lbcb-sci / graphmap2 Goto Github PK

This project forked from isovic/graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1

License: MIT License

Makefile 0.78% Python 1.21% C++ 96.26% C 1.75%

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mjoppich ashuein wook2014 schaudge martin-g

graphmap2's Issues

Segmentation Fault on Yeast Transcriptome

Hi, I am running graphmap2 on the following data:

Reads:
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR598/003/SRR5989373/SRR5989373_1.fastq.gz

Reference GTF:
ftp://ftp.ensembl.org/pub/release-94/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.94.gtf.gz

Reference:
ftp://ftp.ensembl.org/pub/release-94/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz

Using v0.6.3 (git pull and built today) I still get Segmentation Faults:

/mnt/d/dev/git/graphmap2/bin/Linux-x64/graphmap2 align --rebuild-index -x rnaseq --threads 8 -r /home/mjoppich/dev/data/genomes/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.gm2.fa -d fastq/SRR5989373_1.fastq -o graphmap2/SRR5989373_1.unmod.sam
[16:45:22 BuildIndexes] Loading reference sequences.
[16:45:22 SetupIndex_] Building the index for shape: '11110111101111'.
[16:45:22 Create] Allocated memory for a list of 6078553 seeds (128 bits each) (0.00000 sec, diff: 0.03125 sec).
[16:45:22 Create] Memory consumption: [currentRSS = 38 MB, peakRSS = 38 MB]
[16:45:22 Create] Collecting seeds.
[16:45:22 Create] Minimizer seeds will be used. Minimizer window is 5.
[16:45:23 Create] [currentRSS = 170 MB, peakRSS = 223 MB] Sequence: 34/34, len: 1090940, name: 'VII'
[16:45:23 Create] Final memory allocation after collecting seeds: [currentRSS = 176 MB, peakRSS = 223 MB]
[16:45:23 Create] Sorting the seeds using 8 threads.
[16:45:23 Create] Generating the hash table.
[16:45:24 Create] Calculating the distribution statistics for key counts.
[16:45:24 Create] Index statistics: average key count = 2.130736, max key count = 3204.000000, std dev = 3.374890, percentil (99.00%) (count cutoff) = 13.000000
[16:45:25 Create] Memory consumption: [currentRSS = 559 MB, peakRSS = 754 MB]
[16:45:25 SetupIndex_] Finished building index.
[16:45:25 SetupIndex_] Storing the index to file: '/home/mjoppich/dev/data/genomes/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.gm2.fa.gmidx'.
[16:45:26 Index] Memory consumption: [currentRSS = 548 MB, peakRSS = 754 MB]
[16:45:26 Run] Hits will be thresholded at the percentil value (percentil: 99.000000%, frequency: 13).
[16:45:26 Run] Minimizers will be used. Minimizer window length: 5
[16:45:26 Run] Reference genome is assumed to be linear.
[16:45:26 Run] One or more similarly good alignments will be output per mapped read. Will be marked secondary.
[16:45:26 ProcessReads] All reads will be loaded in memory.
[16:45:28 ProcessReads] All reads loaded in 2.56 sec (size around 469 MB). (239685513 bases)
[16:45:28 ProcessReads] Memory consumption: [currentRSS = 1101 MB, peakRSS = 1101 MB]
[16:52:26 ProcessReads] [CPU time: 2825.36 sec, RSS: 5221 MB] Read: 76803/241446 (31.81%) [m: 75674, u: 1122], length = 691, qname: SRR5989373.76804 5859c147-15...runAlignment.sh: line 11:  2125 Segmentation fault      (core dumped) /mnt/d/dev/git/graphmap2/bin/Linux-x64/graphmap2 align --rebuild-index -x rnaseq --threads 8 -r $GENOMEGM2 -d $FASTQ -o graphmap2/$BASENAME.unmod.sam

I can also call graphmap2 in a different fashion:

/mnt/d/dev/git/graphmap2/bin/Linux-x64/graphmap2 align --rebuild-index -x rnaseq --gtf /home/mjoppich/dev/data/genomes/Saccharomyces_cerevisiae.R64-1-1.94.gtf --threads 8 -r /home/mjoppich/dev/data/genomes/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.gm2.fa -d fastq/SRR5989373_1.fastq -o graphmap2/SRR5989373_1.unmod.sam

Then the segmentation fault occurs earlier:

[16:57:43 BuildIndexes] Loading GTF annotations.
[16:57:43 BuildIndexes] Loading genomic sequences.
[16:57:43 BuildIndexes] Generating the transcriptome.
[16:57:43 GenerateTranscriptomeSeqs] Constructing the transcriptome sequences.
[16:57:43 GenerateTranscriptomeSeqs] In total, there are 7036 transcripts.
[16:57:43 SetupIndex_] Building the index for shape: '11110111101111'.
[16:57:43 Create] Allocated memory for a list of 4428323 seeds (128 bits each) (0.00000 sec, diff: 0.03125 sec).
[16:57:43 Create] Memory consumption: [currentRSS = 33 MB, peakRSS = 33 MB]
[16:57:43 Create] Collecting seeds.
[16:57:43 Create] Minimizer seeds will be used. Minimizer window is 5.
[16:57:47 Create] [currentRSS = 133 MB, peakRSS = 169 MB] Sequence: 14072/14072, len: 483, name: 'YGR296C-B_mRNA_VII'''
[16:57:47 Create] Final memory allocation after collecting seeds: [currentRSS = 133 MB, peakRSS = 169 MB]
[16:57:47 Create] Sorting the seeds using 8 threads.
[16:57:48 Create] Generating the hash table.
[16:57:48 Create] Calculating the distribution statistics for key counts.
[16:57:48 Create] Index statistics: average key count = 1.829742, max key count = 273.000000, std dev = 1.723991, percentil (99.00%) (count cutoff) = 9.000000
[16:57:49 Create] Memory consumption: [currentRSS = 325 MB, peakRSS = 424 MB]
[16:57:49 SetupIndex_] Finished building index.
[16:57:49 SetupIndex_] Storing the index to file: '/home/mjoppich/dev/data/genomes/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.gm2.fa.gmidx'.
[16:57:49 Index] Memory consumption: [currentRSS = 325 MB, peakRSS = 424 MB]
[16:57:49 Run] Hits will be thresholded at the percentil value (percentil: 99.000000%, frequency: 9).
[16:57:49 Run] Minimizers will be used. Minimizer window length: 5
[16:57:49 Run] Reference genome is assumed to be linear.
[16:57:49 Run] One or more similarly good alignments will be output per mapped read. Will be marked secondary.
[16:57:49 ProcessReads] All reads will be loaded in memory.
[16:57:52 ProcessReads] All reads loaded in 2.92 sec (size around 469 MB). (239685513 bases)
[16:57:52 ProcessReads] Memory consumption: [currentRSS = 868 MB, peakRSS = 868 MB]
[16:57:53 ProcessReads] [CPU time: 8.52 sec, RSS: 960 MB] Read: 180/241446 (0.07%) [m: 93, u: 80], length = 1743, qname: SRR5989373.181 6b89fcff-b792-4f6a-a00f-...Segmentation fault (core dumped)

I'd be more than happy if you could look into this issue. Given the few introns, the yeast genome might be useful for debugging :)

Segmentation fault

Hi!

I was running graphmap2 (v.0.6.01) on nanopore cDNA reads and got a segmentation fault:

14, qname: 1ae9c3be-6d48-4a45-94ab.../var/slurmd-inter/job103354/slurm_script: line 20: 129981 Segmentation fault (core dumped) graphmap2 align -t 20 -K fastq -L sam -x rnaseq --extcigar -r CBAS_MASURCA-2_final.genome.scf.fasta -d /naslx/projects/uk213/di29vos/cbas/data/ONT/cbas_cDNA_polyA-guppy-3.1.5-hac.porechop_100bp_to_20kb_combined.fastq -o CBAS_MASURCA-2_final.genome.scf._ONT_cdna_graphmap2_combined_raw_100bp.sam

I was running on 20 cores asking for 2000GB RAM. Before I was running on 40 cores asking for 3000GB RAM which gave the same error.

slurm header was this:

#!/bin/bash
#SBATCH --job-name=graphmap2_raw
#SBATCH --error=CBAS_R_graphmap2.log
#SBATCH --clusters=inter
#SBATCH --partition=teramem_inter
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=20
#SBATCH --mem=2000G
#SBATCH --time=48:00:00

How can I prevent segmentation faults?

thanks
Michael

Graphmap2 index in shared memory

Hi, would it be possible to share graphmap2 index among multiple instances of the mapper? Something of the sort was available in STAR-mapper.
It'd be super beneficial for applications with on-the-fly mapping (ie. data coming from the sequencer in small batches) or where multiple instances of the mapper need to be launched simultaneously (my case). Creating/loading index for each instance is waste of time and resources, especially for larger references.
Cheers,

ERROR: CIGAR and query sequence are of different length

Hi!

I am getting an error when converting the graphmap2 (v 0.6.0) generated sam file (of nanopore cDNA reads mapped to a reference assembly) to bam.

These are the logs of the run:

[22:32:53 BuildIndexes] Loading reference sequences.
[22:32:54 SetupIndex_] Loading index from file: '/home/cgarcia/cbas_cDNA/data/CBAS_MASURCA-2_final.genome.scf.fasta.gmidx'.
[22:33:00 Index] Memory consumption: [currentRSS = 4364 MB, peakRSS = 4804 MB]
[22:33:00 Run] Hits will be thresholded at the percentil value (percentil: 99.000000%, frequency: 139).
[22:33:00 Run] Minimizers will be used. Minimizer window length: 5
[22:33:00 Run] Reference genome is assumed to be linear.
[22:33:00 Run] One or more similarly good alignments will be output per mapped read. Will be marked secondary.
[22:33:00 ProcessReads] All reads will be loaded in memory.
[22:33:53 ProcessReads] All reads loaded in 48.67 sec (size around 11231 MB). (9526475634 bases)
[22:33:53 ProcessReads] Memory consumption: [currentRSS = 19168 MB, peakRSS = 19168 MB]
[01:39:48 ProcessReads] [CPU time: 890914.56 sec, RSS: 501212 MB] Read: 11313268/11313268 (100.00%) [m: 9022586, u: 2290682]
[01:40:08 ProcessReads] Memory consumption: [currentRSS = 497484 MB, peakRSS = 502752 MB]

[01:40:08 ProcessReads] All reads processed in 890935.00 sec (or 14848.92 CPU min).
[W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
[E::sam_parse1] CIGAR and query sequence are of different length
[W::sam_read1] Parse error at line 14814
[main_samview] truncated file.
[bam_sort_core] merging from 0 files and 80 in-memory blocks...

my commands were as follows:

Read alignment

graphmap-not_release align -t 80 -x rnaseq -K fasta -L sam --extcigar
-r /home/cgarcia/cbas_cDNA/data/CBAS_MASURCA-2_final.genome.scf.fasta
-d /home/cgarcia/cbas_cDNA/data/cbas_CANU_cDNA_correction-2_combined.correctedReads_100bp.fasta
-o /home/cgarcia/analysis/mapping/graphmap2/corrected2/CBAS_MASURCA-2_final.genome.scf._ONT_cdna_graphmap2_combined_corrected-2_100bp.sam

Convert sam to bam and sort

samtools view -@ 80 -b -S CBAS_MASURCA-2_final.genome.scf._ONT_cdna_graphmap2_combined_corrected-2_100bp.sam | samtools sort -@ 80 \

CBAS_MASURCA-2_final.genome.scf._ONT_cdna_graphmap2_combined_corrected-2_100bp.sorted.bam

The line it complains about is this one (in the sam):

33ef8047-1b3c-4389-aad6-9110103981f5 0 scf7180000042097 35520 0 4=3D3=1X1=44N2D1=1X6=1X3=1I1=1I4=23N1X1=1X1=1X5=1D1=1X4=7D4=1D3I33N1I2=2D1=3D5=2D3=2X2=2I3=1D4=1X2=3I1=1I1=1X2=1D5=1D1=1D1=1D1=1X1=1X1=1X81N1=1I1=1X2=1X3=1X2=2D1X1=1X2=1X1=1X2=1X2=1I1=2D3=1X1=1X1=5D1X1=1X4=1D4=1X4=1I2=1I1=1X1=1X2=2D1X1=1X1=1D1X2=1X6=2D3=48N3=1X1=1X7=1I3=2X1=1X1=1D2=1X1=3X3=1X2=1I1=1X2=148N5=1X6=1D1=2X2=3D3=2D4=133N2=1X2=1D3=3D1=2D2=1X3=2X4=1D1=1X5=214N3=1X6=1I6=1D1=1D2=1X1=3X5=1D2=1X4=1X2=3I1=1X4=2D1=2X5=172N2I1=1X1=1I2=5I1=1X6=1X1=2D1=1D5=1D2=1X3=1X1=17N1=1X4=6D5=3D1X3=4D6=443N * 0 0 TTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTCACCGTGAAACAAAAACAGATTCAGCTATTCAGAAAATAACATGTATACCTAAATTTTATATTTCTATGCAGTTGCTATGCTAATACTACAGCTACTAAACAATATATGTTTTTACACAAAATTCTGTGATCATTCCAGCTTGCTTAGAATAACCTTCTCCAGTTTGACTGTGTCAGCTGCAAATTTGCAGTTCCTTCAGCTAGTTTCTCAGTGGCCATTTGGTCCTCATTTAGCCCACCTGGTGCTTCTCGTTGAGAGATATTTTCTCAATATCAAGTGCCTTTGCTTTATCAGCATCAAATGCTTAGTAACTGATTCAGTTGATTCTTTAGCTTATCCAGAAGGGCAGGGGGAGATAGTAAGGTTATCACAACCCAGCCAATGCAGATTTGGATGACACTAAAGATCCCAGCGAATCGTACTAACATTTGGATAACGATTGAAAGCAAACGTGTCAGGAAATATCTCTCGGCGGAGAAGCAATTCAGGTGGCTGCTTAAATGAAAGGACAAATGGCCGCGCTGAGAAACAACTGAAGAAATCCACCAAGATTTGCTGACAGTGAAGCTGAGAAAATTATTCTAAGCAATAGAATAACATACTCCAGTTTGACCTTGTCTGGCTACTGGTACGGATTCCTTCATTAGTTTCTCGGTGGCCATTTGTGGTCACTCATTTAGCAGCCACTGAATTTGCTTCTCGTTGAGAGATATTTTCTCAATATCAAGTGCCTTTGCTTTATCAGCATCCAAATGTATTAACTGGTTCAGTTGATTCTTTTGAAACTTATCCAGAAAGGGGCAGGAGATAGTGAGTTATCACAACCAGCCAGTACCACCCAAAATTGCCCTGTATTACGGATGCTCCACATGACAATGGTTTTATAGTCAAGCTTCTTGTAATAATTATATGTTTTGGTGACTGATTGAACACCGGGGTCTTCCGGTTGGCTCAAAAGTTTTCTTATCAGTGTTCTTGACATACCAGATCATAGATACGACCAACAAATGGGAAATCAAGTGACTTGTGGCACATGAAACTGCCCCGCAGGCAAACAAAAGCCAAGAAGTCAGATTATGATGGATACCATATTCGCTCTCCAGAATCTGGCTGCTTCATGCCCTCCCATGTTGAACTAAGTTGATTAGTACTCTCTCCTTGCTGATACCTGCCTTTTCATATAGTTCAATAAACCTCTTTGCTTCAGCAATAGGTTCTTCTTTATCAAGCCAGTAACCTTGCATCCGCTAGAGCCCGACCGAGTGCTATCTTCCAAGTCTACAACCCCAAAGTTTACATGGCTTGTCAATAGCAGCGTTACTTGATCGTCAAACTGCCACCCAGCGTCTTTGGCAAACTTAATAGCATCGCAGCAAATGCTGATATTCCGGCATCTGAGCGGCCTGGCCTGGCAAGGATGGGTTAGTAGTTGCATCCGTTGGCTTGTATTGATCAATGGATTTGATATCTCCAGTGTCAGCGACTACCGTAGTAAATTTATTCAATTGGTCAAGCGCTTTCCATAATCTTGCAAGGTGTACGCTTGAAAAGATGTATTGACCTTAATAGGCACTGGAGCGGTCAACACAAAGTTAGATAACGAGAATCAAGGCAGGAATGCAATTTTACCAAAATCATACATCCCCGTAATATATTTCAACAAGAAACACAAAAGAAGACACAAACAACTTTATTGTT * MD:Z:4^TTG3T1 NM:i:347 AS:i:-1134 H0:i:0 ZE:f:0 ZF:f:0 ZQ:i:1735 ZR:i:93581

Can you please help me to figure out what went wrong? I specified to include extended CIGARs with

--extcigar

thanks
Michael

Counting alignment operations error

Hi Ivan,

I get the following error when running graphmap2 on both my ONT cDNA datasets (one dataset can be found here (from this webpage: https://github.com/nanopore-wgs-consortium/NA12878/blob/master/nanopore-human-transcriptome/fastq_fast5_bulk.md)

.graphmap2: src/alignment/cigargen.cc:547: int CountAlignmentOperations(std::vector<unsigned char>&, const int8_t*, const int8_t*, int64_t, int64_t, SeqOrientation, int64_t, int64_t, int64_t, int64_t, bool, int64_t*, int64_t*, int64_t*, int64_t*, int64_t*, int64_t*, int64_t*): Assertion `alignment_position_start >= 0 && "Serious problem in counting alignment operations, stemmed from alignment somewhere."' failed.

Any ideas what this might be?

Best,
Kristoffer

Compile error?

I downloaded graphmap2-0.6.3, and tried to compile it, I got this error:

In file included from src/aligner/anchor_aligner.h:13:0,
from src/aligner/anchor_aligner.cc:8:
./src/containers/results.h:14:37: fatal error: utility/utility_general.h: No such file or directory
compilation terminated.
make: *** [obj_linux/src/aligner/anchor_aligner.o] Error 1

make installation error

Hi,

I am trying to install graphmap2 on a Linux server (see details below). After successfully executing the make modules, it failed on make step. Log pasted below.

Best,
Kristoffer

gcc details

(base) [kris@rackham3 graphmap2]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)

Server details

(base) [kris@rackham3 graphmap2]$ uname -a
Linux rackham3.uppmax.uu.se 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Log

(base) [kris@rackham3 graphmap2]$ make
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp
mkdir -p obj_linux/codebase/gindex/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/main.o codebase/gindex/src/main.cc
mkdir -p obj_linux/codebase/argumentparser/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/argumentparser/src/example.o codebase/argumentparser/src/example.cc
mkdir -p obj_linux/codebase/argumentparser/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/argumentparser/src/argparser.o codebase/argumentparser/src/argparser.cc
mkdir -p obj_linux/codebase/seqlib/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/test.o codebase/seqlib/src/test.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/experimental.o codebase/gindex/src/minimizer_index/experimental.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o codebase/gindex/src/minimizer_index/compiled_shape.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/seed.o codebase/gindex/src/minimizer_index/seed.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o codebase/gindex/src/minimizer_index/minimizer_index.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o codebase/gindex/src/minimizer_index/minimizer_generator.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/index_pos.o codebase/gindex/src/minimizer_index/index_pos.cc
mkdir -p obj_linux/codebase/seqlib/src/utility/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/utility/utility_general.o codebase/seqlib/src/utility/utility_general.cc
mkdir -p obj_linux/codebase/seqlib/src/utility/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/utility/tictoc.o codebase/seqlib/src/utility/tictoc.cc
mkdir -p obj_linux/codebase/seqlib/src/utility/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/utility/evalue_constants.o codebase/seqlib/src/utility/evalue_constants.cc
mkdir -p obj_linux/codebase/seqlib/src/utility/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/utility/evalue.o codebase/seqlib/src/utility/evalue.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o codebase/seqlib/src/sequences/sequence_gfa_test.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_file.o codebase/seqlib/src/sequences/sequence_file.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o codebase/seqlib/src/sequences/sequence_alignment.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o codebase/seqlib/src/sequences/sequence_gfa.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o codebase/seqlib/src/sequences/sequence_alignment_test.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/single_sequence.o codebase/seqlib/src/sequences/single_sequence.cc
mkdir -p obj_linux/codebase/seqlib/src/log_system/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/log_system/log_system.o codebase/seqlib/src/log_system/log_system.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/edlibcigar.o codebase/seqlib/src/libs/edlibcigar.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/alignment.o src/alignment/alignment.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/semiglobal.o src/alignment/semiglobal.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/cigargen.o src/alignment/cigargen.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/transcriptome_mod.o src/alignment/transcriptome_mod.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/anchored.o src/alignment/anchored.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/alignment_wrappers.o src/alignment/alignment_wrappers.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_exts2_sse.o src/ksw2/ksw2_exts2_sse.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_extz2_sse.o src/ksw2/ksw2_extz2_sse.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_extd2_sse.o src/ksw2/ksw2_extd2_sse.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/kalloc.o src/ksw2/kalloc.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_ll_sse.o src/ksw2/ksw2_ll_sse.cc
mkdir -p obj_linux/src/index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/index/index_util.o src/index/index_util.cc
mkdir -p obj_linux/src/aligner/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/aligner/aligner_ksw2.o src/aligner/aligner_ksw2.cc
mkdir -p obj_linux/src/aligner/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/aligner/aligner_util.o src/aligner/aligner_util.cc
mkdir -p obj_linux/src/aligner/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/aligner/anchor_aligner.o src/aligner/anchor_aligner.cc
mkdir -p obj_linux/src/aligner/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/aligner/sam_parser.o src/aligner/sam_parser.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/path_graph_entry.o src/containers/path_graph_entry.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/mapping_data.o src/containers/mapping_data.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/vertices.o src/containers/vertices.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/region.o src/containers/region.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/score_registry.o src/containers/score_registry.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/experimental.o src/graphmap/experimental.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/lcs_anchored.o src/graphmap/lcs_anchored.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/region_selection.o src/graphmap/region_selection.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/process_read.o src/graphmap/process_read.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/rna.o src/graphmap/rna.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/transcriptome.o src/graphmap/transcriptome.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/lcs_semiglobal.o src/graphmap/lcs_semiglobal.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/filter_anchors.o src/graphmap/filter_anchors.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/graphmap.o src/graphmap/graphmap.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/core_graphmap.o src/graphmap/core_graphmap.cc
mkdir -p obj_linux/src/owler/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/owler/owler.o src/owler/owler.cc
mkdir -p obj_linux/src/owler/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/owler/lcsk.o src/owler/lcsk.cc
mkdir -p obj_linux/src/owler/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/owler/process_read.o src/owler/process_read.cc
mkdir -p obj_linux/src/owler/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/owler/owler_experimental.o src/owler/owler_experimental.cc
mkdir -p obj_linux/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/program_parameters.o src/program_parameters.cc
mkdir -p obj_linux/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/main.o src/main.cc
mkdir -p ./bin/Linux-x64/
g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/Linux-x64/graphmap2 ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/gindex/src/main.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_linux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_linux/codebase/gindex/src/minimizer_index/experimental.o ./obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o ./obj_linux/codebase/gindex/src/minimizer_index/seed.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_linux/codebase/gindex/src/minimizer_index/index_pos.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/alignment/alignment.o ./obj_linux/src/alignment/semiglobal.o ./obj_linux/src/alignment/cigargen.o ./obj_linux/src/alignment/transcriptome_mod.o ./obj_linux/src/alignment/anchored.o ./obj_linux/src/alignment/alignment_wrappers.o ./obj_linux/src/ksw2/ksw2_exts2_sse.o ./obj_linux/src/ksw2/ksw2_extz2_sse.o ./obj_linux/src/ksw2/ksw2_extd2_sse.o ./obj_linux/src/ksw2/kalloc.o ./obj_linux/src/ksw2/ksw2_ll_sse.o ./obj_linux/src/index/index_util.o ./obj_linux/src/aligner/aligner_ksw2.o ./obj_linux/src/aligner/aligner_util.o ./obj_linux/src/aligner/anchor_aligner.o ./obj_linux/src/aligner/sam_parser.o ./obj_linux/src/containers/path_graph_entry.o ./obj_linux/src/containers/mapping_data.o ./obj_linux/src/containers/vertices.o ./obj_linux/src/containers/region.o ./obj_linux/src/containers/score_registry.o ./obj_linux/src/graphmap/experimental.o ./obj_linux/src/graphmap/lcs_anchored.o ./obj_linux/src/graphmap/region_selection.o ./obj_linux/src/graphmap/process_read.o ./obj_linux/src/graphmap/rna.o ./obj_linux/src/graphmap/transcriptome.o ./obj_linux/src/graphmap/lcs_semiglobal.o ./obj_linux/src/graphmap/filter_anchors.o ./obj_linux/src/graphmap/graphmap.o ./obj_linux/src/graphmap/core_graphmap.o ./obj_linux/src/owler/owler.o ./obj_linux/src/owler/lcsk.o ./obj_linux/src/owler/process_read.o ./obj_linux/src/owler/owler_experimental.o ./obj_linux/src/program_parameters.o ./obj_linux/src/main.o -lpthread -lgomp -lm -lz
/usr/bin/ld: cannot find -lstdc++
collect2: error: ld returned 1 exit status
make: *** [linux] Error 1

fail to install the graphmap2 v0.6.4

Hi, I am trying to install graphmap2 in linux server (ubuntu16.04.12). After successfully executing the "make modual" step, I failed in the "make" step. Here shows the error information:

Makefile💯 "*** WARNING /home/lhs/miniconda3/bin/x86_64-conda-linux-gnu-gcc minor version <7 ***"
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
/home/lhs/miniconda3/bin/x86_64-conda-linux-gnu-gcc -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/gindex/src -Icodebase/seqlib/src -Icodebase/argumentparser/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp
In file included from codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort_private.h:33:0,
from codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp:29:
/usr/include/stdlib.h:759:11: fatal error: bits/stdlib-bsearch.h: No such file or directory
include <bits/stdlib-bsearch.h>
^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:128: obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o] Error 1

Thanks a lot for any help.

clang error

Hi all,

Has anyone successfully installed this on Mac OS Mojave? After running the make command, I received the following error: clang: error: unsupported option '-fopenmp'. I see that this is a known issue for Mojave, but I'm afraid I'm unable to translate the suggested solutions to this program. I wondered if anyone had a record of how they overcame this and used graphmap2 recently.

Thank you,
Briana

Segmentation fault

Hi!

Recently, I was doing a benchmark for the performance of long spliced reads aligners(minimap2, GMAP, GraphMap2 and deSALT), but when I was running graphmap2 (v.0.6.01) on mouse pacbio SMRT reads and got a segmentation fault when 2.66% reads have been processed using 24 threads, shown in the screenshot:

The source of reads which I used can be found in https://www.ncbi.nlm.nih.gov/sra/?term=SRR6238555

How can I prevent segmentation faults?

thanks
Michael

IGV not finding sequence from bam file generated from a graphmap2 sam file

Hi,
I have Oxford Nanopore DNA sequences (from Plasmidsaurus) that I'm generating sam files through graphmap2, and ultimately making sorted bam files. However, the bam files show no sequence when I load them into IGV. The reference fasta is only 700bp long. My guess you could look at an output sam file and tell me the issue, but I can send you whatever files would help. I would appreciate any kind of direction you might give.

Thanks,

Patrick

Example_part.sam.txt

No reads are aligned?

Hi there,

I used this command to align pacbio reads:

graphmap2 -r hs38DH.fa -d test_100reads.fastq -o graph_map2.test.sam

It seems that NO reads were aligned? Or did I miss anything?

Thanks!

Illegal instruction

Hello, I'm trying to use graphmap2 in a singularity image (which is the only container technology available on the HPC infrastructure I'm working with).

I manage to made a working docker container on my local PC, but when I'm building the singularity image from the docker container, I cannot execute the graphmap2 executable.

Dockerfile :

################## BASE IMAGE ######################
FROM ubuntu:18.04 as base

################## METADATA ######################

LABEL description="Docker image for executing Graphmap2"
LABEL tags="Genomics"

################## INSTALL ######################
RUN apt-get update \
    && apt-get install -y apt-utils build-essential zlib1g-dev libbz2-dev pkg-config cmake libncurses5-dev autoconf git gcc g++ \
    && git clone https://github.com/lbcb-sci/graphmap2 \
    && cd graphmap2 \
    && make modules \
    && make -j 4 testing

Making the docker container :

docker build -f Dockerfile_graphmap2_v1.0 -t tintest/graphmap2:v1.0.0 .
docker push tintest/graphmap2:v1.0.0

The working docker container :

docker run e6323ba65ab2 graphmap2/bin/./graphmap2
Usage:
  graphmap2/bin/./graphmap2 tool

Options
    tool       STR   Specifies the tool to run:
                       align - the entire GraphMap pipeline.
                       owler - Overlapping With Long Erroneous Reads.


GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
GraphMap is licensed under The MIT License.

Version: v0.6.1
Build date: Aug  5 2019 at 14:05:47

Making the singularity image :

singularity build graphmap2.simg docker://tintest/graphmap2:v1.0.0 .
singularity exec graphmap2.simg graphmap2/bin/./graphmap2

The not working singularity images :

singularity exec graphmap2.simg graphmap2/bin/./graphmap2
Illegal instruction

Do you have any experience with singularity or any idea to help me solve this ?

Or if you could add a bioconda recipe for graphmap2, maybe it could help me to execute graphmap2 on a HPC infrastructure without the need of a container technology.

Regards.

`sse` should be used only on x86_64

Related to #21

Trying to build on Linux ARM64 leads to the following error:

g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/seqlib/src -Icodebase/gindex/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_ll_sse.o src/ksw2/ksw2_ll_sse.cc
src/ksw2/ksw2_ll_sse.cc:4:10: fatal error: emmintrin.h: No such file or directory
 #include <emmintrin.h>
          ^~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:124: obj_linux/src/ksw2/ksw2_ll_sse.o] Error 1

SSE and AVX are x86_64 specific features.

Could I please request adding support for Linux ARM64 ?

Alignment failed

I aligned an ONT generated FASTQ file to a reference fasta. The alignment completed with no error however no single read in the output SAM aligned to any region in the reference and all sam flags were equal to 255. There is no issue with the FASTQ or reference file as the alignment worked with minimap2.

Any advice would be appreciated.

Header not contain PG line and duplicate SQ line

Hello
I have tried to align with command ./graphmap2/bin/Linux-x64/graphmap2 align -r ref/ecoliref.fa --gtf ref/ecoliref.gtf -d tex1/tex/call_pass/newbasecalltest/high_tex_chop_trim.fastq -o tex1/tex/call_pass/newbasecalltest/quality_graph.sam
Then I need to convert it into a bam file but it showed an error that the PG line is duplicate and also PG line is missing so I cannot convert them.
Both references were downloaded from ensembl.
Any suggestion to solve this?
Here is a screenshot from sam file output

Thanks in advance.

Segmentation fault

Hi!

I'm trying to run graphmap2 on a SIRV, drosophila, and human dataset using graphmap2. The SIRV and drosophila data are found here

I'm running the version below because I can't build a newer version if any (see my previous installation issue).

Version: v0.6.3
Build date: Nov 21 2019 at 04:42:57

All my runs fail with a segmentation fault, both supplying graphmap2 with and without a gtf file. I have 256Gb available and it looks like graphmap2 is only using about 50-100Gb MaxRSS at failure, so I don't think insufficient memory is the problem.

For example, I run for SIRV:

graphmap2 align --index index.gmidx  --threads 19 -x rnaseq -r SIRV_isoforms_multi-fasta_170612a.fasta -d sirv_reads.fq -o reads.sam

index built with

graphmap2 align --index-only --index index.gmidx  -x rnaseq -r SIRV_isoforms_multi-fasta_170612a.fasta -d sirv_reads.fq

Any ideas?

Best,
Kristoffer

Build fails on Linux ARM64

Trying to build graphmap2 on openEuler 20.03 LTS ARM64 fails with:

mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/seqlib/src -Icodebase/gindex/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp
g++: error: unrecognized command line option ‘-m64’
make: *** [Makefile:128: obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o] Error 1

According to https://stackoverflow.com/a/58244182/497381 -m64 is x86_64 specific flag.
I will try to provide a PR with support for both CPU architectures!

$ g++ --version
g++ (GCC) 7.3.0
$ uname -a
Linux mgrigorov-arm64 4.19.90-2205.3.0.0149.oe1.aarch64 #1 SMP Wed May 11 12:53:17 UTC 2022 aarch64 aarch64 aarch64 GNU/Linux

Sam file not create it killed

/home/aclab/apps/graphmap2/bin/Linux-x64/graphmap2 align -r Homo_sapiens.fa -i /Drive4/graphmap2/Homo_sapiens.fa.gmidx -d combined_T.fastq -o homo.sam

e313594bd264 runi...[19:21:34 BuildIndexes] Loading reference sequences.
[19:28:18 SetupIndex_] Loading index from file: '/Drive4/graphmap2/Homo_sapiens.fa.gmidx'.
[19:40:42 Index] Memory consumption: [currentRSS = 156693 MB, peakRSS = 217297 MB]
[19:40:42 Run] Hits will be thresholded at the percentil value (percentil: 99.000000%, frequency: 1496).
[19:40:42 Run] Minimizers will be used. Minimizer window length: 5
[19:40:42 Run] Automatically setting the maximum allowed number of regions: max. 5101, attempt to reduce after 0
[19:40:42 Run] Reference genome is assumed to be linear.
[19:40:42 Run] Only one alignment will be reported per mapped read.
[19:40:42 ProcessReads] Reads will be loaded in batches of up to 1024 MB in size.
[19:40:47 ProcessReads] Batch of 482940 reads (1024 MiB) loaded in 4.71 sec. (93960397030528 bases)
[19:40:47 ProcessReads] Memory consumption: [currentRSS = 157878 MB, peakRSS = 217297 MB]
[19:40:47 ProcessReads] Using 24 threads.
[19:40:47 ProcessReads] [CPU time: 4.72 sec, RSS: 157878 MB] Read: 10/482940 (0.00%) [m: 0, u: 0], length = 229, qname: bed425b1-097a-4528-a5a0-8e9c41d99ffb run...

After than it killed.
I have memory 500gb so its not a problem i think but it killed always i tried many times. Can you please help me what is the problem.

Graphmap2 can't align dRNAseq reads with U

Could you add U handling to graphmap? Then we won't have to convert U>T for dRNA-seq reads.
Minimap2 handles it just fine ;)

Memory up to 140GB!!!

Hi,
when I was running human RNA-seq simulated reads (5GB fastq reads) and other reads, I found that the memory of GraphMap2 can up to 140GB, maybe there have some bugs in programs, hope the author can check out the source codes to prevent so higher memory.

Best!

Error building with g++ 9.3

Hi,

I'm trying to build GraphMap2 within a Docker with Alpine Linux. I'm running the required make modules && make steps.
The gcc/g++ toolchain is v9.3 and I'm getting the following error. Building with gcc7.5 on my Laptop works fine.
I'm using Graphmap v0.6.4

In file included from codebase/seqlib/src/utility/evalue.cc:10:
codebase/seqlib/src/utility/evalue.h:161:24: error: 'int64_t' was not declared in this scope
161 | int CalculateEValueDNA(int64_t alignment_score, int64_t query_length, int64_t target_length, const EValueParams* eValueParams, double ret_evalue);
| ^~~~~~~
codebase/seqlib/src/utility/evalue.h:161:49: error: 'int64_t' was not declared in this scope
161 | int CalculateEValueDNA(int64_t alignment_score, int64_t query_length, int64_t target_length, const EValueParams eValueParams, double ret_evalue);
| ^~~~~~~
codebase/seqlib/src/utility/evalue.h:161:71: error: 'int64_t' was not declared in this scope
161 | int CalculateEValueDNA(int64_t alignment_score, int64_t query_length, int64_t target_length, const EValueParams eValueParams, double ret_evalue);
| ^~~~~~~
codebase/seqlib/src/utility/evalue.h:161:94: error: expected primary-expression before 'const'
161 | int CalculateEValueDNA(int64_t alignment_score, int64_t query_length, int64_t target_length, const EValueParams eValueParams, double ret_evalue);
| ^~~~~
In file included from codebase/seqlib/src/utility/evalue.cc:10:
codebase/seqlib/src/utility/evalue.h:161:128: error: expected primary-expression before 'double'
161 | int CalculateEValueDNA(int64_t alignment_score, int64_t query_length, int64_t target_length, const EValueParams eValueParams, double ret_evalue);
| ^~~~~~
codebase/seqlib/src/utility/evalue.h:161:146: error: expression list treated as compound expression in initializer [-fpermissive]
161 | int CalculateEValueDNA(int64_t alignment_score, int64_t query_length, int64_t target_length, const EValueParams eValueParams, double ret_evalue);
| ^
codebase/seqlib/src/utility/evalue.h:163:36: error: 'int64_t' has not been declared
163 | int SetupScorer(char matrix_name, int64_t reference_length, int gap_open, int gap_extend, EValueParams ret_eValueParams);
| ^~~~~~~
codebase/seqlib/src/utility/evalue.cc:278:146: error: 'int CalculateEValueDNA(int64_t, int64_t, int64_t, const EValueParams, double)' redeclared as different kind of entity
278 | int CalculateEValueDNA(int64_t alignment_score, int64_t query_length, int64_t target_length, const EValueParams* eValueParams, double ret_evalue) {
| ^
In file included from codebase/seqlib/src/utility/evalue.cc:10:
codebase/seqlib/src/utility/evalue.h:161:5: note: previous declaration 'int CalculateEValueDNA'
161 | int CalculateEValueDNA(int64_t alignment_score, int64_t query_length, int64_t target_length, const EValueParams eValueParams, double *ret_evalue);
| ^~~~~~~~~~~~~~~~~~
make: *** [Makefile:124: obj_linux/codebase/seqlib/src/utility/evalue.o] Error 1

Cheers,

Pay

Calling help return exit-code 1

Calling help should return exit(0) since it prints help (successfully) and then exits.

Please tag a release

Could you tag a release? We can then get the updated version of this in bioconda.

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