isovic / aracon Goto Github PK

Hello!
I tried to install aracon on my Linux service (CentOS release 6.2) with following steps：

1. git clone https://github.com/isovic/aracon.git
2. cd aracon
3. make

The installing process was stoped with the following messages:
[GET MODULES]
Submodule 'components/graphmap' () registered for path 'components/graphmap'
Submodule 'components/miniasm' () registered for path 'components/miniasm'
Submodule 'components/racon' () registered for path 'components/racon'
Submodule 'components/samscripts' () registered for path 'components/samscripts'
Submodule path 'components/graphmap': checked out '1d16f07888b60547094e8257688088d6f00be8af'
Submodule 'codebase/argumentparser' (https://github.com/isovic/graphmap.git) registered for path 'codebase/argumentparser'
Submodule 'codebase/seqlib' (https://github.com/isovic/graphmap.git) registered for path 'codebase/seqlib'
Submodule path 'codebase/argumentparser': checked out 'd0dae52c3d1b029f65f3bf4f0cd671e88dbeb98f'
Submodule path 'codebase/seqlib': checked out 'e0833dc91343ac7a1e33fb6b2f08bc9009bf9a8b'
Submodule path 'components/racon': checked out '0bb2fd6ca9fa4492b0ba7b6751d242795c02f6fa'
Submodule 'codebase/argparser' (https://github.com/isovic/racon.git) registered for path 'codebase/argparser'
Submodule 'codebase/samscripts' (https://github.com/isovic/racon.git) registered for path 'codebase/samscripts'
Submodule 'codebase/seqlib' (https://github.com/isovic/racon.git) registered for path 'codebase/seqlib'
Submodule 'codebase/spoa' (https://github.com/isovic/racon.git) registered for path 'codebase/spoa'
Submodule path 'components/samscripts': checked out 'b40d0663f6a5c477d5f6908f83567758fb627e08'
Entering 'components/graphmap'
From https://github.com/isovic/graphmap

• branch master -> FETCH_HEAD
  Updating 1d16f07..817ba03
  Fast-forward
  Makefile | 2 +-
  README.md | 6 +-
  codebase/argumentparser | 2 +-
  codebase/seqlib | 2 +-
  doc/changelog.md | 6 ++
  src/alignment/anchored.cc | 2 +-
  src/alignment/cigargen.cc | 146 +++++++++++++++++++++++++++-----------
  src/alignment/cigargen.h | 20 ++++++
  src/graphmap/graphmap.cc | 6 +-
  src/graphmap/graphmap.h | 7 ++
  src/graphmap/process_read.cc | 2 +-
  src/graphmap/region_selection.cc | 19 +++--
  src/index/index.h | 67 +----------------
  src/index/index_hash.cc | 10 ++-
  src/program_parameters.cc | 9 +--
  src/program_parameters.h | 3 +-
  16 files changed, 176 insertions(+), 133 deletions(-)
  Entering 'components/miniasm'
  From https://github.com/lh3/miniasm
• branch master -> FETCH_HEAD
  Already up-to-date.
  Entering 'components/racon'
  From https://github.com/isovic/racon
• branch master -> FETCH_HEAD
  Updating 0bb2fd6..bd1a7c1
  Fast-forward
  .gitignore | 1 +
  Makefile | 3 +-
  README.md | 65 ++++-
  codebase/argparser | 2 +-
  codebase/samscripts | 2 +-
  codebase/seqlib | 2 +-
  example1-lambda.sh | 56 ----
  example11-erc-ecoli_map006.sh | 155 -----------
  ...ple12-paf-lambda.sh => example1_1-paf-lambda.sh | 5 +-
  ...le7-mhap-lambda.sh => example1_2-mhap-lambda.sh | 6 +-
  ...hap-ecoli_map006.sh => example1_3-sam-lambda.sh | 53 ++--
  example2-paf-pipe-lambda.sh | 102 +++++++
  example10-erc-lambda.sh => example3-erc-lambda.sh | 7 +-
  example8_1-mhap-ecoli_map006-1111.sh | 122 --------
  example8_2-mhap-ecoli_map006-pileup.sh | 122 --------
  example9-mhap-ecoli_pacbio_160x.sh | 122 --------
  example9_1-mhap-ecoli_pacbio_160x-1111.sh | 122 --------
  run-measure.sh | 13 -
  scripts/edcontigs.py | 2 +-
  scripts/evalcontigs.py | 2 +-
  scripts/intervaltree.py | 2 +-
  scripts/lis.py | 2 +-
  src/consensus/consensus.cc | 195 ++++++++++++-
  src/consensus/consensus.h | 6 +-
  src/consensus/pileup.cc | 2 +-
  src/consensus/pileup.h | 2 +-
  src/main.cc | 205 ++++++++------
  src/mhap.cc | 290 +++++++++++++-------
  src/mhap.h | 20 +-
  29 files changed, 727 insertions(+), 961 deletions(-)
  delete mode 100755 example1-lambda.sh
  delete mode 100755 example11-erc-ecoli_map006.sh
  rename example12-paf-lambda.sh => example1_1-paf-lambda.sh (98%)
  rename example7-mhap-lambda.sh => example1_2-mhap-lambda.sh (95%)
  rename example8-mhap-ecoli_map006.sh => example1_3-sam-lambda.sh (74%)
  create mode 100755 example2-paf-pipe-lambda.sh
  rename example10-erc-lambda.sh => example3-erc-lambda.sh (95%)
  delete mode 100755 example8_1-mhap-ecoli_map006-1111.sh
  delete mode 100755 example8_2-mhap-ecoli_map006-pileup.sh
  delete mode 100755 example9-mhap-ecoli_pacbio_160x.sh
  delete mode 100755 example9_1-mhap-ecoli_pacbio_160x-1111.sh
  delete mode 100755 run-measure.sh
  Entering 'components/samscripts'
  From https://github.com/isovic/samscripts
• branch master -> FETCH_HEAD
  Updating b40d066..8225661
  Fast-forward
  src/alignmentstats.py | 2 +-
  src/apply-consensus.py | 2 +-
  src/consensus.py | 2 +-
  src/count_mapped_reads.py | 2 +-
  src/errorrates.py | 2 +-
  src/fastqfilter.py | 4 +-
  src/fastqparser.py | 2 +-
  src/samfilter.py | 2 +-
  src/svconsensus.py | 2 +-
  src/utility_sam.py | 515 ++++++++++++++++++++++++++++++++-------------
  src/vcffilter.py | 2 +-
  src/venn_of_sams.py | 2 +-
  12 files changed, 385 insertions(+), 154 deletions(-)
  [GraphMap] components/graphmap/bin/Linux-x64/graphmap
  cd components/graphmap; make modules && make -j 4
  make[1]: Entering directory `/share/work2/staff/xingsk/software_install/Minisam_Racon/aracon/components/graphmap'
  git submodule update --init --recursive
  Submodule 'codebase/argumentparser' () registered for path 'codebase/argumentparser'
  Submodule 'codebase/seqlib' () registered for path 'codebase/seqlib'
  Submodule path 'codebase/argumentparser': checked out '72af9764acefbcc92ff76e3aba8a83d9a3e33671'
  Submodule path 'codebase/seqlib': checked out '129d39a97ba56863bea98d3125f4241b26f36341'
  git submodule foreach git pull origin master
  Entering 'codebase/argumentparser'
  From https://github.com/isovic/argumentparser
• branch master -> FETCH_HEAD
  Already up-to-date.
  Entering 'codebase/seqlib'
  From https://github.com/isovic/seqlib
• branch master -> FETCH_HEAD
  Updating 129d39a..a93e7d9
  Fast-forward
  src/utility/utility_general.cc | 8 ++++++--
  src/utility/utility_general.h | 3 ++-
  2 files changed, 8 insertions(+), 3 deletions(-)
  make[1]: Leaving directory /share/work2/staff/xingsk/software_install/Minisam_Racon/aracon/components/graphmap' make[1]: Entering directory /share/work2/staff/xingsk/software_install/Minisam_Racon/aracon/components/graphmap'
  Makefile:97: "*** WARNING g++ minor version <7 ***"
  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 -DRELEASE_VERSION -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/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/seqlib/src -DRELEASE_VERSION -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.cpp
  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/seqlib/src -DRELEASE_VERSION -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.cpp
  mkdir -p obj_linux/codebase/argumentparser/src/
  codebase/seqlib/src/libs/edlib.cpp:4:19: Fatal error: cstdlib：No such file or directory
  compilation terminated
  make[1]: *** [obj_linux/codebase/seqlib/src/libs/edlib.o] error 1
  make[1]: *** waiting for unfinished jobs....
  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 -DRELEASE_VERSION -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
  In file included from codebase/argumentparser/src/argparser.cc:10:0:
  codebase/argumentparser/src/argparser.h:16:18: Fatal error：string：No such file or directory
  compilation terminated
  make[1]: *** [obj_linux/codebase/argumentparser/src/argparser.o] error 1
  make[1]: *** No child processes. Stop.
  make: *** [components/graphmap/bin/Linux-x64/graphmap] error 2

So what can i do now?

Hi,

I wanted to try this tool but I'm having issues installing it. It fails when trying a recursive git pull.

git clone --recursive https://github.com/isovic/aracon

fatal: reference is not a tree: b40d0663f6a5c477d5f6908f83567758fb627e08
Failed to recurse into submodule path 'components/racon'
Unable to checkout 'b40d0663f6a5c477d5f6908f83567758fb627e08' in submodule path 'components/samscripts'

Cheers
Jon

Hi,

I found that the aracon documentation is a little bit out of date. When calling on aracon it gives the following instructions:

A de novo genome assembler for third generation sequencing data which does not requires error >correction.
Usage:
./aracon <reads.fastq> <working_folder> [options]

Options:
--threads INT
--erc Use error correction on the input reads.

Instead the the correct flag to set the number of threads appears to be:

--num_threads INT

Cheers
Jon