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de novo sequence assembler using string graphs

Home Page: http://genome.cshlp.org/content/22/3/549

C++ 94.42% C 0.81% Shell 0.31% Python 2.20% Perl 1.10% HTML 0.17% Makefile 0.47% M4 0.42% Dockerfile 0.10%

sga's Introduction

SGA - String Graph Assembler

SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

For installation and usage instructions see src/README

For running examples see src/examples and the sga wiki

For questions or support contact jared.simpson --at-- oicr.on.ca

sga's People

Contributors

Stargazers

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avilella macmanes hyphaltip nh13 drio bennyyu alicarea mh11 buttonwood nathanhaigh leemendelowitz fmarletaz sjackman kosclose fishjord csf-ngs kenongit richarddurbin mcshane jianbone eernst arturgreensward mateidavid earonesty kimrutherford luo-chengwei bioinformaticsarchive zhaoyanswill deltadev millanek theoryno3 zhangzhen bioinformaticsnl xtmgah peterhj cboursnell sherlockthang snewhouse algolab gdroc coreywischmeyer ashwinkalbhor stepf ktrns jgurtowski shevam yjx1217 fw1121 ambarrio jakevdp mr-c 0mician dbarrell arfourie scchess flopezo kneubert liuchang1437 edawson mmokrejs anomegap kastman pradosj cnyuanh pursue9190 jmg48457 iqbalmorshed attrna cihga39871 xjyx lufuhao atongsa ruolin jianshu93 xfz-creat hercules261188 minghao2016 gashanjakim liulifenyf jonaldlow1605 kvnthomas98

sga's Issues

compile error

DPAlignment.h:132:20: error: ‘c’ may be used uninitialized in this function [-Werror=uninitialized]

sga learn ratio & contig coverage info

Hi,

I am getting a warning message regarding a ratio lower than 0.75 while the reported ratio seems to be 0.83.
Am I misreading?

Also, is there a file that gives us the coverage depth information peer scaffold or per contig? If not, what would be the commands if I had to use a bam file (and which one)?

/bioinformatics/asm/bio_bin/SGA/bin/sga correct -k 37 --discard --learn -t 22 -o reads.ec.k37.fastq A16E04.fastq
[sga correct] Warning: Proportion of kmers greater than the chosen threshold is less than 0.75 (0.831247
[sga correct] This can indicate your chosen kmer size is too large or your data is too low coverage to reliably correct
[sga correct] It is suggest to lower the kmer size and/or choose the threshold manually

Thanks!

Bamtools compile error - Sort.h "missing"

Getting an error compiling on CentOS 6.3, gcc 4.4.6-4.el6, using compiled Bamtools 1.0.2. There is no /api/algorithms folder in the final product, and I had tried placing the Sort.h code file in the bamtools ./src/api/algorithms/ directory; no go. Tried to re-compile on original CentOS5.8 system, this time with jemalloc, but it fails on the DPAlignment pragma issue now.

Any ideas? Thanks — Doug

btw you recently got an email from Amarin that spurred this posting. I'm the HPC applications admin. We had SGA running, but I had compiled it with hoard which presents memory issues on very large databases (crashes)...

g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/app/sga/sparsehash/include -I/app/sga/bamtools-1.0.2/include -I/app/sga/bamtools-1.0.2/include/bamtools -Wall -Wextra -Werror -O3 -MT sga-rewrite-evidence-bam.o -MD -MP -MF .deps/sga-rewrite-evidence-bam.Tpo -c -o sga-rewrite-evidence-bam.o test -f 'rewrite-evidence-bam.cpp' || echo './'rewrite-evidence-bam.cpp
In file included from rewrite-evidence-bam.cpp:18:
/app/sga/bamtools-1.0.2/include/api/algorithms/Sort.h: In static member function ‘static bool BamTools::Algorithms::Sort::sort_helper(const BamTools::Algorithms::Sort::Order&, const ElemType&, const ElemType&)’:
/app/sga/bamtools-1.0.2/include/api/algorithms/Sort.h:38: error: ‘BT_ASSERT_UNREACHABLE’ was not declared in this scope
make[2]: *** [sga-rewrite-evidence-bam.o] Error 1

Flag Modificiation to "keep-headers"

With barcoding included in headers of recent Illumina output it would be nice to keep this information for each sequence in final output.

Currently this is screened out in Utils/SeqReader.cpp

Usage of SGA was preprocess so was looking at implementing flag there. Unfortunately do not have the time to track down all calls to SeqReader(std::string filename, flag) and add another flag for conditionals.

"Assertion `numStrings < MAX_ELEMS' failed"

While running sga index I get this:

Building index for preprocessed.fastq in memory using ropebwt
         done bwt construction, generating .sai file
sga: SampledSuffixArray.cpp:163: void SampledSuffixArray::buildLexicoIndex(const BWT*, int): Assertion `numStrings < MAX_ELEMS' failed.
Aborted (core dumped)

The input file "preprocessed.fastq" was produced by sga preprocess and looks OK as far as I can tell.

The input is rather large: preprocessed.fastq is 1.1 TB. The genome is tuatara which is ~5GB and repetitive. We have very high coverage, hence the 1.1 TB of sequence.

I tried sga index/preqc on a sightly smaller tuatara dataset a month ago and everything worked well. (preqc is very nice!) We added ~100 GB of new data this week so I'm trying again.

I'm using the head of the master branch from GitHub: 6a5dc43 which has worked fine for several other (smaller) datasets.

The core file was truncate by a ulimit limit so probably isn't much use. gdb says:

Reading symbols from /usr/local/sga-v0.9.4-908-g6a5dc43/bin/sga...(no debugging symbols found)...done.
BFD: Warning: /var/scratch/tuatara/v6/sga/core is truncated: expected core file size >= 171233517568, found: 102400000000.
[New LWP 26492]
Cannot access memory at address 0x7f781683b1a8
Cannot access memory at address 0x7f781683b1a0
(gdb) bt
#0  0x00007f7815063475 in ?? ()
Cannot access memory at address 0x7fffda223448

I'm happy to run it again with no ulimit if that would be useful. It takes a day or two to run though.

Thanks for your help.

preprocess --quality-scale bug

In the help and code for sga preprocess there is reference to a non-existent --quality-scale option. I asume this is a relic from before --phred64 flag was implemented?

Compile error

Hey Jared, when I tried to compile the latest version, I ran into this error..
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/home/pacbio/bamtools/include -I/home/pacbio/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas .Wno-unknonw-pragmas-O3 -MT sga-haplotype-filter.o -MD -MP -MF ".deps/sga-haplotype-filter.Tpo" -c -o sga-haplotype-filter.o test -f 'haplotype-filter.cpp' || echo './'haplotype-filter.cpp;
then mv -f ".deps/sga-haplotype-filter.Tpo" ".deps/sga-haplotype-filter.Po"; else rm -f ".deps/sga-haplotype-filter.Tpo"; exit 1; fi
g++: .Wno-unknonw-pragmas-O3: No such file or directory
cc1plus: warnings being treated as errors
haplotype-filter.cpp: In function ‘void runSimulation()’:
haplotype-filter.cpp:302: warning: converting to ‘size_t’ from ‘double’
haplotype-filter.cpp:305: warning: passing NULL to non-pointer argument 1 of ‘void srand(unsigned int)’
haplotype-filter.cpp: In function ‘double LMDiploidNonUniform(const std::vector<double, std::allocator >&, const std::vector<long unsigned int, std::allocator >&)’:
haplotype-filter.cpp:671: warning: passing ‘double’ for argument 1 to ‘double Stats::logPoisson(unsigned int, double)’
haplotype-filter.cpp:679: warning: passing ‘double’ for argument 1 to ‘double Stats::logPoisson(unsigned int, double)’
haplotype-filter.cpp: In function ‘std::vector<long unsigned int, std::allocator > simulateCoverageDiploid(double, size_t, size_t)’:
haplotype-filter.cpp:843: warning: converting to ‘size_t’ from ‘double’
haplotype-filter.cpp:844: warning: converting to ‘size_t’ from ‘double’
haplotype-filter.cpp:859: warning: passing ‘double’ for argument 1 to ‘std::vector<_Tp, _Alloc>::vector(size_t, const _Tp&, const _Alloc&) [with _Tp = long unsigned int, _Alloc = std::allocator]’
haplotype-filter.cpp: In function ‘std::vector<long unsigned int, std::allocator > simulateCoverageHaploidNonUniform(std::vector<double, std::allocator >, size_t, double&)’:
haplotype-filter.cpp:940: warning: passing ‘double’ for argument 1 to ‘std::vector<_Tp, _Alloc>::vector(size_t, const _Tp&, const _Alloc&) [with _Tp = long unsigned int, _Alloc = std::allocator]’
haplotype-filter.cpp: In function ‘std::vector<long unsigned int, std::allocator > simulateCoverageDiploidNonUniform(std::vector<double, std::allocator >, size_t, double&)’:
haplotype-filter.cpp:990: warning: converting to ‘size_t’ from ‘double’
haplotype-filter.cpp:991: warning: converting to ‘size_t’ from ‘double’
haplotype-filter.cpp:1008: warning: passing ‘double’ for argument 1 to ‘std::vector<_Tp, _Alloc>::vector(size_t, const _Tp&, const _Alloc&) [with _Tp = long unsigned int, _Alloc = std::allocator]’
make[2]: *** [sga-haplotype-filter.o] Error 1
make[2]: Leaving directory /home/pacbio/sga/src/SGA' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/pacbio/sga/src'
make: *** [all] Error 2

And idea?

~josh

abort before outputting results

Hi,

I got the following error:

cmd-> terminate called after throwing an instance of 'jellyfish::fastq_hash::ErrorReading'
what(): Bad file type '
/bin/sh: line 1: 29946 Aborted /bioinformatics/asm/bio_bin/Quake/bin/jellyfish qdump -c filelist-un.dbm > filelist-un.txt.qcts
Optimization of distribution likelihood function to choose k-mer cutoff failed. Very likely you have set the value of k too high or not provided adequate coverage (>15x). Inspect the k-mer counts for a clear separation of the error and true k-mer distributions.

real 26m49.410s
user 76m51.239s
sys 2m45.870s

[1]+ Exit 1 time /bioinformatics/asm/bio_bin/Quake/bin/quake.py -f filelist-un.txt -k 15 -p ${CPUS} -q 33

and the kmer counts file was empty:

33G -rw-rw-r-- 1 dbrami employees 33G May 7 16:38 filelist-un.dbm
0 -rw-rw-r-- 1 dbrami employees 0 May 7 16:38 kmers.txt
0 -rw-rw-r-- 1 dbrami employees 0 May 7 16:38 filelist-un.txt.qcts
0 -rw-rw-r-- 1 dbrami employees 0 May 7 16:38 r.log

Any suggestions on what to do other than try with a lower k value?

scaffold2fasta help message is unclear

The --help information for scaffold2fasta implies an uncompressed ASQG file should be given when it in fact expects a gzip-compressed graph.

error: 'tr1/unordered_set' file not found

SGA fails to compile with clang in OS X 10.9 and likely other C++11 compilers that have moved unordered_set from std::tr1 to std.

clang++ -DHAVE_CONFIG_H -I. -I..  -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -I/usr/local/opt/google-sparsehash/include -I/usr/local/opt/bamtools/include -I/usr/local/opt/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -c -o libalgorithm_a-QCProcess.o `test -f 'QCProcess.cpp' || echo './'`QCProcess.cpp
OverlapAlgorithm.cpp:8:10: fatal error: 'tr1/unordered_set' file not found
#include <tr1/unordered_set>
         ^
1 error generated.

Compile error

Hey Jared,
I am trying to install SGA. I installed sparsehash and bamtools.

I get the following error when I try to 'make'.

if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/g/gibson/uyar//include -I/g/gibson/uyar/genome_assembly/tools/other/bamtools-master//include -I/g/gibson/uyar/genome_assembly/tools/other/bamtools-master//include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-preqc.o -MD -MP -MF ".deps/sga-preqc.Tpo" -c -o sga-preqc.o test -f 'preqc.cpp' || echo './'preqc.cpp;
then mv -f ".deps/sga-preqc.Tpo" ".deps/sga-preqc.Po"; else rm -f ".deps/sga-preqc.Tpo"; exit 1; fi
cc1plus: warnings being treated as errors
preqc.cpp: In function ‘void learn_mixture_parameters(const KmerDistribution&, ModelParameters&)’:
preqc.cpp:428: warning: converting to ‘size_t’ from ‘double’
preqc.cpp:455: warning: converting to ‘int’ from ‘double’
preqc.cpp:541: warning: passing ‘double’ for argument 1 to ‘int abs(int)’
make[2]: *** [sga-preqc.o] Error 1
make[2]: Leaving directory /g/gibson/uyar/genome_assembly/tools/Assemblers/sga-master/src/SGA' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/g/gibson/uyar/genome_assembly/tools/Assemblers/sga-master/src'
make: *** [all] Error 2

Do you know how to fix this?

Cheers,
Bora

Linker error: undefined symbol ld_set

bcr.c (ld_set) should be static inline

Undefined symbols for architecture x86_64:
  "_ld_set", referenced from:
      _bcr_append in libthirdparty.a(bcr.o)

Cheers,
Shaun

evaluate with Software Sustainability Institute's criteria-based software evaluation

http://www.software.ac.uk/software-evaluation-guide

http://software.ac.uk/sites/default/files/SSI-SoftwareEvaluationCriteria.pdf

If you're feeling gutsy :-)

fastq.gz support?

I saw that there is SGA has a dependency on zlib library; but i haven't seen in the documentation any explicit support for fastq.gz. format.
I am wrong to assume that SGA can indeed handle fastq.gz files?

sga preprocess only reads first few hundred paired fastq reads when they are pre quality-trimmed

Preprocess -p 1 works fine when the reads aren't yet quality trimmed, but only reads the first few hundred when they are for some reason. There is no error or warning message. The only things I can think of are that 1, the reads are probably different length at some point, and 2, maybe one of my reads is out of order or unmated at that point (I don't think that is the issue because the program I use makes a separate file for singleton reads).

Compile Error

Hello, I'm getting a compile error. Any help would be greatly appreciated.

[rtaylor@Bio-DAP20 src]$ ./configure --prefix=$HOME/local --exec-prefix=$HOME/local --with-sparsehash=$HOME/local/ --with-bamtools=$HOME/local/bin/bamtools --with-jemalloc=$HOME/local/lib/
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for ranlib... ranlib
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for library containing gzopen... -lz
checking for library containing clock_gettime... -lrt
checking for OpenMP flag of C++ compiler... -fopenmp
checking for host type... you are not using osx so multi-threading should work.
checking for malloc in -ljemalloc... yes
checking google/sparse_hash_set usability... yes
checking google/sparse_hash_set presence... yes
checking for google/sparse_hash_set... yes
checking for google/sparse_hash_set... (cached) yes
checking google/sparse_hash_map usability... yes
checking google/sparse_hash_map presence... yes
checking for google/sparse_hash_map... yes
checking unordered_map usability... no
checking unordered_map presence... no
checking for unordered_map... no
checking tr1/unordered_map usability... yes
checking tr1/unordered_map presence... yes
checking for tr1/unordered_map... yes
checking ext/hash_map usability... yes
checking ext/hash_map presence... yes
checking for ext/hash_map... yes
checking unordered_set usability... no
checking unordered_set presence... no
checking for unordered_set... no
checking tr1/unordered_set usability... yes
checking tr1/unordered_set presence... yes
checking for tr1/unordered_set... yes
checking ext/hash_set usability... yes
checking ext/hash_set presence... yes
checking for ext/hash_set... yes
checking api/BamReader.h usability... yes
checking api/BamReader.h presence... yes
checking for api/BamReader.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating Thirdparty/Makefile
config.status: creating Util/Makefile
config.status: creating SQG/Makefile
config.status: creating Bigraph/Makefile
config.status: creating Algorithm/Makefile
config.status: creating StringGraph/Makefile
config.status: creating Concurrency/Makefile
config.status: creating SuffixTools/Makefile
config.status: creating GraphDiff/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SGA/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
[rtaylor@Bio-DAP20 src]$ make

...
... No errors in previous directories
...

make[2]: Entering directory /home/rtaylor/local/src/sga/src/GraphDiff' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelUtil.o -MD -MP -MF .deps/libgraphdiff_a-DindelUtil.Tpo -c -o libgraphdiff_a-DindelUtil.otest -f 'DindelUtil.cpp' || echo './'DindelUtil.cpp mv -f .deps/libgraphdiff_a-DindelUtil.Tpo .deps/libgraphdiff_a-DindelUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelRealignWindow.o -MD -MP -MF .deps/libgraphdiff_a-DindelRealignWindow.Tpo -c -o libgraphdiff_a-DindelRealignWindow.otest -f 'DindelRealignWindow.cpp' || echo './'DindelRealignWindow.cpp mv -f .deps/libgraphdiff_a-DindelRealignWindow.Tpo .deps/libgraphdiff_a-DindelRealignWindow.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelHMM.o -MD -MP -MF .deps/libgraphdiff_a-DindelHMM.Tpo -c -o libgraphdiff_a-DindelHMM.otest -f 'DindelHMM.cpp' || echo './'DindelHMM.cpp mv -f .deps/libgraphdiff_a-DindelHMM.Tpo .deps/libgraphdiff_a-DindelHMM.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-OverlapHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Tpo -c -o libgraphdiff_a-OverlapHaplotypeBuilder.otest -f 'OverlapHaplotypeBuilder.cpp' || echo './'OverlapHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Tpo .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-StringHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-StringHaplotypeBuilder.Tpo -c -o libgraphdiff_a-StringHaplotypeBuilder.otest -f 'StringHaplotypeBuilder.cpp' || echo './'StringHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-StringHaplotypeBuilder.Tpo .deps/libgraphdiff_a-StringHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DeBruijnHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Tpo -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.otest -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'DeBruijnHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Tpo .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Tpo -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.otest -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'PairedDeBruijnHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Tpo .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-HapgenUtil.o -MD -MP -MF .deps/libgraphdiff_a-HapgenUtil.Tpo -c -o libgraphdiff_a-HapgenUtil.otest -f 'HapgenUtil.cpp' || echo './'HapgenUtil.cpp mv -f .deps/libgraphdiff_a-HapgenUtil.Tpo .deps/libgraphdiff_a-HapgenUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-VCFTester.o -MD -MP -MF .deps/libgraphdiff_a-VCFTester.Tpo -c -o libgraphdiff_a-VCFTester.otest -f 'VCFTester.cpp' || echo './'VCFTester.cpp mv -f .deps/libgraphdiff_a-VCFTester.Tpo .deps/libgraphdiff_a-VCFTester.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-GraphCompare.o -MD -MP -MF .deps/libgraphdiff_a-GraphCompare.Tpo -c -o libgraphdiff_a-GraphCompare.otest -f 'GraphCompare.cpp' || echo './'GraphCompare.cpp mv -f .deps/libgraphdiff_a-GraphCompare.Tpo .deps/libgraphdiff_a-GraphCompare.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-OverlapExtractorWithCorrection.o -MD -MP -MF .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo -c -o libgraphdiff_a-OverlapExtractorWithCorrection.otest -f 'OverlapExtractorWithCorrection.cpp' || echo './'OverlapExtractorWithCorrection.cpp mv -f .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/home/rtaylor/local//include -I/home/rtaylor/local/bin/bamtools/include -I/home/rtaylor/local/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DBGPathGuide.o -MD -MP -MF .deps/libgraphdiff_a-DBGPathGuide.Tpo -c -o libgraphdiff_a-DBGPathGuide.otest -f 'DBGPathGuide.cpp' || echo './'DBGPathGuide.cpp DBGPathGuide.cpp: In member function ‘void DBGPathGuide::printStats() const’: DBGPathGuide.cpp:40:132: error: ‘printf’ was not declared in this scope make[2]: *** [libgraphdiff_a-DBGPathGuide.o] Error 1 make[2]: Leaving directory/home/rtaylor/local/src/sga/src/GraphDiff'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/rtaylor/local/src/sga/src'
make: *** [all] Error 2

[rtaylor@Bio-DAP20 src]$ gcc --version
gcc (GCC) 4.6.3 20120306 (Red Hat 4.6.3-2)
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[rtaylor@Bio-DAP20 src]$ cat /proc/version
Linux version 2.6.43.8-1.fc15.x86_64 ([email protected]) (gcc version 4.6.3 20120306 (Red Hat 4.6.3-2) (GCC) ) #1 SMP Mon Jun 4 20:33:44 UTC 2012

error: type qualifiers ignored on function return type

Using bamtools downloaded in July 2011 (BamIndex.h header last modified 19 November 2010), with recent git sources, I get several (identical) compile errors, which are fixed either by removing -Werror or removing const from the "offending" line in BamReader.h.

Details:

make[2]: Entering directory ~/Packages/Assemblers/sga/sga/src/SGA' g++-4.4.5 -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../Thirdparty -Wall -Wextra -Werror -O3 -MT sga-filterBAM.o -MD -MP -MF .deps/sga-filterBAM.Tpo -c -o sga-filterBAM.otest -f 'filterBAM.cpp' || echo './'`filterBAM.cpp
cc1plus: warnings being treated as errors
In file included from api/BamReader.h:16,
from filterBAM.cpp:29:
api/BamIndex.h:77: error: type qualifiers ignored on function return type
make[2]: *** [sga-filterBAM.o] Error 1

Doesn't find bamtools libraries when installed

When bamtools is installed to a custom area (cmake -DCMAKE_INSTALL_PREFIX=/path/to/installation && make && make install), the shared libs and headers are in /path/to/installation/{lib,include}/bamtools, rather than /path/to/installation/{lib,include}.

Currently ./configure fails with a custom installation of bamtools

Can't compile sga!!

Gigven below are the errors : -

g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/home/mayank/bin/bamtools/include -I/home/mayank/bin/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTAlgorithms.o -MD -MP -MF .deps/libsuffixtools_a-BWTAlgorithms.Tpo -c -o libsuffixtools_a-BWTAlgorithms.o test -f 'BWTAlgorithms.cpp' || echo './'BWTAlgorithms.cpp
BWTAlgorithms.cpp: In function ‘void extractRankedPrefixes(const BWT, BWTInterval, const string&, RankedPrefixVector_)’:
BWTAlgorithms.cpp:423:46: error: narrowing conversion of ‘i’ from ‘int64_t {aka long int}’ to ‘size_t {aka long unsigned int}’ inside { } is ill-formed in C++11 [-Werror=narrowing]
cc1plus: all warnings being treated as errors

BWTAlgorithms::updateInterval(interval, '$', pBWT);
for(int64_t i = interval.lower; i <= interval.upper; ++i)
{
// backwards search gives a reversed prefix, fix it
RankedPrefix rp = { i, reverse(curr) };
pOutput->push_back(rp);
}

I changed the int64_t to size_t but I am not sure if this affects my assemblies.
/Mayank

Add strand bias for errors

Strand bias of errors is an interesting aspect of read QC. It should not be too difficult to add something to preqc that measures/quantifies this (he said naively)...

Does not compile with most recent g++

Some warnings treated as errors made this not compile on Arch Linux 64-bit with the most recent version of gcc.
In the generated configure-file on line 195, changing
AM_CXXFLAGS = -Wall -Wextra -Werror -Wno-unknown-pragmas
to
AM_CXXFLAGS = -Wall -Wextra -Werror -Wno-unknown-pragmas -Wno-maybe-uninitialized -Wno-unused-local-typedefs

fixes this.

sga merge fails in trunk

The "sga merge" command fails in trunk:
[nwatson-haigh@awrivm1 sga]$ ~/sga-trunk/bin/sga --version
String Graph Assembler (sga) Version 0.9.30
Written by Jared Simpson.

[nwatson-haigh@awrivm1 sga]$ /home/nwatson-haigh/sga-trunk/bin/sga merge -r -t 30 merged.8.fastq merged.27.fastq
Merge1: [0,-1] merged.bwt merged.sai merged.8.fastq
Merge2: [0,-1] merged.bwt merged.sai merged.27.fastq
Error: could not open merged.bwt for read

An earlier version worked:

[nwatson-haigh@awrivm1 sga]$ ~/sga/bin/sga --version
String Graph Assembler (sga) Version 0.9.20
Written by Jared Simpson.

[nwatson-haigh@awrivm1 index_raw]$ /home/nwatson-haigh/sga/bin/sga merge -r -t 30 merged.8.fastq merged.27.fastq
Merge1: [0,-1] merged.8.bwt merged.8.sai merged.8.fastq
Merge2: [0,-1] merged.27.bwt merged.27.sai merged.27.fastq
[sga::process] processed 151923 sequences in 3.246327s (46798.427885 sequences/s)

Indexing crashes with -t 30, but works with -t 10 on a 64 core system

I also used a really large -d for the -t 30 run when it crashed. Something like 200000000. Now I am using -d 4000000 like you suggest, maybe that was the issue that caused pthread_create to crash?

I get a return of "Error 12" from pthread_create. I think I read somewhere that people were having that issue with other programs when pthread_destroy wasn't called at the right time? In that case though I don't know why it works with -t10...

bad shebang in python scripts

I need to use a python version that is not /usr/bin/python to get ruffus to work.

You could change the shebang at the top of the sga-pipeline python script from:

!/usr/bin/python

to:

!/usr/bin/env python

so that the python version that is used is chosen from the user's environment.

Thanks!

sga-mergeDriver.pl improvements

Needs help text if nothing is passed in

Needs to be able to suppress `-r' being passed to sga merge

Have option to run the jobs in sequential (locally) instead of outputting the command line

CentOS 5.8 install

Does anyone know if this is possible? The biggest issue I've run into is that there is no Sparsehash package available in the respositories for this, and trying to install from the downloaded rpm from the google site results in an error:

rpm -i sparsehash-2.0.2-1.noarch.rpm
error: Failed dependencies:
rpmlib(FileDigests) <= 4.6.0-1 is needed by sparsehash-2.0.2-1.noarch
rpmlib(PayloadIsXz) <= 5.2-1 is needed by sparsehash-2.0.2-1.noarch

I don't know what provides these, anyone have any success installing on a slightly older Redhat or CentOS install? I have hope, because there does appear to be a CentOS 6 version of this in the repositories.

SGA requires OpenMP

Hi Jared,

The previous release of SGA (0.9.37) built without OpenMP, but the current HEAD requires OpenMP:

../Concurrency/SequenceProcessFramework.h:279:5: error: use of undeclared
      identifier 'omp_set_num_threads'
    omp_set_num_threads(numThreads);

Just wanted to check whether this change was intentional. It's fine either way. If OpenMP is a required dependency, perhaps ./configure could output an error message if it's not available.

I ask because the default compile on OS X is clang, which doesn't provide OpenMP. GCC is available though.

Cheers,
Shaun

SGA/src/bin/sga-bam2de.pl has invalid default values

Hi,

My pipeline is not completing successfully. When I reach the said portion of the pipeline, I get the pasted error.
It seems the default value of '0' for the --seed-length falg, given in the perl code as $minLength = 0 is not playing nice.
incidentally, the -s flag in the 'DistanceEst' command is set twice (to same value).

Please advise on a better default value

cmd-> /bioinformatics/asm/bio_bin/SGA/src/bin/sga-bam2de.pl -n 5 --prefix libPE A15H06.pe.bam
abyss-fixmate -h libPE.tmp.hist A15H06.pe.bam | samtools view -Sb - > libPE.diffcontigs.bam
[samopen] SAM header is present: 1181 sequences.
Mateless 0
Unaligned 83624 0.883%
Singleton 417487 4.41%
FR 8595667 90.8%
RF 2260 0.0239%
FF 729 0.0077%
Different 367979 3.89%
Total 9467746
awk '$2 >= 3' libPE.tmp.hist > libPE.hist
samtools sort libPE.diffcontigs.bam libPE.diffcontigs.sorted
DistanceEst -s 0 -n 5 -k 99 -j 1 -o libPE.de libPE.hist libPE.diffcontigs.sorted.bam
DistanceEst: missing -s,--seed-length option
Try `DistanceEst --help' for more information.

division by zero error on output for sga-astat.py

In the final printing step of sga-astat.py, there's a line that includes a division:
print '%s\t%d\t%d\t%d\t%f\t%f' % (cd.name, cd.len, cd.nlen, cd.n, cd.n / (cd.nlen * arrivalRate), cd.astat)

This line resulted in an error when I ran it on my bowtie2-mapped reads (with no minimum contig length set) against assembled contigs:

$ ~/bin/sga-astat.py enterococci_all_vs_supergenome.bam > contigs.astat
Reading alignments from enterococci_all_vs_supergenome.bam
Initial arrival rate: 2.67734681196
Initial genome size estimate: 8412774
Iteration 0 arrival rate: 1.63762399084
Iteration 0 genome size estimate: 13754021
Iteration 1 arrival rate: 1.27047154511
Iteration 1 genome size estimate: 17728783
Iteration 2 arrival rate: 1.17208944432
Iteration 2 genome size estimate: 19216890
Using genome size: 19216890
Using arrival rate: 1.17208950043
Traceback (most recent call last):
File "/home/gringer/bin/sga-astat.py", line 175, in
print '%s\t%d\t%d\t%d\t%f\t%f' % (cd.name, cd.len, cd.nlen, cd.n, cd.n / (cd.nlen * arrivalRate), cd.astat)
ZeroDivisionError: float division by zero

Obviously this error is happening because cd.nlen is zero, which can only happen if the contig size is one less than the average read length:

[line 121] cd.nlen = cd.len - avgReadLen + 1

Other bits in the code seem to assume that this value, cd.nlen, is positive, e.g. line 131: [bootstrapLen += cd.nlen].

One fix for this particular division by zero error is to ensure that cd.nlen is always positive by making the following change:

[line 121] cd.nlen = cd.len - avgReadLen + 1 if (cd.len > avgReadLen) else 1

I'm not sure how this would affect other code regions. Based on the description, "number of positions
that can generate a read of length avgReadLen", this should probably be 'else 0' rather than 'else 1', but then the division by zero error would occur for all situations where the contig length is less than the read length, rather than the current state of only when it's exactly one bp less. Given that it gets through the code fine until this point, an alternative change consistent with this description would be the following:

[line 121] cd.nlen = cd.len - avgReadLen + 1 if (cd.len > avgReadLen) else 0
[line 175-176]
nstat = cd.n / (cd.nlen * arrivalRate) if (cd.nlen > 0) else 0
print '%s\t%d\t%d\t%d\t%f\t%f' % (cd.name, cd.len, cd.nlen, nstat, cd.astat)

Bearing in mind that this would push the zero problem further downstream. I haven't looked at what would happen to sga scaffold if it found a zero value (or negative value) in this column.

COMPILE error: BamTools has not been declared

Hello,

Issue occurs at make step:

...
Making all in GraphDiff
make[2]: Entering directory /shared/reads/velvet_1.2.07/contrib/VelvetOptimiser-2.2.0/pseudoloma/sga/sga/src/GraphDiff' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I../../bamtools//include -I../../bamtools//include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelUtil.o -MD -MP -MF .deps/libgraphdiff_a-DindelUtil.Tpo -c -o libgraphdiff_a-DindelUtil.otest -f 'DindelUtil.cpp' || echo './'DindelUtil.cpp In file included from DindelUtil.h:14, from DindelUtil.cpp:11: GraphCompare.h:31:27: error: api/BamWriter.h: No such file or directory In file included from DindelUtil.h:14, from DindelUtil.cpp:11: GraphCompare.h:234: error: \u2018BamTools\u2019 has not been declared GraphCompare.h:234: error: ISO C++ forbids declaration of \u2018BamWriter\u2019 with no type GraphCompare.h:234: error: expected \u2018;\u2019 before \u2018m_evidenceBamFile\u2019 make[2]: *** [libgraphdiff_a-DindelUtil.o] Error 1 make[2]: Leaving directory/shared/reads/velvet_1.2.07/contrib/VelvetOptimiser-2.2.0/pseudoloma/sga/sga/src/GraphDiff'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/shared/reads/velvet_1.2.07/contrib/VelvetOptimiser-2.2.0/pseudoloma/sga/sga/src'
make: *** [all] Error 2

$ gcc --version
gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ uname -a
Linux BioPower 2.6.32-279.5.1.el6.x86_64 #1 SMP Tue Aug 14 16:11:42 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux

Bamtools: bamtools-2.2.3
Config cmd:
$ ./configure --with-bamtools=../../bamtools/ --with-jemalloc=../../jemalloc/lib
...
checking api/BamReader.h usability... yes
checking api/BamReader.h presence... yes
checking for api/BamReader.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating Thirdparty/Makefile
config.status: creating Util/Makefile
config.status: creating SQG/Makefile
config.status: creating Bigraph/Makefile
config.status: creating Algorithm/Makefile
config.status: creating StringGraph/Makefile
config.status: creating Concurrency/Makefile
config.status: creating SuffixTools/Makefile
config.status: creating GraphDiff/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SGA/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands

Any thoughts would be appreciated,
Adrian

sga preprocess disable primer screen

I had assumed from the docs that unless I supplied a STRING for -r and/or -c they primer screening would not be enabled.

I'm trying to preprocess some 454 data and it's screening for sequences defined in src/Util/PrimerScreen.cpp. Is there a way to disable this?

Compile error on ubuntu 64bit

Hi,

I tried to compile sga on our ubuntu server (64 bit) and got the following error message:

... (no errors in previous directories)
make[2]: Entering directory /home1/ctx/software/sga/src/SGA' g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/ctx/software/bamtools/include -I/ctx/software/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-haplotype-filter.o -MD -MP -MF .deps/sga-haplotype-filter.Tpo -c -o sga-haplotype-filter.otest -f 'haplotype-filter.cpp' || echo './'haplotype-filter.cpp haplotype-filter.cpp: In function 'double LMDiploidNonUniform(const std::vector<double>&, const std::vector<long unsigned int>&)': haplotype-filter.cpp:659:12: error: variable 'best_M' set but not used [-Werror=unused-but-set-variable] cc1plus: all warnings being treated as errors make[2]: *** [sga-haplotype-filter.o] Error 1 make[2]: Leaving directory/home1/ctx/software/sga/src/SGA'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home1/ctx/software/sga/src'
make: *** [all] Error 2

Any suggestions? If you need any more info, contact me!
Thanks in advance,
Chris

sga index output unexpectedly placed in working directory

When running

sga index --no-reverse directory/file.fastq

I would have expected the index files that are created to be directory/file.bwt and directory/file.sai, but they are actually put into the working directory as file.bwt and file.sai. This can be worked-around by using the -p option, but is still unexpected behavior that makes sga index a little harder to use in automated workflows.

Compile error on 32-bit Ubuntu

When compiling on a 32-bit system, I received this compilation error:

LRAlignment.cpp: In function ‘void LRAlignment::removeDuplicateCells(LRAlignment::LRStackEntry*, LRAlignment::LRHash&)’:
LRAlignment.cpp:560:37: error: left shift count >= width of type [-Werror]
LRAlignment.cpp:566:30: error: left shift count >= width of type [-Werror]
cc1plus: all warnings being treated as errors

Assertion failed in scaffold2fasta

Failed assertion causes a crash in scaffold2fasta:

/home/mvermaat1/bin/sga scaffold2fasta --use-overlap --write-unplaced -m 200 -o R52c.scaffolds.fa -a R52c.ec.k41.filter.pass.asqg.gz R52c.scaffolds.scaf
Warning: removed Graph best: 0
Graph unique: 1
Find overlaps: 4
Deleted edges for 0 super repetitive vertices
16 duplicate edges
sga: ScaffoldSequenceCollection.cpp:26: virtual std::string GraphSequenceCollection::getSequence(const string&) const: Assertion `pVertex != __null' failed.
Vertices: 10774002 Edges: 85142090 Islands: 63761 Tips: 558513 Monobranch: 3560421 Dibranch: 680564 Simple: 9801302

Please let me know what's needed to debug this. I use current git master sga.

Option (flag) to restrict output to read quality plots

Motivation: I sometimes see preqc showing read QC problems that were missed with fastqc. So adding this to a standard read QC pipeline would be very useful, but the full preqc pipeline takes quite some time.

Request: option to restrict output to 'Mean quality score by position', 'Fraction of bases at least Q30' and any other plots that can be made once the analysis has come far enough for these. Perhaps also 'Estimated Fragment Size Histogram' and Est. PCR Duplicate Proportion. In the hope that it is faster than full preqc, that is...

Issue running 'make'

Hello,

Trying to install sga to run preqc on some reads I'm having trouble assembling. When I run make in the src directory I get the following output and the install files arent created. Let me know what you think when you get time. I'm running GCC version 4.8.1 on Ubuntu 13.10. Thanks,

Justin

make[2]: Entering directory /home/justin/sga-master/src/Algorithm' g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/home/justin/sga-master/src/bamtools/include -I/home/justin/sga-master/src/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-DPAlignment.o -MD -MP -MF .deps/libalgorithm_a-DPAlignment.Tpo -c -o libalgorithm_a-DPAlignment.otest -f 'DPAlignment.cpp' || echo './'DPAlignment.cpp In file included from DPAlignment.cpp:9:0: DPAlignment.h: In member function ‘void DPAlignment::fillMatrix(const string&, const string&)’: DPAlignment.h:133:20: error: ‘a’ may be used uninitialized in this function [-Werror=maybe-uninitialized] inline int compare3(int a, int b, int c) const ^ DPAlignment.h:133:20: error: ‘b’ may be used uninitialized in this function [-Werror=maybe-uninitialized] DPAlignment.h:133:20: error: ‘c’ may be used uninitialized in this function [-Werror=maybe-uninitialized] DPAlignment.h:133:20: error: ‘c’ may be used uninitialized in this function [-Werror=maybe-uninitialized] DPAlignment.h:133:20: error: ‘a’ may be used uninitialized in this function [-Werror=maybe-uninitialized] DPAlignment.h:133:20: error: ‘b’ may be used uninitialized in this function [-Werror=maybe-uninitialized] cc1plus: all warnings being treated as errors make[2]: *** [libalgorithm_a-DPAlignment.o] Error 1 make[2]: Leaving directory/home/justin/sga-master/src/Algorithm'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/justin/sga-master/src'
make: *** [all] Error 2

Could not getVertex(id), when id is the first one in scaffolds.m200.u25.scaf file

Here is the output:
"
Constructed 2068245 scaffolds from 2068974 contigs (2067788 singleton scaffolds)
Total bases: 2561.80Mbp
Total span: 2561.81Mbp
Max scaffold span: 44310 bp
N50 scaffold span: 2878 bp
Mean scaffold span: 1239 bp
Graph best: 0
Graph unique: 1
Find overlaps: 4
Deleted edges for 0 super repetitive vertices
Vertices: 0 Edges: 0 Islands: 0 Tips: 0 Monobranch: 0 Dibranch: 0 Simple: 0
Error: could not find the contig record with id contig-5530055
Check to make sure you have loaded the correct set of contigs
"
In fact, this contig shows up in every file related to scaffold and scaffold2fa procedure.
Besides, this contig is the first item in scaf file, I wonder what is wrong here.

Describe the ASQG file format

Here's a relevant posting.

Some error in preqc after compile

preqc.cpp: In function 'void generate_branch_classification(JSONWriter_, GenomeEstimates, const BWTIndexSet&)':
preqc.cpp:1396: warning: passing 'double' for argument 1 to 'double probability_diploid_copy(size_t, size_t)'
preqc.cpp: In function 'void generate_de_bruijn_simulation(JSONWriter_, GenomeEstimates, const BWTIndexSet&)':
preqc.cpp:1633: warning: passing 'double' for argument 1 to 'double probability_diploid_copy(size_t, size_t)'
make[2]: * [sga-preqc.o] Error 1
make[2]: Leaving directory /home/****/temp/SGA/sga-master/src/SGA' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/*_/temp/SGA/sga-master/src'
make: *_* [all] Error 2

sga preqc command fails with "unrecognized command: preqc"

Bubble Orientation Issue

SGSearch::findVariantWalks looks for situations where all walks that exit a node X pass through a common node Y. If the sequences of these alternative walks are similar enough, and if the variant walks can be cleanly removed, then one walk from X to Y is retained and the nodes on the variant walks are removed.

However, findVariantWalks fails to check that Y has the same orientation in all walks. There may be rare cases where all walks which leave one end of X enter Y, but the orientation of Y differs between walks. Without checking that the orientation is consistent, the graph will still be smoothed.

Error in overlap step

The error I am getting is as follows.

Error: the top level block in irreducible-overlap computation does not have the expected terminal character

Not sure exactly what is causing it, however in the initial preprocessing step I trimmed reads based on quality scores, so it could be that some reads are trimmed too short perhaps? If you have any ideas what I could look at to see what is causing the error let me know.

Compile error on MacOS X 10.7.4

I've received the following compile error from SGA downloaded 21.03.13. I also have the newest version of Xcode 4.6.1

rsb-33-059:src meganm$ sudo make
Password:
make all-recursive
Making all in bin
make[2]: Nothing to be done for all'. Making all in Thirdparty g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT gzstream.o -MD -MP -MF .deps/gzstream.Tpo -c -o gzstream.o gzstream.C mv -f .deps/gzstream.Tpo .deps/gzstream.Po gcc -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -O3 -MT stdaln.o -MD -MP -MF .deps/stdaln.Tpo -c -o stdaln.o stdaln.c mv -f .deps/stdaln.Tpo .deps/stdaln.Po g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT overlapper.o -MD -MP -MF .deps/overlapper.Tpo -c -o overlapper.o overlapper.cpp mv -f .deps/overlapper.Tpo .deps/overlapper.Po g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT multiple_alignment.o -MD -MP -MF .deps/multiple_alignment.Tpo -c -o multiple_alignment.o multiple_alignment.cpp mv -f .deps/multiple_alignment.Tpo .deps/multiple_alignment.Po gcc -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -O3 -MT bcr.o -MD -MP -MF .deps/bcr.Tpo -c -o bcr.o bcr.c mv -f .deps/bcr.Tpo .deps/bcr.Po g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT MurmurHash3.o -MD -MP -MF .deps/MurmurHash3.Tpo -c -o MurmurHash3.o MurmurHash3.cpp mv -f .deps/MurmurHash3.Tpo .deps/MurmurHash3.Po g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT count_min_sketch.o -MD -MP -MF .deps/count_min_sketch.Tpo -c -o count_min_sketch.o count_min_sketch.cpp mv -f .deps/count_min_sketch.Tpo .deps/count_min_sketch.Po rm -f libthirdparty.a ar cru libthirdparty.a gzstream.o stdaln.o overlapper.o multiple_alignment.o bcr.o MurmurHash3.o count_min_sketch.o ranlib libthirdparty.a Making all in Util g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Util.o -MD -MP -MF .deps/libutil_a-Util.Tpo -c -o libutil_a-Util.otest -f 'Util.cpp' || echo './'Util.cpp mv -f .deps/libutil_a-Util.Tpo .deps/libutil_a-Util.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Alphabet.o -MD -MP -MF .deps/libutil_a-Alphabet.Tpo -c -o libutil_a-Alphabet.otest -f 'Alphabet.cpp' || echo './'Alphabet.cpp mv -f .deps/libutil_a-Alphabet.Tpo .deps/libutil_a-Alphabet.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Contig.o -MD -MP -MF .deps/libutil_a-Contig.Tpo -c -o libutil_a-Contig.otest -f 'Contig.cpp' || echo './'Contig.cpp mv -f .deps/libutil_a-Contig.Tpo .deps/libutil_a-Contig.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-ReadTable.o -MD -MP -MF .deps/libutil_a-ReadTable.Tpo -c -o libutil_a-ReadTable.otest -f 'ReadTable.cpp' || echo './'ReadTable.cpp mv -f .deps/libutil_a-ReadTable.Tpo .deps/libutil_a-ReadTable.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-ReadInfoTable.o -MD -MP -MF .deps/libutil_a-ReadInfoTable.Tpo -c -o libutil_a-ReadInfoTable.otest -f 'ReadInfoTable.cpp' || echo './'ReadInfoTable.cpp mv -f .deps/libutil_a-ReadInfoTable.Tpo .deps/libutil_a-ReadInfoTable.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-SeqReader.o -MD -MP -MF .deps/libutil_a-SeqReader.Tpo -c -o libutil_a-SeqReader.otest -f 'SeqReader.cpp' || echo './'SeqReader.cpp mv -f .deps/libutil_a-SeqReader.Tpo .deps/libutil_a-SeqReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-DNAString.o -MD -MP -MF .deps/libutil_a-DNAString.Tpo -c -o libutil_a-DNAString.otest -f 'DNAString.cpp' || echo './'DNAString.cpp mv -f .deps/libutil_a-DNAString.Tpo .deps/libutil_a-DNAString.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Match.o -MD -MP -MF .deps/libutil_a-Match.Tpo -c -o libutil_a-Match.otest -f 'Match.cpp' || echo './'Match.cpp mv -f .deps/libutil_a-Match.Tpo .deps/libutil_a-Match.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Pileup.o -MD -MP -MF .deps/libutil_a-Pileup.Tpo -c -o libutil_a-Pileup.otest -f 'Pileup.cpp' || echo './'Pileup.cpp mv -f .deps/libutil_a-Pileup.Tpo .deps/libutil_a-Pileup.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-BitChar.o -MD -MP -MF .deps/libutil_a-BitChar.Tpo -c -o libutil_a-BitChar.otest -f 'BitChar.cpp' || echo './'BitChar.cpp mv -f .deps/libutil_a-BitChar.Tpo .deps/libutil_a-BitChar.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Interval.o -MD -MP -MF .deps/libutil_a-Interval.Tpo -c -o libutil_a-Interval.otest -f 'Interval.cpp' || echo './'Interval.cpp mv -f .deps/libutil_a-Interval.Tpo .deps/libutil_a-Interval.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-SeqCoord.o -MD -MP -MF .deps/libutil_a-SeqCoord.Tpo -c -o libutil_a-SeqCoord.otest -f 'SeqCoord.cpp' || echo './'SeqCoord.cpp mv -f .deps/libutil_a-SeqCoord.Tpo .deps/libutil_a-SeqCoord.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-MultiOverlap.o -MD -MP -MF .deps/libutil_a-MultiOverlap.Tpo -c -o libutil_a-MultiOverlap.otest -f 'MultiOverlap.cpp' || echo './'MultiOverlap.cpp mv -f .deps/libutil_a-MultiOverlap.Tpo .deps/libutil_a-MultiOverlap.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-QualityVector.o -MD -MP -MF .deps/libutil_a-QualityVector.Tpo -c -o libutil_a-QualityVector.otest -f 'QualityVector.cpp' || echo './'QualityVector.cpp mv -f .deps/libutil_a-QualityVector.Tpo .deps/libutil_a-QualityVector.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Stats.o -MD -MP -MF .deps/libutil_a-Stats.Tpo -c -o libutil_a-Stats.otest -f 'Stats.cpp' || echo './'Stats.cpp mv -f .deps/libutil_a-Stats.Tpo .deps/libutil_a-Stats.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-Quality.o -MD -MP -MF .deps/libutil_a-Quality.Tpo -c -o libutil_a-Quality.otest -f 'Quality.cpp' || echo './'Quality.cpp mv -f .deps/libutil_a-Quality.Tpo .deps/libutil_a-Quality.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-PrimerScreen.o -MD -MP -MF .deps/libutil_a-PrimerScreen.Tpo -c -o libutil_a-PrimerScreen.otest -f 'PrimerScreen.cpp' || echo './'PrimerScreen.cpp mv -f .deps/libutil_a-PrimerScreen.Tpo .deps/libutil_a-PrimerScreen.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-BitVector.o -MD -MP -MF .deps/libutil_a-BitVector.Tpo -c -o libutil_a-BitVector.otest -f 'BitVector.cpp' || echo './'BitVector.cpp mv -f .deps/libutil_a-BitVector.Tpo .deps/libutil_a-BitVector.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-CorrectionThresholds.o -MD -MP -MF .deps/libutil_a-CorrectionThresholds.Tpo -c -o libutil_a-CorrectionThresholds.otest -f 'CorrectionThresholds.cpp' || echo './'CorrectionThresholds.cpp mv -f .deps/libutil_a-CorrectionThresholds.Tpo .deps/libutil_a-CorrectionThresholds.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-KmerDistribution.o -MD -MP -MF .deps/libutil_a-KmerDistribution.Tpo -c -o libutil_a-KmerDistribution.otest -f 'KmerDistribution.cpp' || echo './'KmerDistribution.cpp mv -f .deps/libutil_a-KmerDistribution.Tpo .deps/libutil_a-KmerDistribution.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-ClusterReader.o -MD -MP -MF .deps/libutil_a-ClusterReader.Tpo -c -o libutil_a-ClusterReader.otest -f 'ClusterReader.cpp' || echo './'ClusterReader.cpp mv -f .deps/libutil_a-ClusterReader.Tpo .deps/libutil_a-ClusterReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-MultiAlignment.o -MD -MP -MF .deps/libutil_a-MultiAlignment.Tpo -c -o libutil_a-MultiAlignment.otest -f 'MultiAlignment.cpp' || echo './'MultiAlignment.cpp mv -f .deps/libutil_a-MultiAlignment.Tpo .deps/libutil_a-MultiAlignment.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-StdAlnTools.o -MD -MP -MF .deps/libutil_a-StdAlnTools.Tpo -c -o libutil_a-StdAlnTools.otest -f 'StdAlnTools.cpp' || echo './'StdAlnTools.cpp mv -f .deps/libutil_a-StdAlnTools.Tpo .deps/libutil_a-StdAlnTools.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-VCFUtil.o -MD -MP -MF .deps/libutil_a-VCFUtil.Tpo -c -o libutil_a-VCFUtil.otest -f 'VCFUtil.cpp' || echo './'VCFUtil.cpp mv -f .deps/libutil_a-VCFUtil.Tpo .deps/libutil_a-VCFUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-QualityTable.o -MD -MP -MF .deps/libutil_a-QualityTable.Tpo -c -o libutil_a-QualityTable.otest -f 'QualityTable.cpp' || echo './'QualityTable.cpp mv -f .deps/libutil_a-QualityTable.Tpo .deps/libutil_a-QualityTable.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libutil_a-BloomFilter.o -MD -MP -MF .deps/libutil_a-BloomFilter.Tpo -c -o libutil_a-BloomFilter.otest -f 'BloomFilter.cpp' || echo './'BloomFilter.cpp mv -f .deps/libutil_a-BloomFilter.Tpo .deps/libutil_a-BloomFilter.Po rm -f libutil.a ar cru libutil.a libutil_a-Util.o libutil_a-Alphabet.o libutil_a-Contig.o libutil_a-ReadTable.o libutil_a-ReadInfoTable.o libutil_a-SeqReader.o libutil_a-DNAString.o libutil_a-Match.o libutil_a-Pileup.o libutil_a-BitChar.o libutil_a-Interval.o libutil_a-SeqCoord.o libutil_a-MultiOverlap.o libutil_a-QualityVector.o libutil_a-Stats.o libutil_a-Quality.o libutil_a-PrimerScreen.o libutil_a-BitVector.o libutil_a-CorrectionThresholds.o libutil_a-KmerDistribution.o libutil_a-ClusterReader.o libutil_a-MultiAlignment.o libutil_a-StdAlnTools.o libutil_a-VCFUtil.o libutil_a-QualityTable.o libutil_a-BloomFilter.o ranlib libutil.a Making all in SQG g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsqg_a-SQG.o -MD -MP -MF .deps/libsqg_a-SQG.Tpo -c -o libsqg_a-SQG.otest -f 'SQG.cpp' || echo './'SQG.cpp mv -f .deps/libsqg_a-SQG.Tpo .deps/libsqg_a-SQG.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -I../Util -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsqg_a-ASQG.o -MD -MP -MF .deps/libsqg_a-ASQG.Tpo -c -o libsqg_a-ASQG.otest -f 'ASQG.cpp' || echo './'ASQG.cpp mv -f .deps/libsqg_a-ASQG.Tpo .deps/libsqg_a-ASQG.Po rm -f libsqg.a ar cru libsqg.a libsqg_a-SQG.o libsqg_a-ASQG.o ranlib libsqg.a Making all in Bigraph g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libbigraph_a-Bigraph.o -MD -MP -MF .deps/libbigraph_a-Bigraph.Tpo -c -o libbigraph_a-Bigraph.otest -f 'Bigraph.cpp' || echo './'Bigraph.cpp mv -f .deps/libbigraph_a-Bigraph.Tpo .deps/libbigraph_a-Bigraph.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libbigraph_a-Vertex.o -MD -MP -MF .deps/libbigraph_a-Vertex.Tpo -c -o libbigraph_a-Vertex.otest -f 'Vertex.cpp' || echo './'Vertex.cpp mv -f .deps/libbigraph_a-Vertex.Tpo .deps/libbigraph_a-Vertex.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libbigraph_a-Edge.o -MD -MP -MF .deps/libbigraph_a-Edge.Tpo -c -o libbigraph_a-Edge.otest -f 'Edge.cpp' || echo './'Edge.cpp mv -f .deps/libbigraph_a-Edge.Tpo .deps/libbigraph_a-Edge.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libbigraph_a-EdgeDesc.o -MD -MP -MF .deps/libbigraph_a-EdgeDesc.Tpo -c -o libbigraph_a-EdgeDesc.otest -f 'EdgeDesc.cpp' || echo './'EdgeDesc.cpp mv -f .deps/libbigraph_a-EdgeDesc.Tpo .deps/libbigraph_a-EdgeDesc.Po rm -f libbigraph.a ar cru libbigraph.a libbigraph_a-Bigraph.o libbigraph_a-Vertex.o libbigraph_a-Edge.o libbigraph_a-EdgeDesc.o ranlib libbigraph.a Making all in Algorithm g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-OverlapAlgorithm.o -MD -MP -MF .deps/libalgorithm_a-OverlapAlgorithm.Tpo -c -o libalgorithm_a-OverlapAlgorithm.otest -f 'OverlapAlgorithm.cpp' || echo './'OverlapAlgorithm.cpp mv -f .deps/libalgorithm_a-OverlapAlgorithm.Tpo .deps/libalgorithm_a-OverlapAlgorithm.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-SearchSeed.o -MD -MP -MF .deps/libalgorithm_a-SearchSeed.Tpo -c -o libalgorithm_a-SearchSeed.otest -f 'SearchSeed.cpp' || echo './'SearchSeed.cpp mv -f .deps/libalgorithm_a-SearchSeed.Tpo .deps/libalgorithm_a-SearchSeed.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-OverlapBlock.o -MD -MP -MF .deps/libalgorithm_a-OverlapBlock.Tpo -c -o libalgorithm_a-OverlapBlock.otest -f 'OverlapBlock.cpp' || echo './'OverlapBlock.cpp mv -f .deps/libalgorithm_a-OverlapBlock.Tpo .deps/libalgorithm_a-OverlapBlock.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-SearchHistory.o -MD -MP -MF .deps/libalgorithm_a-SearchHistory.Tpo -c -o libalgorithm_a-SearchHistory.otest -f 'SearchHistory.cpp' || echo './'SearchHistory.cpp mv -f .deps/libalgorithm_a-SearchHistory.Tpo .deps/libalgorithm_a-SearchHistory.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ErrorCorrectProcess.o -MD -MP -MF .deps/libalgorithm_a-ErrorCorrectProcess.Tpo -c -o libalgorithm_a-ErrorCorrectProcess.otest -f 'ErrorCorrectProcess.cpp' || echo './'ErrorCorrectProcess.cpp mv -f .deps/libalgorithm_a-ErrorCorrectProcess.Tpo .deps/libalgorithm_a-ErrorCorrectProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-QCProcess.o -MD -MP -MF .deps/libalgorithm_a-QCProcess.Tpo -c -o libalgorithm_a-QCProcess.otest -f 'QCProcess.cpp' || echo './'QCProcess.cpp mv -f .deps/libalgorithm_a-QCProcess.Tpo .deps/libalgorithm_a-QCProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-OverlapTools.o -MD -MP -MF .deps/libalgorithm_a-OverlapTools.Tpo -c -o libalgorithm_a-OverlapTools.otest -f 'OverlapTools.cpp' || echo './'OverlapTools.cpp mv -f .deps/libalgorithm_a-OverlapTools.Tpo .deps/libalgorithm_a-OverlapTools.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-DPAlignment.o -MD -MP -MF .deps/libalgorithm_a-DPAlignment.Tpo -c -o libalgorithm_a-DPAlignment.otest -f 'DPAlignment.cpp' || echo './'DPAlignment.cpp mv -f .deps/libalgorithm_a-DPAlignment.Tpo .deps/libalgorithm_a-DPAlignment.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ConnectProcess.o -MD -MP -MF .deps/libalgorithm_a-ConnectProcess.Tpo -c -o libalgorithm_a-ConnectProcess.otest -f 'ConnectProcess.cpp' || echo './'ConnectProcess.cpp mv -f .deps/libalgorithm_a-ConnectProcess.Tpo .deps/libalgorithm_a-ConnectProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-StringGraphGenerator.o -MD -MP -MF .deps/libalgorithm_a-StringGraphGenerator.Tpo -c -o libalgorithm_a-StringGraphGenerator.otest -f 'StringGraphGenerator.cpp' || echo './'StringGraphGenerator.cpp mv -f .deps/libalgorithm_a-StringGraphGenerator.Tpo .deps/libalgorithm_a-StringGraphGenerator.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-FMMergeProcess.o -MD -MP -MF .deps/libalgorithm_a-FMMergeProcess.Tpo -c -o libalgorithm_a-FMMergeProcess.otest -f 'FMMergeProcess.cpp' || echo './'FMMergeProcess.cpp mv -f .deps/libalgorithm_a-FMMergeProcess.Tpo .deps/libalgorithm_a-FMMergeProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-StatsProcess.o -MD -MP -MF .deps/libalgorithm_a-StatsProcess.Tpo -c -o libalgorithm_a-StatsProcess.otest -f 'StatsProcess.cpp' || echo './'StatsProcess.cpp mv -f .deps/libalgorithm_a-StatsProcess.Tpo .deps/libalgorithm_a-StatsProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ClusterProcess.o -MD -MP -MF .deps/libalgorithm_a-ClusterProcess.Tpo -c -o libalgorithm_a-ClusterProcess.otest -f 'ClusterProcess.cpp' || echo './'ClusterProcess.cpp mv -f .deps/libalgorithm_a-ClusterProcess.Tpo .deps/libalgorithm_a-ClusterProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ReadCluster.o -MD -MP -MF .deps/libalgorithm_a-ReadCluster.Tpo -c -o libalgorithm_a-ReadCluster.otest -f 'ReadCluster.cpp' || echo './'ReadCluster.cpp mv -f .deps/libalgorithm_a-ReadCluster.Tpo .deps/libalgorithm_a-ReadCluster.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-LRAlignment.o -MD -MP -MF .deps/libalgorithm_a-LRAlignment.Tpo -c -o libalgorithm_a-LRAlignment.otest -f 'LRAlignment.cpp' || echo './'LRAlignment.cpp mv -f .deps/libalgorithm_a-LRAlignment.Tpo .deps/libalgorithm_a-LRAlignment.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-StringThreader.o -MD -MP -MF .deps/libalgorithm_a-StringThreader.Tpo -c -o libalgorithm_a-StringThreader.otest -f 'StringThreader.cpp' || echo './'StringThreader.cpp mv -f .deps/libalgorithm_a-StringThreader.Tpo .deps/libalgorithm_a-StringThreader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-ExtensionDP.o -MD -MP -MF .deps/libalgorithm_a-ExtensionDP.Tpo -c -o libalgorithm_a-ExtensionDP.otest -f 'ExtensionDP.cpp' || echo './'ExtensionDP.cpp mv -f .deps/libalgorithm_a-ExtensionDP.Tpo .deps/libalgorithm_a-ExtensionDP.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-HaplotypeBuilder.o -MD -MP -MF .deps/libalgorithm_a-HaplotypeBuilder.Tpo -c -o libalgorithm_a-HaplotypeBuilder.otest -f 'HaplotypeBuilder.cpp' || echo './'HaplotypeBuilder.cpp mv -f .deps/libalgorithm_a-HaplotypeBuilder.Tpo .deps/libalgorithm_a-HaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-GapFillProcess.o -MD -MP -MF .deps/libalgorithm_a-GapFillProcess.Tpo -c -o libalgorithm_a-GapFillProcess.otest -f 'GapFillProcess.cpp' || echo './'GapFillProcess.cpp mv -f .deps/libalgorithm_a-GapFillProcess.Tpo .deps/libalgorithm_a-GapFillProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-VariationBuilderCommon.o -MD -MP -MF .deps/libalgorithm_a-VariationBuilderCommon.Tpo -c -o libalgorithm_a-VariationBuilderCommon.otest -f 'VariationBuilderCommon.cpp' || echo './'VariationBuilderCommon.cpp mv -f .deps/libalgorithm_a-VariationBuilderCommon.Tpo .deps/libalgorithm_a-VariationBuilderCommon.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../GraphDiff -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libalgorithm_a-KmerOverlaps.o -MD -MP -MF .deps/libalgorithm_a-KmerOverlaps.Tpo -c -o libalgorithm_a-KmerOverlaps.otest -f 'KmerOverlaps.cpp' || echo './'KmerOverlaps.cpp mv -f .deps/libalgorithm_a-KmerOverlaps.Tpo .deps/libalgorithm_a-KmerOverlaps.Po rm -f libalgorithm.a ar cru libalgorithm.a libalgorithm_a-OverlapAlgorithm.o libalgorithm_a-SearchSeed.o libalgorithm_a-OverlapBlock.o libalgorithm_a-SearchHistory.o libalgorithm_a-ErrorCorrectProcess.o libalgorithm_a-QCProcess.o libalgorithm_a-OverlapTools.o libalgorithm_a-DPAlignment.o libalgorithm_a-ConnectProcess.o libalgorithm_a-StringGraphGenerator.o libalgorithm_a-FMMergeProcess.o libalgorithm_a-StatsProcess.o libalgorithm_a-ClusterProcess.o libalgorithm_a-ReadCluster.o libalgorithm_a-LRAlignment.o libalgorithm_a-StringThreader.o libalgorithm_a-ExtensionDP.o libalgorithm_a-HaplotypeBuilder.o libalgorithm_a-GapFillProcess.o libalgorithm_a-VariationBuilderCommon.o libalgorithm_a-KmerOverlaps.o ranlib libalgorithm.a Making all in StringGraph g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGUtil.o -MD -MP -MF .deps/libstringgraph_a-SGUtil.Tpo -c -o libstringgraph_a-SGUtil.otest -f 'SGUtil.cpp' || echo './'SGUtil.cpp mv -f .deps/libstringgraph_a-SGUtil.Tpo .deps/libstringgraph_a-SGUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGAlgorithms.o -MD -MP -MF .deps/libstringgraph_a-SGAlgorithms.Tpo -c -o libstringgraph_a-SGAlgorithms.otest -f 'SGAlgorithms.cpp' || echo './'SGAlgorithms.cpp mv -f .deps/libstringgraph_a-SGAlgorithms.Tpo .deps/libstringgraph_a-SGAlgorithms.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGVisitors.o -MD -MP -MF .deps/libstringgraph_a-SGVisitors.Tpo -c -o libstringgraph_a-SGVisitors.otest -f 'SGVisitors.cpp' || echo './'SGVisitors.cpp mv -f .deps/libstringgraph_a-SGVisitors.Tpo .deps/libstringgraph_a-SGVisitors.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-CompleteOverlapSet.o -MD -MP -MF .deps/libstringgraph_a-CompleteOverlapSet.Tpo -c -o libstringgraph_a-CompleteOverlapSet.otest -f 'CompleteOverlapSet.cpp' || echo './'CompleteOverlapSet.cpp mv -f .deps/libstringgraph_a-CompleteOverlapSet.Tpo .deps/libstringgraph_a-CompleteOverlapSet.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-RemovalAlgorithm.o -MD -MP -MF .deps/libstringgraph_a-RemovalAlgorithm.Tpo -c -o libstringgraph_a-RemovalAlgorithm.otest -f 'RemovalAlgorithm.cpp' || echo './'RemovalAlgorithm.cpp mv -f .deps/libstringgraph_a-RemovalAlgorithm.Tpo .deps/libstringgraph_a-RemovalAlgorithm.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGSearch.o -MD -MP -MF .deps/libstringgraph_a-SGSearch.Tpo -c -o libstringgraph_a-SGSearch.otest -f 'SGSearch.cpp' || echo './'SGSearch.cpp mv -f .deps/libstringgraph_a-SGSearch.Tpo .deps/libstringgraph_a-SGSearch.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../Thirdparty -I../Algorithm -I../SQG -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libstringgraph_a-SGWalk.o -MD -MP -MF .deps/libstringgraph_a-SGWalk.Tpo -c -o libstringgraph_a-SGWalk.otest -f 'SGWalk.cpp' || echo './'SGWalk.cpp mv -f .deps/libstringgraph_a-SGWalk.Tpo .deps/libstringgraph_a-SGWalk.Po rm -f libstringgraph.a ar cru libstringgraph.a libstringgraph_a-SGUtil.o libstringgraph_a-SGAlgorithms.o libstringgraph_a-SGVisitors.o libstringgraph_a-CompleteOverlapSet.o libstringgraph_a-RemovalAlgorithm.o libstringgraph_a-SGSearch.o libstringgraph_a-SGWalk.o ranlib libstringgraph.a Making all in Concurrency g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libconcurrency_a-OverlapProcess.o -MD -MP -MF .deps/libconcurrency_a-OverlapProcess.Tpo -c -o libconcurrency_a-OverlapProcess.otest -f 'OverlapProcess.cpp' || echo './'OverlapProcess.cpp mv -f .deps/libconcurrency_a-OverlapProcess.Tpo .deps/libconcurrency_a-OverlapProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../SuffixTools -I../Thirdparty -I../Algorithm -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libconcurrency_a-RmdupProcess.o -MD -MP -MF .deps/libconcurrency_a-RmdupProcess.Tpo -c -o libconcurrency_a-RmdupProcess.otest -f 'RmdupProcess.cpp' || echo './'RmdupProcess.cpp mv -f .deps/libconcurrency_a-RmdupProcess.Tpo .deps/libconcurrency_a-RmdupProcess.Po rm -f libconcurrency.a ar cru libconcurrency.a libconcurrency_a-OverlapProcess.o libconcurrency_a-RmdupProcess.o ranlib libconcurrency.a Making all in SuffixTools g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-STCommon.o -MD -MP -MF .deps/libsuffixtools_a-STCommon.Tpo -c -o libsuffixtools_a-STCommon.otest -f 'STCommon.cpp' || echo './'STCommon.cpp mv -f .deps/libsuffixtools_a-STCommon.Tpo .deps/libsuffixtools_a-STCommon.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-Occurrence.o -MD -MP -MF .deps/libsuffixtools_a-Occurrence.Tpo -c -o libsuffixtools_a-Occurrence.otest -f 'Occurrence.cpp' || echo './'Occurrence.cpp mv -f .deps/libsuffixtools_a-Occurrence.Tpo .deps/libsuffixtools_a-Occurrence.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SuffixArray.o -MD -MP -MF .deps/libsuffixtools_a-SuffixArray.Tpo -c -o libsuffixtools_a-SuffixArray.otest -f 'SuffixArray.cpp' || echo './'SuffixArray.cpp mv -f .deps/libsuffixtools_a-SuffixArray.Tpo .deps/libsuffixtools_a-SuffixArray.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SuffixCompare.o -MD -MP -MF .deps/libsuffixtools_a-SuffixCompare.Tpo -c -o libsuffixtools_a-SuffixCompare.otest -f 'SuffixCompare.cpp' || echo './'SuffixCompare.cpp mv -f .deps/libsuffixtools_a-SuffixCompare.Tpo .deps/libsuffixtools_a-SuffixCompare.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-InverseSuffixArray.o -MD -MP -MF .deps/libsuffixtools_a-InverseSuffixArray.Tpo -c -o libsuffixtools_a-InverseSuffixArray.otest -f 'InverseSuffixArray.cpp' || echo './'InverseSuffixArray.cpp mv -f .deps/libsuffixtools_a-InverseSuffixArray.Tpo .deps/libsuffixtools_a-InverseSuffixArray.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SACAInducedCopying.o -MD -MP -MF .deps/libsuffixtools_a-SACAInducedCopying.Tpo -c -o libsuffixtools_a-SACAInducedCopying.otest -f 'SACAInducedCopying.cpp' || echo './'SACAInducedCopying.cpp mv -f .deps/libsuffixtools_a-SACAInducedCopying.Tpo .deps/libsuffixtools_a-SACAInducedCopying.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTAlgorithms.o -MD -MP -MF .deps/libsuffixtools_a-BWTAlgorithms.Tpo -c -o libsuffixtools_a-BWTAlgorithms.otest -f 'BWTAlgorithms.cpp' || echo './'BWTAlgorithms.cpp mv -f .deps/libsuffixtools_a-BWTAlgorithms.Tpo .deps/libsuffixtools_a-BWTAlgorithms.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTDiskConstruction.o -MD -MP -MF .deps/libsuffixtools_a-BWTDiskConstruction.Tpo -c -o libsuffixtools_a-BWTDiskConstruction.otest -f 'BWTDiskConstruction.cpp' || echo './'BWTDiskConstruction.cpp mv -f .deps/libsuffixtools_a-BWTDiskConstruction.Tpo .deps/libsuffixtools_a-BWTDiskConstruction.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTReader.o -MD -MP -MF .deps/libsuffixtools_a-BWTReader.Tpo -c -o libsuffixtools_a-BWTReader.otest -f 'BWTReader.cpp' || echo './'BWTReader.cpp mv -f .deps/libsuffixtools_a-BWTReader.Tpo .deps/libsuffixtools_a-BWTReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTWriter.o -MD -MP -MF .deps/libsuffixtools_a-BWTWriter.Tpo -c -o libsuffixtools_a-BWTWriter.otest -f 'BWTWriter.cpp' || echo './'BWTWriter.cpp mv -f .deps/libsuffixtools_a-BWTWriter.Tpo .deps/libsuffixtools_a-BWTWriter.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SAReader.o -MD -MP -MF .deps/libsuffixtools_a-SAReader.Tpo -c -o libsuffixtools_a-SAReader.otest -f 'SAReader.cpp' || echo './'SAReader.cpp mv -f .deps/libsuffixtools_a-SAReader.Tpo .deps/libsuffixtools_a-SAReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SAWriter.o -MD -MP -MF .deps/libsuffixtools_a-SAWriter.Tpo -c -o libsuffixtools_a-SAWriter.otest -f 'SAWriter.cpp' || echo './'SAWriter.cpp mv -f .deps/libsuffixtools_a-SAWriter.Tpo .deps/libsuffixtools_a-SAWriter.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-GapArray.o -MD -MP -MF .deps/libsuffixtools_a-GapArray.Tpo -c -o libsuffixtools_a-GapArray.otest -f 'GapArray.cpp' || echo './'GapArray.cpp mv -f .deps/libsuffixtools_a-GapArray.Tpo .deps/libsuffixtools_a-GapArray.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-RankProcess.o -MD -MP -MF .deps/libsuffixtools_a-RankProcess.Tpo -c -o libsuffixtools_a-RankProcess.otest -f 'RankProcess.cpp' || echo './'RankProcess.cpp mv -f .deps/libsuffixtools_a-RankProcess.Tpo .deps/libsuffixtools_a-RankProcess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SBWT.o -MD -MP -MF .deps/libsuffixtools_a-SBWT.Tpo -c -o libsuffixtools_a-SBWT.otest -f 'SBWT.cpp' || echo './'SBWT.cpp mv -f .deps/libsuffixtools_a-SBWT.Tpo .deps/libsuffixtools_a-SBWT.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-RLBWT.o -MD -MP -MF .deps/libsuffixtools_a-RLBWT.Tpo -c -o libsuffixtools_a-RLBWT.otest -f 'RLBWT.cpp' || echo './'RLBWT.cpp mv -f .deps/libsuffixtools_a-RLBWT.Tpo .deps/libsuffixtools_a-RLBWT.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTWriterBinary.o -MD -MP -MF .deps/libsuffixtools_a-BWTWriterBinary.Tpo -c -o libsuffixtools_a-BWTWriterBinary.otest -f 'BWTWriterBinary.cpp' || echo './'BWTWriterBinary.cpp mv -f .deps/libsuffixtools_a-BWTWriterBinary.Tpo .deps/libsuffixtools_a-BWTWriterBinary.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTReaderBinary.o -MD -MP -MF .deps/libsuffixtools_a-BWTReaderBinary.Tpo -c -o libsuffixtools_a-BWTReaderBinary.otest -f 'BWTReaderBinary.cpp' || echo './'BWTReaderBinary.cpp mv -f .deps/libsuffixtools_a-BWTReaderBinary.Tpo .deps/libsuffixtools_a-BWTReaderBinary.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTWriterAscii.o -MD -MP -MF .deps/libsuffixtools_a-BWTWriterAscii.Tpo -c -o libsuffixtools_a-BWTWriterAscii.otest -f 'BWTWriterAscii.cpp' || echo './'BWTWriterAscii.cpp mv -f .deps/libsuffixtools_a-BWTWriterAscii.Tpo .deps/libsuffixtools_a-BWTWriterAscii.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTReaderAscii.o -MD -MP -MF .deps/libsuffixtools_a-BWTReaderAscii.Tpo -c -o libsuffixtools_a-BWTReaderAscii.otest -f 'BWTReaderAscii.cpp' || echo './'BWTReaderAscii.cpp mv -f .deps/libsuffixtools_a-BWTReaderAscii.Tpo .deps/libsuffixtools_a-BWTReaderAscii.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTIntervalCache.o -MD -MP -MF .deps/libsuffixtools_a-BWTIntervalCache.Tpo -c -o libsuffixtools_a-BWTIntervalCache.otest -f 'BWTIntervalCache.cpp' || echo './'BWTIntervalCache.cpp mv -f .deps/libsuffixtools_a-BWTIntervalCache.Tpo .deps/libsuffixtools_a-BWTIntervalCache.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-QuickBWT.o -MD -MP -MF .deps/libsuffixtools_a-QuickBWT.Tpo -c -o libsuffixtools_a-QuickBWT.otest -f 'QuickBWT.cpp' || echo './'QuickBWT.cpp mv -f .deps/libsuffixtools_a-QuickBWT.Tpo .deps/libsuffixtools_a-QuickBWT.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-SampledSuffixArray.o -MD -MP -MF .deps/libsuffixtools_a-SampledSuffixArray.Tpo -c -o libsuffixtools_a-SampledSuffixArray.otest -f 'SampledSuffixArray.cpp' || echo './'SampledSuffixArray.cpp mv -f .deps/libsuffixtools_a-SampledSuffixArray.Tpo .deps/libsuffixtools_a-SampledSuffixArray.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTCABauerCoxRosone.o -MD -MP -MF .deps/libsuffixtools_a-BWTCABauerCoxRosone.Tpo -c -o libsuffixtools_a-BWTCABauerCoxRosone.otest -f 'BWTCABauerCoxRosone.cpp' || echo './'BWTCABauerCoxRosone.cpp mv -f .deps/libsuffixtools_a-BWTCABauerCoxRosone.Tpo .deps/libsuffixtools_a-BWTCABauerCoxRosone.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTCARopebwt.o -MD -MP -MF .deps/libsuffixtools_a-BWTCARopebwt.Tpo -c -o libsuffixtools_a-BWTCARopebwt.otest -f 'BWTCARopebwt.cpp' || echo './'BWTCARopebwt.cpp mv -f .deps/libsuffixtools_a-BWTCARopebwt.Tpo .deps/libsuffixtools_a-BWTCARopebwt.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-PopulationIndex.o -MD -MP -MF .deps/libsuffixtools_a-PopulationIndex.Tpo -c -o libsuffixtools_a-PopulationIndex.otest -f 'PopulationIndex.cpp' || echo './'PopulationIndex.cpp mv -f .deps/libsuffixtools_a-PopulationIndex.Tpo .deps/libsuffixtools_a-PopulationIndex.Po rm -f libsuffixtools.a ar cru libsuffixtools.a libsuffixtools_a-STCommon.o libsuffixtools_a-Occurrence.o libsuffixtools_a-SuffixArray.o libsuffixtools_a-SuffixCompare.o libsuffixtools_a-InverseSuffixArray.o libsuffixtools_a-SACAInducedCopying.o libsuffixtools_a-BWTAlgorithms.o libsuffixtools_a-BWTDiskConstruction.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-SAReader.o libsuffixtools_a-SAWriter.o libsuffixtools_a-GapArray.o libsuffixtools_a-RankProcess.o libsuffixtools_a-SBWT.o libsuffixtools_a-RLBWT.o libsuffixtools_a-BWTReader.o libsuffixtools_a-BWTWriter.o libsuffixtools_a-BWTWriterBinary.o libsuffixtools_a-BWTReaderBinary.o libsuffixtools_a-BWTWriterAscii.o libsuffixtools_a-BWTReaderAscii.o libsuffixtools_a-BWTIntervalCache.o libsuffixtools_a-QuickBWT.o libsuffixtools_a-SampledSuffixArray.o libsuffixtools_a-BWTCABauerCoxRosone.o libsuffixtools_a-BWTCARopebwt.o libsuffixtools_a-PopulationIndex.o ranlib libsuffixtools.a Making all in Scaffold g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldVertex.o -MD -MP -MF .deps/libscaffold_a-ScaffoldVertex.Tpo -c -o libscaffold_a-ScaffoldVertex.otest -f 'ScaffoldVertex.cpp' || echo './'ScaffoldVertex.cpp mv -f .deps/libscaffold_a-ScaffoldVertex.Tpo .deps/libscaffold_a-ScaffoldVertex.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldEdge.o -MD -MP -MF .deps/libscaffold_a-ScaffoldEdge.Tpo -c -o libscaffold_a-ScaffoldEdge.otest -f 'ScaffoldEdge.cpp' || echo './'ScaffoldEdge.cpp mv -f .deps/libscaffold_a-ScaffoldEdge.Tpo .deps/libscaffold_a-ScaffoldEdge.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldGraph.o -MD -MP -MF .deps/libscaffold_a-ScaffoldGraph.Tpo -c -o libscaffold_a-ScaffoldGraph.otest -f 'ScaffoldGraph.cpp' || echo './'ScaffoldGraph.cpp mv -f .deps/libscaffold_a-ScaffoldGraph.Tpo .deps/libscaffold_a-ScaffoldGraph.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldVisitors.o -MD -MP -MF .deps/libscaffold_a-ScaffoldVisitors.Tpo -c -o libscaffold_a-ScaffoldVisitors.otest -f 'ScaffoldVisitors.cpp' || echo './'ScaffoldVisitors.cpp mv -f .deps/libscaffold_a-ScaffoldVisitors.Tpo .deps/libscaffold_a-ScaffoldVisitors.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldLink.o -MD -MP -MF .deps/libscaffold_a-ScaffoldLink.Tpo -c -o libscaffold_a-ScaffoldLink.otest -f 'ScaffoldLink.cpp' || echo './'ScaffoldLink.cpp mv -f .deps/libscaffold_a-ScaffoldLink.Tpo .deps/libscaffold_a-ScaffoldLink.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldRecord.o -MD -MP -MF .deps/libscaffold_a-ScaffoldRecord.Tpo -c -o libscaffold_a-ScaffoldRecord.otest -f 'ScaffoldRecord.cpp' || echo './'ScaffoldRecord.cpp mv -f .deps/libscaffold_a-ScaffoldRecord.Tpo .deps/libscaffold_a-ScaffoldRecord.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldGroup.o -MD -MP -MF .deps/libscaffold_a-ScaffoldGroup.Tpo -c -o libscaffold_a-ScaffoldGroup.otest -f 'ScaffoldGroup.cpp' || echo './'ScaffoldGroup.cpp mv -f .deps/libscaffold_a-ScaffoldGroup.Tpo .deps/libscaffold_a-ScaffoldGroup.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldSearch.o -MD -MP -MF .deps/libscaffold_a-ScaffoldSearch.Tpo -c -o libscaffold_a-ScaffoldSearch.otest -f 'ScaffoldSearch.cpp' || echo './'ScaffoldSearch.cpp mv -f .deps/libscaffold_a-ScaffoldSearch.Tpo .deps/libscaffold_a-ScaffoldSearch.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldWalk.o -MD -MP -MF .deps/libscaffold_a-ScaffoldWalk.Tpo -c -o libscaffold_a-ScaffoldWalk.otest -f 'ScaffoldWalk.cpp' || echo './'ScaffoldWalk.cpp mv -f .deps/libscaffold_a-ScaffoldWalk.Tpo .deps/libscaffold_a-ScaffoldWalk.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldAlgorithms.o -MD -MP -MF .deps/libscaffold_a-ScaffoldAlgorithms.Tpo -c -o libscaffold_a-ScaffoldAlgorithms.otest -f 'ScaffoldAlgorithms.cpp' || echo './'ScaffoldAlgorithms.cpp mv -f .deps/libscaffold_a-ScaffoldAlgorithms.Tpo .deps/libscaffold_a-ScaffoldAlgorithms.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../SQG -I../Algorithm -I../StringGraph -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libscaffold_a-ScaffoldSequenceCollection.o -MD -MP -MF .deps/libscaffold_a-ScaffoldSequenceCollection.Tpo -c -o libscaffold_a-ScaffoldSequenceCollection.otest -f 'ScaffoldSequenceCollection.cpp' || echo './'ScaffoldSequenceCollection.cpp mv -f .deps/libscaffold_a-ScaffoldSequenceCollection.Tpo .deps/libscaffold_a-ScaffoldSequenceCollection.Po rm -f libscaffold.a ar cru libscaffold.a libscaffold_a-ScaffoldVertex.o libscaffold_a-ScaffoldEdge.o libscaffold_a-ScaffoldGraph.o libscaffold_a-ScaffoldVisitors.o libscaffold_a-ScaffoldLink.o libscaffold_a-ScaffoldRecord.o libscaffold_a-ScaffoldGroup.o libscaffold_a-ScaffoldSearch.o libscaffold_a-ScaffoldWalk.o libscaffold_a-ScaffoldAlgorithms.o libscaffold_a-ScaffoldSequenceCollection.o ranlib libscaffold.a Making all in GraphDiff g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelUtil.o -MD -MP -MF .deps/libgraphdiff_a-DindelUtil.Tpo -c -o libgraphdiff_a-DindelUtil.otest -f 'DindelUtil.cpp' || echo './'DindelUtil.cpp mv -f .deps/libgraphdiff_a-DindelUtil.Tpo .deps/libgraphdiff_a-DindelUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelRealignWindow.o -MD -MP -MF .deps/libgraphdiff_a-DindelRealignWindow.Tpo -c -o libgraphdiff_a-DindelRealignWindow.otest -f 'DindelRealignWindow.cpp' || echo './'DindelRealignWindow.cpp mv -f .deps/libgraphdiff_a-DindelRealignWindow.Tpo .deps/libgraphdiff_a-DindelRealignWindow.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DindelHMM.o -MD -MP -MF .deps/libgraphdiff_a-DindelHMM.Tpo -c -o libgraphdiff_a-DindelHMM.otest -f 'DindelHMM.cpp' || echo './'DindelHMM.cpp mv -f .deps/libgraphdiff_a-DindelHMM.Tpo .deps/libgraphdiff_a-DindelHMM.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-OverlapHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Tpo -c -o libgraphdiff_a-OverlapHaplotypeBuilder.otest -f 'OverlapHaplotypeBuilder.cpp' || echo './'OverlapHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Tpo .deps/libgraphdiff_a-OverlapHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-StringHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-StringHaplotypeBuilder.Tpo -c -o libgraphdiff_a-StringHaplotypeBuilder.otest -f 'StringHaplotypeBuilder.cpp' || echo './'StringHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-StringHaplotypeBuilder.Tpo .deps/libgraphdiff_a-StringHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-DeBruijnHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Tpo -c -o libgraphdiff_a-DeBruijnHaplotypeBuilder.otest -f 'DeBruijnHaplotypeBuilder.cpp' || echo './'DeBruijnHaplotypeBuilder.cpp mv -f .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Tpo .deps/libgraphdiff_a-DeBruijnHaplotypeBuilder.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-HapgenUtil.o -MD -MP -MF .deps/libgraphdiff_a-HapgenUtil.Tpo -c -o libgraphdiff_a-HapgenUtil.otest -f 'HapgenUtil.cpp' || echo './'HapgenUtil.cpp mv -f .deps/libgraphdiff_a-HapgenUtil.Tpo .deps/libgraphdiff_a-HapgenUtil.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-VCFTester.o -MD -MP -MF .deps/libgraphdiff_a-VCFTester.Tpo -c -o libgraphdiff_a-VCFTester.otest -f 'VCFTester.cpp' || echo './'VCFTester.cpp mv -f .deps/libgraphdiff_a-VCFTester.Tpo .deps/libgraphdiff_a-VCFTester.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-GraphCompare.o -MD -MP -MF .deps/libgraphdiff_a-GraphCompare.Tpo -c -o libgraphdiff_a-GraphCompare.otest -f 'GraphCompare.cpp' || echo './'GraphCompare.cpp mv -f .deps/libgraphdiff_a-GraphCompare.Tpo .deps/libgraphdiff_a-GraphCompare.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libgraphdiff_a-OverlapExtractorWithCorrection.o -MD -MP -MF .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo -c -o libgraphdiff_a-OverlapExtractorWithCorrection.otest -f 'OverlapExtractorWithCorrection.cpp' || echo './'OverlapExtractorWithCorrection.cpp mv -f .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Po rm -f libgraphdiff.a ar cru libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o ranlib libgraphdiff.a Making all in SGA g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-sga.o -MD -MP -MF .deps/sga-sga.Tpo -c -o sga-sga.otest -f 'sga.cpp' || echo './'sga.cpp mv -f .deps/sga-sga.Tpo .deps/sga-sga.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-index.o -MD -MP -MF .deps/sga-index.Tpo -c -o sga-index.otest -f 'index.cpp' || echo './'index.cpp mv -f .deps/sga-index.Tpo .deps/sga-index.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-overlap.o -MD -MP -MF .deps/sga-overlap.Tpo -c -o sga-overlap.otest -f 'overlap.cpp' || echo './'overlap.cpp mv -f .deps/sga-overlap.Tpo .deps/sga-overlap.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-assemble.o -MD -MP -MF .deps/sga-assemble.Tpo -c -o sga-assemble.otest -f 'assemble.cpp' || echo './'assemble.cpp mv -f .deps/sga-assemble.Tpo .deps/sga-assemble.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-correct.o -MD -MP -MF .deps/sga-correct.Tpo -c -o sga-correct.otest -f 'correct.cpp' || echo './'correct.cpp mv -f .deps/sga-correct.Tpo .deps/sga-correct.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-oview.o -MD -MP -MF .deps/sga-oview.Tpo -c -o sga-oview.otest -f 'oview.cpp' || echo './'oview.cpp mv -f .deps/sga-oview.Tpo .deps/sga-oview.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-preprocess.o -MD -MP -MF .deps/sga-preprocess.Tpo -c -o sga-preprocess.otest -f 'preprocess.cpp' || echo './'preprocess.cpp mv -f .deps/sga-preprocess.Tpo .deps/sga-preprocess.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-rmdup.o -MD -MP -MF .deps/sga-rmdup.Tpo -c -o sga-rmdup.otest -f 'rmdup.cpp' || echo './'rmdup.cpp mv -f .deps/sga-rmdup.Tpo .deps/sga-rmdup.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-merge.o -MD -MP -MF .deps/sga-merge.Tpo -c -o sga-merge.otest -f 'merge.cpp' || echo './'merge.cpp mv -f .deps/sga-merge.Tpo .deps/sga-merge.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-subgraph.o -MD -MP -MF .deps/sga-subgraph.Tpo -c -o sga-subgraph.otest -f 'subgraph.cpp' || echo './'subgraph.cpp mv -f .deps/sga-subgraph.Tpo .deps/sga-subgraph.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-scaffold.o -MD -MP -MF .deps/sga-scaffold.Tpo -c -o sga-scaffold.otest -f 'scaffold.cpp' || echo './'scaffold.cpp mv -f .deps/sga-scaffold.Tpo .deps/sga-scaffold.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-scaffold2fasta.o -MD -MP -MF .deps/sga-scaffold2fasta.Tpo -c -o sga-scaffold2fasta.otest -f 'scaffold2fasta.cpp' || echo './'scaffold2fasta.cpp mv -f .deps/sga-scaffold2fasta.Tpo .deps/sga-scaffold2fasta.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-connect.o -MD -MP -MF .deps/sga-connect.Tpo -c -o sga-connect.otest -f 'connect.cpp' || echo './'connect.cpp mv -f .deps/sga-connect.Tpo .deps/sga-connect.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-walk.o -MD -MP -MF .deps/sga-walk.Tpo -c -o sga-walk.otest -f 'walk.cpp' || echo './'walk.cpp mv -f .deps/sga-walk.Tpo .deps/sga-walk.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-filter.o -MD -MP -MF .deps/sga-filter.Tpo -c -o sga-filter.otest -f 'filter.cpp' || echo './'filter.cpp mv -f .deps/sga-filter.Tpo .deps/sga-filter.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-stats.o -MD -MP -MF .deps/sga-stats.Tpo -c -o sga-stats.otest -f 'stats.cpp' || echo './'`stats.cpp
mv -f .deps/sga-stats.Tpo .deps/sga-stats.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -fopenmp -I/usr/local/bin/include -I/usr/local/bin/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT sga-fm-merge.o -MD -MP -MF .deps/sga-fm-merge.Tpo -c -o s

Vertex coverage information is not retained when using sga fm-merge

Merging sequences prior to sga assemble losing the vertex coverage information. This information must be kept to avoid popping bubbles and retaining the lower-coverage branch.

Compile Error

Hi Jared,
I'm getting a compile error on Ubuntu 12.10

g++ -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Thirdparty -I../Bigraph -I../Concurrency -fopenmp -I/home/rwtaylor/downloads/bamtools/include -I/home/rwtaylor/downloads/bamtools/include/bamtools -Wall -Wextra -Werror -Wno-unknown-pragmas -O3 -MT libsuffixtools_a-BWTAlgorithms.o -MD -MP -MF .deps/libsuffixtools_a-BWTAlgorithms.Tpo -c -o libsuffixtools_a-BWTAlgorithms.o test -f 'BWTAlgorithms.cpp' || echo './'BWTAlgorithms.cpp
BWTAlgorithms.cpp: In function ‘void extractRankedPrefixes(const BWT, BWTInterval, const string&, RankedPrefixVector_)’:
BWTAlgorithms.cpp:423:46: error: narrowing conversion of ‘i’ from ‘int64_t {aka long int}’ to ‘size_t {aka long unsigned int}’ inside { } is ill-formed in C++11 [-Werror=narrowing]
cc1plus: all warnings being treated as errors
make[2]: *** [libsuffixtools_a-BWTAlgorithms.o] Error 1
make[2]: Leaving directory /home/rwtaylor/downloads/sga/src/SuffixTools' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/rwtaylor/downloads/sga/src'
make: *** [all] Error 2

Thanks,
Ryan

sga depends on some abyss programs, no errors to indicate this

It might be worth noting somewhere that sga (or more specifically sga-bam2de.pl) depends on two programs from ABySS, abyss-fixmate and DistanceEst. On my debian system I was able to install abyss, but needed to modify this file to point at '/usr/lib/abyss/abyss-fixmate' and '/usr/lib/abyss/DistanceEst' for the functions to work (these programs are not in the default path). No errors were produced to indicate that these programs were missing, so it took a while for me to work out why my scaffolding wasn't joining any contigs.

FWIW, it might be possible to remove the dependance on abyss-fixmate without too much additional work. Generating the histogram of average distances (e.g. pe.hist) can be done fairly fast with a combination of samtools and awk, using the 'view' command to filter on the first read of a pair when the pairs are properly mapped (bowtie2 seems to define this as correct orientation with not too much distance between reads):

samtools view -f 0x42 mappedreads.bam | awk '{print sqrt($9*$9)}' | sort -n | uniq -c | sort -k 2,2n | awk '{print $2"\t"$1}' > pe.hist

Creating the contig distance file (e.g. pe.de) will probably require things beyond simple command line pipes. I can generate a sorted BAM file containing only pairs with different contigs:

(samtools view -H mappedreads.bam; samtools view -F 0x02 mappedreads.bam | cut -f 1-11 | awk -v 'OFS=\t' '{if($7 != "="){$1="";$10="";$11="*";print $0}}') | samtools view -Sb - | samtools sort - pe.diffcontigs.sorted

However, altering the template length (field 9) would (I expect) need a knowledge of the most likely read-pair distance.

sga stats does not compute error rates when --no-overlap parameter is given

This should be fixed by making the documentation/output clear or by using one of the new forward-index only overlap algorithms (like in KmerOverlaps.h).

sga index aborts when input file is empty

When given an empty input file, sga index will throw an assertion either when writing the BWT (if -d is not given) or when trying to merge the BWTs (if -d is given). This should be changed to warn the user that no data was given and exit gracefully.

sga index: -d does not make sense with -a ropebwt

When both '-d N' and '-a ropebwt' options are used with sga index, the slow disk-based SAIS algorithm will be used. This is counter-intuitive and leads to very long indexing time. This should be resolved by printing an error and useful help text if the user specifies both options.

How to handle high depth data?

When I tried to deal with a 80x data from 8 Lanes, the first thing I tried is to merge all the fa files into a single one, however, it turns out that the program aborted saying that cannot std:allocate sth. like that, I guess it is because the data is too much for one time running. So I ran it separately in 8 different tasks, it finished normally on preprocess stage. But the problem is that I can't find a way to use these 8 different fa data to do the following assembly, most of the parameters only accept two files read1 and read2 as far as I know. Should I correct them separately and assemble them separately? Or is there a way that I missed on the manual?
Thanks!

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