSAM(std::string const&, std::vector<int, std::allocator > const&)':
/public1/home/stu_yanhansong/software/boost_1_61_0//include/boost/filesystem/operations.hpp:455: undefined reference to boost::filesystem::detai l::status(boost::filesystem::path const&, boost::system::error_code*)'Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::LoadFromSAMDeNovo(std::vector<std::string, std::allocatorstd::string > const&)':
/public1/home/stu_yanhansong/software/boost_1_61_0//include/boost/filesystem/operations.hpp:455: undefined reference to boost::filesystem::detai l::status(boost::filesystem::path const&, boost::system::error_code*)'Lachesis-GenomeLinkMatrix.o:/public1/home/stu_yanhansong/software/boost_1_61_0//include/boost/filesystem/operations.hpp:455: more undefined refer ences to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' followcollect2: error: ld returned 1 exit status
make[2]: *** [Lachesis] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
Segmentation fault (core dumped) using reference
Hi
I am scaffolding contigs generated by CANU using Lachesis. I faced a bug “Segmentation fault (core dumped)” when I use the reference (USE_REFERENCE = 1). The bug also existed when I used the test data.
When I don’t use the reference (USE_REFERENCE = 0), it is good for my data and test data. How can I fix it?
Thanks.
bam/sam.h
Hi
After a successful ./configure I run make I get an fatal error that reads:
make[1]: Entering directory `.../shendurelab-LACHESIS-2e27abb/src/include/gtools'
g++ -c SAMStepper.cc -Wall -ansi -pedantic -g -O3 -std=c++11
In file included from SAMStepper.cc:18:0:
**SAMStepper.h:65:21: fatal error: bam/sam.h: No such file or directory**
**#include <bam/sam.h>**
^
compilation terminated.
make[1]: *** [SAMStepper.o] Error 1
I tried to get around the issue by creating a symbolic link back into samtools to where sam.h is within 'src/include/gtools/' (creating the bam folder 'src/include/gtools/bam/') but it still fails to read the file.
Any help would be really appreciated.
Thanks,
Simon
error: Assertion `c1.pos == c2.mpos' failed
Filling 21 clusters with Hi-C data from SAM file /public/msq/WHF4-1/script//Mi.REduced.paired_only.bam (dot = 1M alignments)
Lachesis: ChromLinkMatrix.cc:2186: void LoadDeNovoCLMsFromSAM(const string&, const string&, const ClusterVec&, std::vector<ChromLinkMatrix*>): Assertion `c1.pos == c2.mpos' failed.
samtools-0.1.18 boost_1_52_0
make[2]: Entering directory /export1/workdir/group1/liyang/software/LACHESIS-master/src' /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -static -lz -lpthread -Linclude -lJtime -lJgtools -lJmarkov -L/export1/workdir/group1/liyang/software/boost_1_52_0/lib -Wl,-R,/export1/workdir/group1/liyang/software/boost_1_52_0/lib -L/export1/workdir/group1/liyang/software/boost_1_52_0/lib -Wl,-R,/export1/workdir/group1/liyang/software/boost_1_52_0/lib -L/export1/workdir/group1/liyang/software/zlib-1.2.11/lib -L/export1/workdir/group1/liyang/software/bzip2-1.0.6/lib -L/export1/workdir/group1/liyang/software/xz-5.2.2/lib -L/export1/workdir/group1/liyang/software/pcre-8.41/lib -L/export1/workdir/group1/liyang/software/curl-7.47.1/lib -L/export1/workdir/group1/liyang/software/boost_1_52_0/stage/lib -L/export1/public/software/samtools-0.1.18/lib -lz -lpthread -lm -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -lboost_system -lboost_program_options -lboost_filesystem-mt -lbam -lz libtool: link: g++ -g -O2 -Wl,-R -Wl,/export1/workdir/group1/liyang/software/boost_1_52_0/lib -Wl,-R -Wl,/export1/workdir/group1/liyang/software/boost_1_52_0/lib -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -Linclude -lJtime -lJgtools -lJmarkov -L/export1/workdir/group1/liyang/software/boost_1_52_0/lib -L/export1/workdir/group1/liyang/software/zlib-1.2.11/lib -L/export1/workdir/group1/liyang/software/bzip2-1.0.6/lib -L/export1/workdir/group1/liyang/software/xz-5.2.2/lib -L/export1/workdir/group1/liyang/software/pcre-8.41/lib -L/export1/workdir/group1/liyang/software/curl-7.47.1/lib -L/export1/workdir/group1/liyang/software/boost_1_52_0/stage/lib -L/export1/public/software/samtools-0.1.18/lib -lpthread -lm -lboost_system -lboost_program_options -lboost_filesystem-mt -lbam -lz Lachesis-ChromLinkMatrix.o: In function is_regular_file':
/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::NonDeNovoTrueMapping() const':
/export1/workdir/group1/liyang/software/LACHESIS-master/src/GenomeLinkMatrix.cc:1062: undefined reference to HumanGenome_chroms()' /export1/workdir/group1/liyang/software/LACHESIS-master/src/GenomeLinkMatrix.cc:1063: undefined reference to HumanGenome_chrom_lengths()'
Lachesis-GenomeLinkMatrix.o: In function GenomeLinkMatrix::BinsPerChromInHumanGenome() const': /export1/workdir/group1/liyang/software/LACHESIS-master/src/GenomeLinkMatrix.cc:1558: undefined reference to HumanGenome_chroms()'
/export1/workdir/group1/liyang/software/LACHESIS-master/src/GenomeLinkMatrix.cc:1559: undefined reference to HumanGenome_chrom_lengths()' Lachesis-GenomeLinkMatrix.o: In function is_regular_file':
/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' Lachesis-GenomeLinkMatrix.o:/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: more undefined references to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' follow
Lachesis-TrueMapping.o: In function TrueMapping': /export1/workdir/group1/liyang/software/LACHESIS-master/src/TrueMapping.cc:128: undefined reference to HumanGenome_chroms()'
/export1/workdir/group1/liyang/software/LACHESIS-master/src/TrueMapping.cc:134: undefined reference to HumanGenome_chrom_lengths()' /export1/workdir/group1/liyang/software/LACHESIS-master/src/TrueMapping.cc:136: undefined reference to HumanGenome_centromere_locs()'
Lachesis-TrueMapping.o: In function TrueMapping::TargetToHumanChromIDs() const': /export1/workdir/group1/liyang/software/LACHESIS-master/src/TrueMapping.cc:664: undefined reference to HumanGenome_chroms()'
Lachesis-TrueMapping.o: In function is_regular_file': /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
Lachesis-LinkSizeDistribution.o: In function is_regular_file': /export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' Lachesis-ContigOrdering.o: In function is_regular_file':
/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' Lachesis-RunParams.o: In function is_regular_file':
/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' Lachesis-RunParams.o:/export1/workdir/group1/liyang/software/boost_1_52_0/include/boost/filesystem/operations.hpp:299: more undefined references to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' follow
collect2: ld returned 1 exit status
make[2]: *** [Lachesis] Error 1
make[2]: Leaving directory /export1/workdir/group1/liyang/software/LACHESIS-master/src' make[1]: *** [all] Error 2 make[1]: Leaving directory /export1/workdir/group1/liyang/software/LACHESIS-master/src'
make: *** [all-recursive] Error 1
Assemble bone fish genome
Hi,
Just finish reading your fabulous article on Nature Biotechnology, I couldn't help wondering if I can use LACHESIS to assemble the bone fish draft genome I am working on. However I found it hard to find any Hi-C data sets for any kind of fish. With such an emerging model organism, I guess the best shot I can get is using Zebrafish data set, but I couldn't find any Hi-C experiments done on Zebrafish either. Do You have any option/suggestion for the genome-wide chromatin interaction data set for assembling bone fish genome?
Thank You Very Much,
by the way NICE name for the tool, Fates are my favorite goddess :)
GenomeLinkMatrix error
Hi, I have one problem.
When I run LACHESIS, I got this error.
How can I do if I want to solve this problem?
N_clusters = 31, N_singletons = 6
Total length in singleton clusters = 31570
Total length of all clustered contigs = 2921503406 out of 2944539404 (99.2177%)
Lachesis: GenomeLinkMatrix.cc:1133: void GenomeLinkMatrix::ValidateClusters(const TrueMapping*, bool) const: Assertion `( same_cluster ? N_links_same_cluster : N_links_diff_cluster ) >= 0' failed.
Aborted
Bareword found where operator expected at PreprocessSAMs.pl
Hi,
I got the following errors:
Bareword found where operator expected at /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl line 6, near "// This"
(Missing operator before This?)
Number found where operator expected at /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl line 6, near ") 2014"
(Missing operator before 2014?)
Bareword found where operator expected at /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl line 6, near "2015 by"
(Missing operator before by?)
syntax error at /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl line 6, near "// This software "
Unknown regexp modifier "/B" at /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl line 24, at end of line
(Might be a runaway multi-line // string starting on line 17)
Unknown regexp modifier "/A" at /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl line 24, at end of line
Unknown regexp modifier "/M" at /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl line 24, at end of line
"use" not allowed in expression at /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl line 24, at end of line
Execution of /work/waterhouse_team/apps/lachesis/bin/PreprocessSAMs.pl aborted due to compilation errors.
What did I miss?
Thank you in advance,
Michal
Doesn't build against new Samtools 1.0 release
LACHESIS no longer builds with the introduction of the htslib library and the release of the 1.0 version of Samtools. The includes in the gtools (and possibly other places in the code base) need to be fixed. This can be avoided by building against the 0.1.19 version.
version number?
I'm writing up some experiments for publication where I used your software. I'm going to cite it, but I'm having difficulties figuring out what version I used. I don't think I got it from github, so I don't have the git info to help me. You should really consider adding some --help or --version functionality.
Testing out Lachesis on a sample dataset: error while loading shared libraries: libboost_system.so.1.62.0
Hi,
when I run the test
$ ./Lachesis INIs/test_case.ini
I get the following error message:
./Lachesis: error while loading shared libraries: libboost_system.so.1.62.0: cannot open shared object file: No such file or directory
I am using boost 1.6.2
It took me a while to be able to compile Lachesis, to make it compile i did the following:
removed "-std=c++11" option from CFLAGS in the Makefile of "include/markov" folder as suggested in another issue post. Then I realized that I had to build the boost libraries, to do that I ran in the "boost_1_62_0" folder:
$ ./boostrap.sh --prefix=/my_path_to/boost_1_62_0
$ ./b2 install
this generated a "lib" and "include" folder in the "boost_1_62_0" folder
then, to satisfy the directory structure required by lachesis i made a "stage" folder in "boost_1_62_0" folder and made a link to the newly generated "lib" folder (as it is also suggested in another issue post):
$ ln -s /my_path_to/boost_1_62_0/lib /my_path_to/boost_1_62_0/stage/lib
Set the required environmental variables:
$ export LACHESIS_SAMTOOLS_DIR=/my_path_to/samtools-0.1.19/
$ export LACHESIS_BOOST_DIR=/my_path_to/boost_1_62_0/
Changed the memory limit to 10 Mb:
$ ulimit -s 10240
Then I ran make in the lachesis folder, and it compiled correctly, although many warning messages appeared.
It seems to me that it is not looking for the library into the correct folder but, as I understand, the library is in the correct place: "my_path_to/boost_1_62_0/stage/lib/libboost_system.so.1.62.0"
Could somebody help me?
I am running this in a Computer with Ubuntu 15.10 ,16GB of memory, gcc 5.2.1 , zlib 1.2.8 , samtools 0.1.19
lack file of dotplot.20.renumbered.txt
Hi!
I had installed LACHESIS recently, but when I test it with demo, it output following error as follow, then lead to the failure of "QuickDotplot.SKY.R". I couldn't find any script that would output "dotplot.20.renumbered.txt". Is this a pre-exists file?
Any suggestion would be grateful!
Best wishes!
In addition: Warning message:
In file(file, "rt") :
cannot open file '/myHome/vol10/src/Lachesis/dotplot.20.renumbered.txt': No such file or directory
Execution halted
mv: cannot stat `/myHome/public_html/dotplot.SKY.jpg': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
Lachesis: Lachesis.cc:158: void LachesisOrdering(const RunParams&): Assertion `(int) clusters.size() >= run_params._cluster_N' failed.
Lachesis: Lachesis.cc:158: void LachesisOrdering(const RunParams&): Assertion `(int) clusters.size() >= run_params._cluster_N' failed.
get a very big clusters
I have recently used LACHESIS for the long read assemblies(the assembly contig N50 10Mb). I get a very big clusters(60Mb,50% genome) no matter what the parameter adjusted. Could you help me?
LIBEVENT_CHECK_CONFIG
make fails with error
./configure: line 10288: syntax error near unexpected token no' ./configure: line 10288: LIBEVENT_CHECK_CONFIG(no)'
Fail to build lachesis
Hi,
I have all the prerequisites installed but when installing lachesis, I encounter some problems.
There are also a lot of stray 'xxx' in program errors. Please let me know how to resolve this issue.
/usr/bin/locale:127: error: stray ‘\1’ in program
/usr/bin/locale:127:1334: warning: null character(s) ignored
/usr/bin/locale:127: error: stray ‘\1’ in program
/usr/bin/locale:127:1349: warning: null character(s) ignored
In file included from /home/gmsljk/boost_1_58_0/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast/detail/converter_lexical.hpp:53,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast/try_lexical_convert.hpp:34,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast.hpp:32,
from VCF_variant_info.h:22,
from ChromInterval.h:32,
from ChromInterval.cc:2:
/usr/bin/locale:1: error: expected constructor, destructor, or type conversion before ‘>’ token
In file included from /home/gmsljk/boost_1_58_0/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast/detail/converter_lexical.hpp:53,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast/try_lexical_convert.hpp:34,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast.hpp:32,
from VCF_variant_info.h:22,
from ChromInterval.h:32,
from ChromInterval.cc:2:
/usr/bin/locale:3: error: expected constructor, destructor, or type conversion before numeric constant
In file included from /home/gmsljk/boost_1_58_0/boost/lexical_cast/detail/converter_lexical_streams.hpp:44,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast/detail/converter_lexical.hpp:53,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast/try_lexical_convert.hpp:34,
from /home/gmsljk/boost_1_58_0/boost/lexical_cast.hpp:32,
from VCF_variant_info.h:22,
from ChromInterval.h:32,
from ChromInterval.cc:2:
/usr/bin/locale:4: error: expected constructor, destructor, or type conversion before ‘:’ token
/usr/bin/locale:4: error: expected declaration before ‘}’ token
make[2]: *** [ChromInterval.o] Error 1
make[2]: Leaving directory /home/gmsljk/LACHESIS-master/include/gtools' make[1]: *** [libJgtools.a] Error 2 make[1]: Leaving directory/home/gmsljk/LACHESIS-master/include'
make: *** [libs] Error 2
Thank you.
Regards,
Kevin
./configure: line 16192: syntax error near unexpected token `BOOST_REQUIRE'
I keep failing to get LACHESIS to get past the './configure' step. The error messages at which the build shrieks and dies are:
"""
./configure: line 16192: syntax error near unexpected token BOOST_REQUIRE' ./configure: line 16192: BOOST_REQUIRE(1.52.0)'
"""
Here are the line-commands with which I have failed to get the .configure to work:
cd /mnt/home/emsch/src ;
zcat /mnt/home/emsch/TGZ/shendurelab-LACHESIS-9b16824.tar.gz | tar xf - ;
cd /mnt/home/emsch/src/shendurelab-LACHESIS-9b16824 ;
module load Boost/1.52.0 ; # apparently, LACHESIS requires this version or later
module load SAMTools/0.1.19 ; # apparently, LACHESIS will not build/run with any later version
# I'm guessing, from the instruction "LACHESIS_BOOST_DIR should have the subdirectory stage/lib/",
# that this should be a simple 'boost' rather than 'boost/1.52.0--GCC-4.4.5':
export LACHESIS_BOOST_DIR=/opt/software/boost/ ;
export LACHESIS_SAMTOOLS_DIR=/opt/software/SAMTools/0.1.19--GCC-4.4.5/bin/ ;
autoreconf --install ;
./configure --prefix=/mnt/home/emsch ;
[... and things run merrily along for a while before failing with:]
"""
./configure: line 16192: syntax error near unexpected token BOOST_REQUIRE' ./configure: line 16192: BOOST_REQUIRE(1.52.0)'
"""
If anybody can tell me what I am doing wrong and how to get the ./configure to complete, I'd appreciate it!
Broken commit?
ChromLinkMatrix.cc doesn't compile after last commit (probably due to merge issues). I found traces of git junk signature from commit 65454ff in current last commit ddd9d8f which causes compilation failure.
I workarounded by temporary modifying lines manually (delete lines from 734 to 739 and line 744) in my local build.
when donging 'make', it appeared 'collect2: ld returned 1 exit status'
Samtools 0.1.18. Boost 1.63.
When donging 'make', it appeared 'collect2: ld returned 1 exit status', like the message below.
[root@tc6000 LACHESIS-master]# make
Making all in src/include/gtools
make[1]: Entering directory /public/software/apps/LACHESIS-master/src/include/gtools' ar crv libJgtools.a N50.o ChromInterval.o HumanGenome.o CopyNumberProfile.o FileParsers.o SAMStepper.o; mv libJgtools.a .. a - N50.o a - ChromInterval.o a - HumanGenome.o a - CopyNumberProfile.o a - FileParsers.o a - SAMStepper.o make[1]: Leaving directory /public/software/apps/LACHESIS-master/src/include/gtools'
Making all in src/include/markov
make[1]: Entering directory /public/software/apps/LACHESIS-master/src/include/markov' ar crv libJmarkov.a SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o; mv libJmarkov.a .. a - SymbolSet.o a - WDAG.o a - MarkovModel.o a - MarkovChain.o a - HMM.o make[1]: Leaving directory /public/software/apps/LACHESIS-master/src/include/markov'
Making all in src/include
make[1]: Entering directory /public/software/apps/LACHESIS-master/src/include' make[1]: Nothing to be done for all'.
make[1]: Leaving directory /public/software/apps/LACHESIS-master/src/include' Making all in src make[1]: Entering directory /public/software/apps/LACHESIS-master/src'
make all-am
make[2]: Entering directory /public/software/apps/LACHESIS-master/src' /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -static -lz -lpthread -Linclude -lJtime -lJgtools -lJmarkov -L/usr/local/lib -Wl,-R,/usr/local/lib -L/usr/local/lib -Wl,-R,/usr/local/lib -L/public/software/apps/samtools-0.1.18 -lz -lpthread -lm -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -lboost_system -lboost_program_options -lboost_filesystem-mt -lbam -lz libtool: link: g++ -g -O2 -Wl,-R -Wl,/usr/local/lib -Wl,-R -Wl,/usr/local/lib -o Lachesis Lachesis-Reporter.o Lachesis-ChromLinkMatrix.o Lachesis-GenomeLinkMatrix.o Lachesis-TrueMapping.o Lachesis-LinkSizeDistribution.o Lachesis-ContigOrdering.o Lachesis-ClusterVec.o Lachesis-RunParams.o Lachesis-TextFileParsers.o Lachesis-Lachesis.o -Linclude -lJtime -lJgtools -lJmarkov -L/usr/local/lib -L/public/software/apps/samtools-0.1.18 -lpthread -lm -lboost_system -lboost_program_options -lboost_filesystem-mt -lbam -lz include/libJmarkov.a(WDAG.o): In function WDAG::ReadFromFile(std::basic_string<char, std::char_traits, std::allocator > const&)':
/usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' include/libJmarkov.a(WDAG.o): In function boost::exception_detail::error_info_injectorstd::overflow_error::~error_info_injector()':
/usr/local/include/boost/exception/exception.hpp:360: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o): In function boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::overflow_error >::~clone_impl()':
/usr/local/include/boost/exception/exception.hpp:360: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o): In function boost::exception_detail::error_info_injectorstd::overflow_error::~error_info_injector()':
/usr/local/include/boost/exception/exception.hpp:360: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o): In function boost::exception_detail::clone_impl<boost::exception_detail::error_info_injectorstd::overflow_error >::~clone_impl()':
/usr/local/include/boost/exception/exception.hpp:360: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o): In function error_info_injector':
/usr/local/include/boost/exception/exception.hpp:348: undefined reference to std::overflow_error::~overflow_error()' include/libJmarkov.a(WDAG.o):/usr/local/include/boost/exception/exception.hpp:348: more undefined references to std::overflow_error::~overflow_error()' follow
Lachesis-ChromLinkMatrix.o: In function is_regular_file': /usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
/usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' /usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
Lachesis-GenomeLinkMatrix.o: In function is_regular_file': /usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)'
/usr/local/include/boost/filesystem/operations.hpp:456: undefined reference to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' Lachesis-GenomeLinkMatrix.o:/usr/local/include/boost/filesystem/operations.hpp:456: more undefined references to boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)' follow
collect2: ld returned 1 exit status
make[2]: *** [Lachesis] Error 1
make[2]: Leaving directory /public/software/apps/LACHESIS-master/src' make[1]: *** [all] Error 2 make[1]: Leaving directory /public/software/apps/LACHESIS-master/src'
make: *** [all-recursive] Error 1
Can you give some advices to solve this problem.
errors about SAMStepper.cc and SAMStepper.h in sam.h
While install the LACHESIS in precession make . Fllowing errors appeared, Is anyone knows what's wrong with it and how to fix it ?@shendurelab
Making all in src/include/gtools
make[1]: Entering directory /home/software/LACHESIS/src/include/gtools' g++ -c SAMStepper.cc -Wall -ansi -pedantic -g -O3 -std=c++11 In file included from SAMStepper.cc:18:0: SAMStepper.h:65:58: error: too many decimal points in number /home/software/samtools-0.1.18/sam.h ^ SAMStepper.cc:32:58: error: too many decimal points in number /home/software/samtools-0.1.18/sam.h ^ In file included from SAMStepper.cc:18:0: SAMStepper.h:65:1: error: expected unqualified-id before ‘/’ token /home/software/samtools-0.1.18/sam.h ^ In file included from /public/software/gcc4.8/include/c++/4.8.1/functional:53:0, from /public/software/gcc4.8/include/c++/4.8.1/bits/stl_algo.h:66, from /public/software/gcc4.8/include/c++/4.8.1/algorithm:62, from /public/software/gcc4.8/include/c++/4.8.1/ext/slist:47, from /usr/local/include/boost/algorithm/string/std/slist_traits.hpp:16, from /usr/local/include/boost/algorithm/string/std_containers_traits.hpp:23, from /usr/local/include/boost/algorithm/string.hpp:18, from SAMStepper.cc:28: /public/software/gcc4.8/include/c++/4.8.1/typeinfo:39:37: error: expected declaration before end of line #pragma GCC visibility push(default) ^ make[1]: *** [SAMStepper.o] Error 1 make[1]: Leaving directory /home/software/LACHESIS/src/include/gtools'
make: *** [all-recursive] Error 1
Many thanks!
configure: error: cannot run /bin/sh ./config.sub
Hi,
When I run ./configure I always get the following message:
configure: error: cannot run /bin/sh ./config.sub
In the configure file I found:
# These three variables are undocumented and unsupported,
# and are intended to be withdrawn in a future Autoconf release.
# They can cause serious problems if a builder's source tree is in a directory
# whose full name contains unusual characters.
ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
I wonder if perhaps config.sub and config.guess are missing in the repository?
null_score != 0
Hi,
It run correctly at first, then it showed some messasge and Lachesis stoped. The message are as follows, and I don't know how to solve it.
Reinserting 14 shreds
OrientContigs
ContigOrdering with 2 contigs used (17 unused): 0_fw,3_fw
Full ordering: Order contains 2 of 19 contigs (10.526316%), with a total length of 379396 of 1399223 (27.114763%).
Lachesis: ChromLinkMatrix.cc:739: double ChromLinkMatrix::EnrichmentScore(const ContigOrdering&) const: Assertion `null_score != 0' failed.
Aborted (core dumped)
Thanks.
ivy
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