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cschin / Peregrine

Peregrine: Fast Genome Assembler Using SHIMMER Index
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Peregrine wihout Docker? #31

Open Tdanis opened 4 years ago

Tdanis commented 4 years ago

Hello, I have one quick question. Is any other way to use peregrine without Docker ? Because my machine does not support Docker.

Thank you

jelber2 commented 4 years ago

I had done this awhile ago, but I think the below should work

git clone https://github.com/cschin/Peregrine.git
cd Peregrine
# try running the commands in install_with_conda.sh individually or
bash install_with_conda.sh

# when you are ready to use peregrine
conda activate peregrine

find /genetics/elbers/illumina-or-pacbio2/purge_haplotigs -name "random_reads_ccs.fasta.gz" | sort > seqdata.lst

# NOTE set the values such as 75 to fit the number of cores and amount of memory for your system
pg_run.py asm \
/genetics/elbers/illumina-or-pacbio2/purge_haplotigs/seqdata.lst 75 75 75 75 75 75 75 75 75 \
--with-consensus --shimmer-r 3 --best_n_ovlp 8 \
--output /genetics/elbers/illumina-or-pacbio2/purge_haplotigs/peregrine-shimmer-r_3-best_n_ovlp_8

# output for contigs is in peregrine-shimmer-r_3-best_n_ovlp_8/4-cns/cns-merge/ctg_cns.fa

conda deactivate
Tdanis commented 4 years ago

Thank you very much.

Theodoros Danis

From: Jean Elbers notifications@github.com Sent: Wednesday, February 26, 2020 1:01:48 PM To: cschin/Peregrine Peregrine@noreply.github.com Cc: Tdanis danis_theo@hotmail.com; Author author@noreply.github.com Subject: Re: [cschin/Peregrine] Peregrine wihout Docker? (#31)

I had done this awhile ago, but I think the below should work

git clone https://github.com/cschin/Peregrine.git cd Peregrine

try running the commands in install_with_conda.sh individually or

bash install_with_conda.sh

when you are ready to use peregrine

conda activate peregrine

find /genetics/elbers/illumina-or-pacbio2/purge_haplotigs -name "random_reads_ccs.fasta.gz" | sort > seqdata.lst

NOTE set the values such as 75 to fit the number of cores and amount of memory for your system

pg_run.py asm \ /genetics/elbers/illumina-or-pacbio2/purge_haplotigs/seqdata.lst 75 75 75 75 75 75 75 75 75 \ --with-consensus --shimmer-r 3 --best_n_ovlp 8 \ --output /genetics/elbers/illumina-or-pacbio2/purge_haplotigs/peregrine-shimmer-r_3-best_n_ovlp_8

output for contigs is in peregrine-shimmer-r_3-best_n_ovlp_8/4-cns/cns-merge/ctg_cns.fa

conda deactivate

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cschin commented 4 years ago

Thank you @jelber2.

Yedomon commented 3 years ago

Hello Dear @cschin.

I encountered some problems following conda installation.

Here is my installation process


git clone https://github.com/cschin/Peregrine.git

cd Peregrine

bash install_with_conda.sh

I saw this info


Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/kplee/miniconda3/envs/peregrine

  added / updated specs:
    - python=3.7

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
  certifi            conda-forge/linux-64::certifi-2020.12.5-py37h89c1867_1
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_18
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_18
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  openssl            conda-forge/linux-64::openssl-1.1.1i-h7f98852_0
  pip                conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.7.9-hffdb5ce_0_cpython
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py37h89c1867_3
  sqlite             conda-forge/linux-64::sqlite-3.34.0-h74cdb3f_0
  tk                 conda-forge/linux-64::tk-8.6.10-h21135ba_1
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate peregrine
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: done

## Package Plan ##

  environment location: /home/kplee/miniconda3/envs/peregrine

  added / updated specs:
    - pypy3.6

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  expat              conda-forge/linux-64::expat-2.2.10-h9c3ff4c_0
  gdbm               conda-forge/linux-64::gdbm-1.18-h0a1914f_2
  pypy3.6            conda-forge/linux-64::pypy3.6-7.3.2-h45e8706_2

The following packages will be DOWNGRADED:

  libffi                                     3.3-h58526e2_2 --> 3.2.1-he1b5a44_1007
  python                           3.7.9-hffdb5ce_0_cpython --> 3.7.8-h8bdb77d_2_cpython

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
~/program/Peregrine/py ~/program/Peregrine
running install
running bdist_egg
running egg_info
creating peregrine.egg-info
writing peregrine.egg-info/PKG-INFO
writing dependency_links to peregrine.egg-info/dependency_links.txt
writing requirements to peregrine.egg-info/requires.txt
writing top-level names to peregrine.egg-info/top_level.txt
writing manifest file 'peregrine.egg-info/SOURCES.txt'
reading manifest file 'peregrine.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'peregrine.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/peregrine
copying peregrine/__init__.py -> build/lib.linux-x86_64-3.7/peregrine
copying peregrine/_version.py -> build/lib.linux-x86_64-3.7/peregrine
copying peregrine/build_falcon4py.py -> build/lib.linux-x86_64-3.7/peregrine
copying peregrine/build_shimmer4py.py -> build/lib.linux-x86_64-3.7/peregrine
copying peregrine/utils.py -> build/lib.linux-x86_64-3.7/peregrine
UPDATING build/lib.linux-x86_64-3.7/peregrine/_version.py
set build/lib.linux-x86_64-3.7/peregrine/_version.py to '1.6.3+3.g008082a.dirty'
running build_ext
generating cffi module 'build/temp.linux-x86_64-3.7/peregrine._falcon4py.c'
creating build/temp.linux-x86_64-3.7
generating cffi module 'build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c'
building 'peregrine._shimmer4py' extension
creating build/temp.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/home
creating build/temp.linux-x86_64-3.7/home/kplee
creating build/temp.linux-x86_64-3.7/home/kplee/program
creating build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine
creating build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c -o build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7/peregrine._shimmer4py.o
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c: In function ‘_cffi_d_build_shimmer_map4py’:
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c:777:3: warning: implicit declaration of function ‘build_shimmer_map4py’ [-Wimplicit-function-declaration]
   build_shimmer_map4py(x0, x1, x2, x3, x4, x5, x6);
   ^
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c: In function ‘_cffi_d_get_mmer_count’:
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c:1034:3: warning: implicit declaration of function ‘get_mmer_count’ [-Wimplicit-function-declaration]
   return get_mmer_count(x0, x1);
   ^
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c: In function ‘_cffi_d_get_shimmer_hits’:
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c:1082:3: warning: implicit declaration of function ‘get_shimmer_hits’ [-Wimplicit-function-declaration]
   get_shimmer_hits(x0, x1, x2, x3);
   ^
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c: In function ‘_cffi_d_get_shimmers_for_read’:
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c:1145:3: warning: implicit declaration of function ‘get_shimmers_for_read’ [-Wimplicit-function-declaration]
   get_shimmers_for_read(x0, x1, x2);
   ^
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/src/shimmer4py.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shimmer4py.o
/home/kplee/program/Peregrine/src/shimmer4py.c: In function ‘build_shimmer_map4py’:
/home/kplee/program/Peregrine/src/shimmer4py.c:101:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
   for (uint8_t i = 0; i < p.we_wordc; i++) {
   ^
/home/kplee/program/Peregrine/src/shimmer4py.c:101:3: note: use option -std=c99 or -std=gnu99 to compile your code
/home/kplee/program/Peregrine/src/shimmer4py.c:115:16: error: redefinition of ‘i’
   for (uint8_t i = 0; i < p.we_wordc; i++) {
                ^
/home/kplee/program/Peregrine/src/shimmer4py.c:101:16: note: previous definition of ‘i’ was here
   for (uint8_t i = 0; i < p.we_wordc; i++) {
                ^
/home/kplee/program/Peregrine/src/shimmer4py.c:115:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
   for (uint8_t i = 0; i < p.we_wordc; i++) {
   ^
/home/kplee/program/Peregrine/src/shimmer4py.c:78:7: warning: variable ‘written’ set but not used [-Wunused-but-set-variable]
   int written;
       ^
/home/kplee/program/Peregrine/src/shimmer4py.c: In function ‘get_shimmer_hits’:
/home/kplee/program/Peregrine/src/shimmer4py.c:181:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
   for (khiter_t __j = kh_begin(mmer1_map); __j != kh_end(mmer1_map); ++__j) {
   ^
/home/kplee/program/Peregrine/src/shimmer4py.c:188:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
     for (size_t __k0 = 0; __k0 < (mpv->n); __k0++) {
     ^
error: command 'gcc' failed with exit status 1
running clean
removing 'build/temp.linux-x86_64-3.7' (and everything under it)
removing 'build/lib.linux-x86_64-3.7' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.7' does not exist -- can't clean it
removing 'build'
~/program/Peregrine
fatal: destination path 'pypeFLOW' already exists and is not an empty directory.
~/program/Peregrine/pypeFLOW ~/program/Peregrine
/home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/setuptools/dist.py:458: UserWarning: Normalizing '2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476
' to '2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476'
  warnings.warn(tmpl.format(**locals()))
running install
running bdist_egg
running egg_info
writing pypeflow.egg-info/PKG-INFO
writing dependency_links to pypeflow.egg-info/dependency_links.txt
writing entry points to pypeflow.egg-info/entry_points.txt
writing requirements to pypeflow.egg-info/requires.txt
writing top-level names to pypeflow.egg-info/top_level.txt
reading manifest file 'pypeflow.egg-info/SOURCES.txt'
writing manifest file 'pypeflow.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/pwatcher
copying build/lib/pwatcher/__init__.py -> build/bdist.linux-x86_64/egg/pwatcher
copying build/lib/pwatcher/blocking.py -> build/bdist.linux-x86_64/egg/pwatcher
copying build/lib/pwatcher/fs_based.py -> build/bdist.linux-x86_64/egg/pwatcher
copying build/lib/pwatcher/network_based.py -> build/bdist.linux-x86_64/egg/pwatcher
creating build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/__init__.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/fs_heartbeat.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/network_heartbeat.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/pwatcher.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/pypeflow_example.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/query_server.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/job_start.sh -> build/bdist.linux-x86_64/egg/pwatcher/mains
creating build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/__init__.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/do_support.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/do_task.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/io.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/pwatcher_workflow.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/sample_tasks.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/simple_pwatcher_bridge.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/tasks.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/util.py -> build/bdist.linux-x86_64/egg/pypeflow
creating build/bdist.linux-x86_64/egg/pypeflow/mains
copying build/lib/pypeflow/mains/__init__.py -> build/bdist.linux-x86_64/egg/pypeflow/mains
creating build/bdist.linux-x86_64/egg/src
copying build/lib/src/__init__.py -> build/bdist.linux-x86_64/egg/src
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/blocking.py to blocking.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/fs_based.py to fs_based.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/network_based.py to network_based.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/fs_heartbeat.py to fs_heartbeat.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/network_heartbeat.py to network_heartbeat.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/pwatcher.py to pwatcher.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/pypeflow_example.py to pypeflow_example.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/query_server.py to query_server.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/do_support.py to do_support.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/do_task.py to do_task.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/io.py to io.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/pwatcher_workflow.py to pwatcher_workflow.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/sample_tasks.py to sample_tasks.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/simple_pwatcher_bridge.py to simple_pwatcher_bridge.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/tasks.py to tasks.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/util.py to util.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/mains/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/src/__init__.py to __init__.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg
creating /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg
Extracting pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding pypeflow 2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476 to easy-install.pth file
Installing heartbeat-wrapper script to /home/kplee/miniconda3/envs/peregrine/bin
Installing pwatcher-main script to /home/kplee/miniconda3/envs/peregrine/bin
Installing pwatcher-pypeflow-example script to /home/kplee/miniconda3/envs/peregrine/bin

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg
Processing dependencies for pypeflow==2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476
Searching for networkx>=1.9.1
Reading https://pypi.org/simple/networkx/
Downloading https://files.pythonhosted.org/packages/9b/cd/dc52755d30ba41c60243235460961fc28022e5b6731f16c268667625baea/networkx-2.5-py3-none-any.whl#sha256=8c5812e9f798d37c50570d15c4a69d5710a18d77bafc903ee9c5fba7454c616c
Best match: networkx 2.5
Processing networkx-2.5-py3-none-any.whl
Installing networkx-2.5-py3-none-any.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding networkx 2.5 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/networkx-2.5-py3.7.egg
Searching for decorator>=4.3.0
Reading https://pypi.org/simple/decorator/
Downloading https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl#sha256=41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760
Best match: decorator 4.4.2
Processing decorator-4.4.2-py2.py3-none-any.whl
Installing decorator-4.4.2-py2.py3-none-any.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding decorator 4.4.2 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/decorator-4.4.2-py3.7.egg
Finished processing dependencies for pypeflow==2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476
~/program/Peregrine
~/program/Peregrine/py ~/program/Peregrine
Collecting pip
  Using cached pip-21.0.1-py3-none-any.whl (1.5 MB)
Collecting setuptools
  Using cached setuptools-53.0.0-py3-none-any.whl (784 kB)
Collecting wheel
  Using cached wheel-0.36.2-py2.py3-none-any.whl (35 kB)
Installing collected packages: wheel, setuptools, pip
Successfully installed pip-21.0.1 setuptools-53.0.0 wheel-0.36.2
running install
running bdist_egg
running egg_info
creating peregrine_pypy.egg-info
writing peregrine_pypy.egg-info/PKG-INFO
writing dependency_links to peregrine_pypy.egg-info/dependency_links.txt
writing requirements to peregrine_pypy.egg-info/requires.txt
writing top-level names to peregrine_pypy.egg-info/top_level.txt
writing manifest file 'peregrine_pypy.egg-info/SOURCES.txt'
reading manifest file 'peregrine_pypy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'peregrine_pypy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
warning: install_lib: 'build/lib' does not exist -- no Python modules to install

creating build
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.6
copying scripts/ovlp_to_graph.py -> build/scripts-3.6
copying scripts/graph_to_path.py -> build/scripts-3.6
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/ovlp_to_graph.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/graph_to_path.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/ovlp_to_graph.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/graph_to_path.py to 775
copying peregrine_pypy.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine_pypy.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine_pypy.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine_pypy.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine_pypy.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/peregrine_pypy-0.1-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing peregrine_pypy-0.1-py3.6.egg
Copying peregrine_pypy-0.1-py3.6.egg to /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages
Adding peregrine-pypy 0.1 to easy-install.pth file
Installing graph_to_path.py script to /home/kplee/miniconda3/envs/peregrine/bin
Installing ovlp_to_graph.py script to /home/kplee/miniconda3/envs/peregrine/bin

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages/peregrine_pypy-0.1-py3.6.egg
Processing dependencies for peregrine-pypy==0.1
Searching for networkx==2.4
Reading https://pypi.org/simple/networkx/
Downloading https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl#sha256=cdfbf698749a5014bf2ed9db4a07a5295df1d3a53bf80bf3cbd61edf9df05fa1
Best match: networkx 2.4
Processing networkx-2.4-py3-none-any.whl
Installing networkx-2.4-py3-none-any.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages
Adding networkx 2.4 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages/networkx-2.4-py3.6.egg
Searching for decorator>=4.3.0
Reading https://pypi.org/simple/decorator/
Downloading https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl#sha256=41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760
Best match: decorator 4.4.2
Processing decorator-4.4.2-py2.py3-none-any.whl
Installing decorator-4.4.2-py2.py3-none-any.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages
Adding decorator 4.4.2 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages/decorator-4.4.2-py3.6.egg
Finished processing dependencies for peregrine-pypy==0.1
~/program/Peregrine
~/program/Peregrine/src ~/program/Peregrine
gcc -O3  -Wall -Wno-unused-result -Wno-unused-function -Werror   -c -o shmr_utils.o shmr_utils.c
shmr_utils.c: In function ‘build_map’:
shmr_utils.c:321:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
   for (size_t i = s + 1; i < mmers->n; i++) {
   ^
shmr_utils.c:321:3: note: use option -std=c99 or -std=gnu99 to compile your code
make: *** [shmr_utils.o] Error 1
cp shmr_mkseqdb shmr_index shmr_gather_mc shmr_overlap shmr_dedup shmr_map /home/kplee/miniconda3/envs/peregrine/bin
cp: cannot stat ‘shmr_mkseqdb’: No such file or directory
cp: cannot stat ‘shmr_index’: No such file or directory
cp: cannot stat ‘shmr_gather_mc’: No such file or directory
cp: cannot stat ‘shmr_overlap’: No such file or directory
cp: cannot stat ‘shmr_dedup’: No such file or directory
cp: cannot stat ‘shmr_map’: No such file or directory
make: *** [install] Error 1
~/program/Peregrine

I notice this error message:


error: command 'gcc' failed with exit status 1

Is there a problem relative to the gcc version? How can I fix it?

I am using Centos 7

Here is my GGC version

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)

Yedomon

cschin commented 3 years ago

@Yedomon the error is 

gcc -O3  -Wall -Wno-unused-result -Wno-unused-function -Werror   -c -o shmr_utils.o shmr_utils.c
shmr_utils.c: In function ‘build_map’:
shmr_utils.c:321:3: error: ‘for’ loop initial declarations are only allowed in C99 mode
   for (size_t i = s + 1; i < mmers->n; i++) {

I am using this gcc

gcc --version
gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 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.

and I just test to compile 

gcc -O3  -Wall -Wno-unused-result -Wno-unused-function -Werror   -c -o shmr_utils.o shmr_utils.c

it works fine.

GCC 4.8.5 is rather old. You might be able to compile it with suggested option (you can edit the Makefile to add the options), but I suggest to upgrade your system to a more recent one.

Hope this helps.

Yedomon commented 3 years ago

Thank you very.

It works....... nicely!

After trying to update the gcc of the Centos by doing:


$ yum -y install centos-release-scl
$ yum -y install devtoolset-7-gcc devtoolset-7-gcc-c++ devtoolset-7-binutils
$ scl enable devtoolset-7 bash

I ran again 


$ bash install_with_conda.sh

Info file:

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/kplee/miniconda3/envs/peregrine

  added / updated specs:
    - python=3.7

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0
  certifi            conda-forge/linux-64::certifi-2020.12.5-py37h89c1867_1
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_18
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_18
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  openssl            conda-forge/linux-64::openssl-1.1.1i-h7f98852_0
  pip                conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.7.9-hffdb5ce_0_cpython
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py37h89c1867_3
  sqlite             conda-forge/linux-64::sqlite-3.34.0-h74cdb3f_0
  tk                 conda-forge/linux-64::tk-8.6.10-h21135ba_1
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate peregrine
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/kplee/miniconda3/envs/peregrine

  added / updated specs:
    - pypy3.6

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  expat              conda-forge/linux-64::expat-2.2.10-h9c3ff4c_0
  gdbm               conda-forge/linux-64::gdbm-1.18-h0a1914f_2
  pypy3.6            conda-forge/linux-64::pypy3.6-7.3.2-h45e8706_2

The following packages will be DOWNGRADED:

  libffi                                     3.3-h58526e2_2 --> 3.2.1-he1b5a44_1007
  python                           3.7.9-hffdb5ce_0_cpython --> 3.7.8-h8bdb77d_2_cpython

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
~/program/Peregrine/py ~/program/Peregrine
running install
running bdist_egg
running egg_info
creating peregrine.egg-info
writing peregrine.egg-info/PKG-INFO
writing dependency_links to peregrine.egg-info/dependency_links.txt
writing requirements to peregrine.egg-info/requires.txt
writing top-level names to peregrine.egg-info/top_level.txt
writing manifest file 'peregrine.egg-info/SOURCES.txt'
reading manifest file 'peregrine.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'peregrine.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/peregrine
copying peregrine/__init__.py -> build/lib.linux-x86_64-3.7/peregrine
copying peregrine/_version.py -> build/lib.linux-x86_64-3.7/peregrine
copying peregrine/build_falcon4py.py -> build/lib.linux-x86_64-3.7/peregrine
copying peregrine/build_shimmer4py.py -> build/lib.linux-x86_64-3.7/peregrine
copying peregrine/utils.py -> build/lib.linux-x86_64-3.7/peregrine
UPDATING build/lib.linux-x86_64-3.7/peregrine/_version.py
set build/lib.linux-x86_64-3.7/peregrine/_version.py to '1.6.3+3.g008082a.dirty'
running build_ext
generating cffi module 'build/temp.linux-x86_64-3.7/peregrine._falcon4py.c'
creating build/temp.linux-x86_64-3.7
generating cffi module 'build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c'
building 'peregrine._shimmer4py' extension
creating build/temp.linux-x86_64-3.7/build
creating build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/home
creating build/temp.linux-x86_64-3.7/home/kplee
creating build/temp.linux-x86_64-3.7/home/kplee/program
creating build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine
creating build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c -o build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7/peregrine._shimmer4py.o
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c: In function ‘_cffi_d_build_shimmer_map4py’:
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c:777:3: warning: implicit declaration of function ‘build_shimmer_map4py’; did you mean ‘_cffi_d_build_shimmer_map4py’? [-Wimplicit-function-declaration]
   build_shimmer_map4py(x0, x1, x2, x3, x4, x5, x6);
   ^~~~~~~~~~~~~~~~~~~~
   _cffi_d_build_shimmer_map4py
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c: In function ‘_cffi_d_get_mmer_count’:
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c:1034:10: warning: implicit declaration of function ‘get_mmer_count’; did you mean ‘read_mm_count’? [-Wimplicit-function-declaration]
   return get_mmer_count(x0, x1);
          ^~~~~~~~~~~~~~
          read_mm_count
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c: In function ‘_cffi_d_get_shimmer_hits’:
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c:1082:3: warning: implicit declaration of function ‘get_shimmer_hits’; did you mean ‘_cffi_d_get_shimmer_hits’? [-Wimplicit-function-declaration]
   get_shimmer_hits(x0, x1, x2, x3);
   ^~~~~~~~~~~~~~~~
   _cffi_d_get_shimmer_hits
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c: In function ‘_cffi_d_get_shimmers_for_read’:
build/temp.linux-x86_64-3.7/peregrine._shimmer4py.c:1145:3: warning: implicit declaration of function ‘get_shimmers_for_read’; did you mean ‘_cffi_d_get_shimmers_for_read’? [-Wimplicit-function-declaration]
   get_shimmers_for_read(x0, x1, x2);
   ^~~~~~~~~~~~~~~~~~~~~
   _cffi_d_get_shimmers_for_read
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/src/shimmer4py.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shimmer4py.o
/home/kplee/program/Peregrine/src/shimmer4py.c: In function ‘build_shimmer_map4py’:
/home/kplee/program/Peregrine/src/shimmer4py.c:78:7: warning: variable ‘written’ set but not used [-Wunused-but-set-variable]
   int written;
       ^~~~~~~
/home/kplee/program/Peregrine/src/shimmer4py.c:75:5: warning: argument 1 null where non-null expected [-Wnonnull]
     snprintf(shimmer_prefix, 8191, "shimmer-L2");
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/kplee/program/Peregrine/src/shimmer4py.c:75:5: note: in a call to built-in function ‘__builtin_memcpy’
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/src/DWmatch.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/DWmatch.o
/home/kplee/program/Peregrine/src/DWmatch.c: In function ‘ovlp_match’:
/home/kplee/program/Peregrine/src/DWmatch.c:148:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if ((x - x1 > longest_match)) {
                   ^
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/src/shmr_align.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shmr_align.o
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/src/shmr_utils.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shmr_utils.o
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/src/shmr_reduce.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shmr_reduce.o
/home/kplee/program/Peregrine/src/shmr_reduce.c: In function ‘mm_reduce’:
/home/kplee/program/Peregrine/src/shmr_reduce.c:79:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (r_offset < rs - 1) {
                  ^
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/src/mm_sketch.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/mm_sketch.o
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/src/kalloc.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/kalloc.o
gcc -pthread -shared -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -L/home/kplee/miniconda3/envs/peregrine/lib -Wl,-rpath=/home/kplee/miniconda3/envs/peregrine/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7/peregrine._shimmer4py.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shimmer4py.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/DWmatch.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shmr_align.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shmr_utils.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/shmr_reduce.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/mm_sketch.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/src/kalloc.o -o build/lib.linux-x86_64-3.7/peregrine/_shimmer4py.abi3.so
building 'peregrine._falcon4py' extension
creating build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/falcon
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c build/temp.linux-x86_64-3.7/peregrine._falcon4py.c -o build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7/peregrine._falcon4py.o
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/falcon/falcon.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/falcon/falcon.o
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/falcon/DW_banded.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/falcon/DW_banded.o
gcc -pthread -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/kplee/miniconda3/envs/peregrine/include/python3.7m -c /home/kplee/program/Peregrine/falcon/kalloc.c -o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/falcon/kalloc.o
gcc -pthread -shared -B /home/kplee/miniconda3/envs/peregrine/compiler_compat -L/home/kplee/miniconda3/envs/peregrine/lib -Wl,-rpath=/home/kplee/miniconda3/envs/peregrine/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/build/temp.linux-x86_64-3.7/peregrine._falcon4py.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/falcon/falcon.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/falcon/DW_banded.o build/temp.linux-x86_64-3.7/home/kplee/program/Peregrine/falcon/kalloc.o -o build/lib.linux-x86_64-3.7/peregrine/_falcon4py.abi3.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/peregrine
copying build/lib.linux-x86_64-3.7/peregrine/__init__.py -> build/bdist.linux-x86_64/egg/peregrine
copying build/lib.linux-x86_64-3.7/peregrine/build_falcon4py.py -> build/bdist.linux-x86_64/egg/peregrine
copying build/lib.linux-x86_64-3.7/peregrine/build_shimmer4py.py -> build/bdist.linux-x86_64/egg/peregrine
copying build/lib.linux-x86_64-3.7/peregrine/utils.py -> build/bdist.linux-x86_64/egg/peregrine
copying build/lib.linux-x86_64-3.7/peregrine/_version.py -> build/bdist.linux-x86_64/egg/peregrine
copying build/lib.linux-x86_64-3.7/peregrine/_shimmer4py.abi3.so -> build/bdist.linux-x86_64/egg/peregrine
copying build/lib.linux-x86_64-3.7/peregrine/_falcon4py.abi3.so -> build/bdist.linux-x86_64/egg/peregrine
byte-compiling build/bdist.linux-x86_64/egg/peregrine/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/peregrine/build_falcon4py.py to build_falcon4py.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/peregrine/build_shimmer4py.py to build_shimmer4py.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/peregrine/utils.py to utils.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/peregrine/_version.py to _version.cpython-37.pyc
creating stub loader for peregrine/_shimmer4py.abi3.so
creating stub loader for peregrine/_falcon4py.abi3.so
byte-compiling build/bdist.linux-x86_64/egg/peregrine/_shimmer4py.py to _shimmer4py.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/peregrine/_falcon4py.py to _falcon4py.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.7
copying and adjusting scripts/path_to_contig.py -> build/scripts-3.7
copying and adjusting scripts/pg_asm_cns.py -> build/scripts-3.7
copying scripts/pg_run.py -> build/scripts-3.7
copying scripts/pg_run_dev.py -> build/scripts-3.7
changing mode of build/scripts-3.7/path_to_contig.py from 664 to 775
changing mode of build/scripts-3.7/pg_asm_cns.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/path_to_contig.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/pg_asm_cns.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/pg_run.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/pg_run_dev.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/path_to_contig.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pg_asm_cns.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pg_run.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pg_run_dev.py to 775
copying peregrine.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
peregrine.__pycache__._falcon4py.cpython-37: module references __file__
peregrine.__pycache__._shimmer4py.cpython-37: module references __file__
creating dist
creating 'dist/peregrine-1.6.3+3.g008082a.dirty-py3.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing peregrine-1.6.3+3.g008082a.dirty-py3.7-linux-x86_64.egg
creating /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/peregrine-1.6.3+3.g008082a.dirty-py3.7-linux-x86_64.egg
Extracting peregrine-1.6.3+3.g008082a.dirty-py3.7-linux-x86_64.egg to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding peregrine 1.6.3+3.g008082a.dirty to easy-install.pth file
Installing path_to_contig.py script to /home/kplee/miniconda3/envs/peregrine/bin
Installing pg_asm_cns.py script to /home/kplee/miniconda3/envs/peregrine/bin
Installing pg_run.py script to /home/kplee/miniconda3/envs/peregrine/bin
Installing pg_run_dev.py script to /home/kplee/miniconda3/envs/peregrine/bin

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/peregrine-1.6.3+3.g008082a.dirty-py3.7-linux-x86_64.egg
Processing dependencies for peregrine==1.6.3+3.g008082a.dirty
Searching for numpy>=1.16.2
Reading https://pypi.org/simple/numpy/
Downloading https://files.pythonhosted.org/packages/73/0d/20355061d7c382c973d9c62803c6f1bdb2e2eb9e5f3623dff2f94c0e253c/numpy-1.20.0-cp37-cp37m-manylinux1_x86_64.whl#sha256=e9c5fd330d2fedf06051bafb996252de9b032fcb2ec03eefc9a543e56efa66d4
Best match: numpy 1.20.0
Processing numpy-1.20.0-cp37-cp37m-manylinux1_x86_64.whl
Installing numpy-1.20.0-cp37-cp37m-manylinux1_x86_64.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding numpy 1.20.0 to easy-install.pth file
Installing f2py script to /home/kplee/miniconda3/envs/peregrine/bin
Installing f2py3 script to /home/kplee/miniconda3/envs/peregrine/bin
Installing f2py3.7 script to /home/kplee/miniconda3/envs/peregrine/bin

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/numpy-1.20.0-py3.7-linux-x86_64.egg
Searching for docopt>=0.6.2
Reading https://pypi.org/simple/docopt/
Downloading https://files.pythonhosted.org/packages/a2/55/8f8cab2afd404cf578136ef2cc5dfb50baa1761b68c9da1fb1e4eed343c9/docopt-0.6.2.tar.gz#sha256=49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491
Best match: docopt 0.6.2
Processing docopt-0.6.2.tar.gz
Writing /tmp/easy_install-198dp41z/docopt-0.6.2/setup.cfg
Running docopt-0.6.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-198dp41z/docopt-0.6.2/egg-dist-tmp-i8hg2bo2
zip_safe flag not set; analyzing archive contents...
Moving docopt-0.6.2-py3.7.egg to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding docopt 0.6.2 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/docopt-0.6.2-py3.7.egg
Searching for cffi==1.14.4
Best match: cffi 1.14.4
Processing cffi-1.14.4-py3.7-linux-x86_64.egg
Adding cffi 1.14.4 to easy-install.pth file

Using /home/kplee/program/Peregrine/py/.eggs/cffi-1.14.4-py3.7-linux-x86_64.egg
Searching for pycparser==2.20
Best match: pycparser 2.20
Processing pycparser-2.20-py3.7.egg
Adding pycparser 2.20 to easy-install.pth file

Using /home/kplee/program/Peregrine/py/.eggs/pycparser-2.20-py3.7.egg
Finished processing dependencies for peregrine==1.6.3+3.g008082a.dirty
running clean
removing 'build/temp.linux-x86_64-3.7' (and everything under it)
removing 'build/lib.linux-x86_64-3.7' (and everything under it)
removing 'build/bdist.linux-x86_64' (and everything under it)
removing 'build/scripts-3.7' (and everything under it)
removing 'build'
~/program/Peregrine
fatal: destination path 'pypeFLOW' already exists and is not an empty directory.
~/program/Peregrine/pypeFLOW ~/program/Peregrine
/home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/setuptools/dist.py:458: UserWarning: Normalizing '2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476
' to '2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476'
  warnings.warn(tmpl.format(**locals()))
running install
running bdist_egg
running egg_info
writing pypeflow.egg-info/PKG-INFO
writing dependency_links to pypeflow.egg-info/dependency_links.txt
writing entry points to pypeflow.egg-info/entry_points.txt
writing requirements to pypeflow.egg-info/requires.txt
writing top-level names to pypeflow.egg-info/top_level.txt
reading manifest file 'pypeflow.egg-info/SOURCES.txt'
writing manifest file 'pypeflow.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/pwatcher
copying build/lib/pwatcher/__init__.py -> build/bdist.linux-x86_64/egg/pwatcher
copying build/lib/pwatcher/blocking.py -> build/bdist.linux-x86_64/egg/pwatcher
copying build/lib/pwatcher/fs_based.py -> build/bdist.linux-x86_64/egg/pwatcher
copying build/lib/pwatcher/network_based.py -> build/bdist.linux-x86_64/egg/pwatcher
creating build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/__init__.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/fs_heartbeat.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/network_heartbeat.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/pwatcher.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/pypeflow_example.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/query_server.py -> build/bdist.linux-x86_64/egg/pwatcher/mains
copying build/lib/pwatcher/mains/job_start.sh -> build/bdist.linux-x86_64/egg/pwatcher/mains
creating build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/__init__.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/do_support.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/do_task.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/io.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/pwatcher_workflow.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/sample_tasks.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/simple_pwatcher_bridge.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/tasks.py -> build/bdist.linux-x86_64/egg/pypeflow
copying build/lib/pypeflow/util.py -> build/bdist.linux-x86_64/egg/pypeflow
creating build/bdist.linux-x86_64/egg/pypeflow/mains
copying build/lib/pypeflow/mains/__init__.py -> build/bdist.linux-x86_64/egg/pypeflow/mains
creating build/bdist.linux-x86_64/egg/src
copying build/lib/src/__init__.py -> build/bdist.linux-x86_64/egg/src
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/blocking.py to blocking.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/fs_based.py to fs_based.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/network_based.py to network_based.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/fs_heartbeat.py to fs_heartbeat.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/network_heartbeat.py to network_heartbeat.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/pwatcher.py to pwatcher.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/pypeflow_example.py to pypeflow_example.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/query_server.py to query_server.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/do_support.py to do_support.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/do_task.py to do_task.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/io.py to io.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/pwatcher_workflow.py to pwatcher_workflow.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/sample_tasks.py to sample_tasks.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/simple_pwatcher_bridge.py to simple_pwatcher_bridge.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/tasks.py to tasks.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/util.py to util.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/pypeflow/mains/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.linux-x86_64/egg/src/__init__.py to __init__.cpython-37.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pypeflow.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg
creating /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg
Extracting pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding pypeflow 2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476 to easy-install.pth file
Installing heartbeat-wrapper script to /home/kplee/miniconda3/envs/peregrine/bin
Installing pwatcher-main script to /home/kplee/miniconda3/envs/peregrine/bin
Installing pwatcher-pypeflow-example script to /home/kplee/miniconda3/envs/peregrine/bin

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg
Processing dependencies for pypeflow==2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476
Searching for networkx>=1.9.1
Reading https://pypi.org/simple/networkx/
Downloading https://files.pythonhosted.org/packages/9b/cd/dc52755d30ba41c60243235460961fc28022e5b6731f16c268667625baea/networkx-2.5-py3-none-any.whl#sha256=8c5812e9f798d37c50570d15c4a69d5710a18d77bafc903ee9c5fba7454c616c
Best match: networkx 2.5
Processing networkx-2.5-py3-none-any.whl
Installing networkx-2.5-py3-none-any.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding networkx 2.5 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/networkx-2.5-py3.7.egg
Searching for decorator>=4.3.0
Reading https://pypi.org/simple/decorator/
Downloading https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl#sha256=41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760
Best match: decorator 4.4.2
Processing decorator-4.4.2-py2.py3-none-any.whl
Installing decorator-4.4.2-py2.py3-none-any.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages
Adding decorator 4.4.2 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.7/site-packages/decorator-4.4.2-py3.7.egg
Finished processing dependencies for pypeflow==2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476
~/program/Peregrine
~/program/Peregrine/py ~/program/Peregrine
Collecting pip
  Using cached pip-21.0.1-py3-none-any.whl (1.5 MB)
Collecting setuptools
  Using cached setuptools-53.0.0-py3-none-any.whl (784 kB)
Collecting wheel
  Using cached wheel-0.36.2-py2.py3-none-any.whl (35 kB)
Installing collected packages: wheel, setuptools, pip
Successfully installed pip-21.0.1 setuptools-53.0.0 wheel-0.36.2
running install
running bdist_egg
running egg_info
creating peregrine_pypy.egg-info
writing peregrine_pypy.egg-info/PKG-INFO
writing dependency_links to peregrine_pypy.egg-info/dependency_links.txt
writing requirements to peregrine_pypy.egg-info/requires.txt
writing top-level names to peregrine_pypy.egg-info/top_level.txt
writing manifest file 'peregrine_pypy.egg-info/SOURCES.txt'
reading manifest file 'peregrine_pypy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'peregrine_pypy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
warning: install_lib: 'build/lib' does not exist -- no Python modules to install

creating build
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.6
copying scripts/ovlp_to_graph.py -> build/scripts-3.6
copying scripts/graph_to_path.py -> build/scripts-3.6
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/ovlp_to_graph.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/graph_to_path.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/ovlp_to_graph.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/graph_to_path.py to 775
copying peregrine_pypy.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine_pypy.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine_pypy.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine_pypy.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying peregrine_pypy.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/peregrine_pypy-0.1-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing peregrine_pypy-0.1-py3.6.egg
Copying peregrine_pypy-0.1-py3.6.egg to /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages
Adding peregrine-pypy 0.1 to easy-install.pth file
Installing graph_to_path.py script to /home/kplee/miniconda3/envs/peregrine/bin
Installing ovlp_to_graph.py script to /home/kplee/miniconda3/envs/peregrine/bin

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages/peregrine_pypy-0.1-py3.6.egg
Processing dependencies for peregrine-pypy==0.1
Searching for networkx==2.4
Reading https://pypi.org/simple/networkx/
Downloading https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl#sha256=cdfbf698749a5014bf2ed9db4a07a5295df1d3a53bf80bf3cbd61edf9df05fa1
Best match: networkx 2.4
Processing networkx-2.4-py3-none-any.whl
Installing networkx-2.4-py3-none-any.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages
Adding networkx 2.4 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages/networkx-2.4-py3.6.egg
Searching for decorator>=4.3.0
Reading https://pypi.org/simple/decorator/
Downloading https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl#sha256=41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760
Best match: decorator 4.4.2
Processing decorator-4.4.2-py2.py3-none-any.whl
Installing decorator-4.4.2-py2.py3-none-any.whl to /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages
Adding decorator 4.4.2 to easy-install.pth file

Installed /home/kplee/miniconda3/envs/peregrine/lib/python3.6/site-packages/decorator-4.4.2-py3.6.egg
Finished processing dependencies for peregrine-pypy==0.1
~/program/Peregrine
~/program/Peregrine/src ~/program/Peregrine
make: Nothing to be done for `all'.
cp shmr_mkseqdb shmr_index shmr_gather_mc shmr_overlap shmr_dedup shmr_map /home/kplee/miniconda3/envs/peregrine/bin
~/program/Peregrine

Activate the peregrine environment


source activate peregrine

See the help


$ pg_run.py -h

Got this:


Peregrine Assembler & SHIMMER ASMKit(1.6.3+3.g008082a.dirty)
pypeflow 2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476

Peregrine
=========

Peregrine is a fast genome assembler for accurate long
reads (length > 10kb, accuraccy > 99%). It can assemble
a human genome from 30x reads within 20 cpu hours from
reads to polished consensus. It uses Sparse HIereachical
MimiMizER (SHIMMER) for fast read-to-read overlaps without
explicitly quadratic comparisions used in other OLC
assemblers.

Peregrine Assembler and SHIMMER Genome Assembly Toolkit
Copyright (c) 2019- by Jason, Chen-Shan, Chin

Peregrine Assembler and  SHIMMER Genome Assembly Toolkit
is licensed under a Creative Commons
Attribution-NonCommercial-ShareAlike 4.0 International
License.

You should have received a copy of the license along with
this work. If not, see
<http://creativecommons.org/licenses/by-nc-sa/4.0/>.

************************************************************
If you want to use it for any commericial purposes
(including promotion activity for a commerical product),
please contact Jason Chin for a commericial license.
************************************************************

run `pg_run.py -h` for help and other license information

using pypeflow 2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476

This is a pre-release, please do not re-distribute without permission.

I agree that I am not using this software for any commericial purposes (yes/no): yes
Peregrine
===============================================================
Peregrine is a fast genome assembler for accurate long
reads (length > 10kb, accuraccy > 99%). It can assemble
a human genome from 30x reads within 20 cpu hours from
reads to polished consensus. It uses Sparse HIereachical
MimiMizER (SHIMMER) for fast read-to-read overlaps without
explicitly quadratic comparisions used in other OLC
assemblers.

Currently, the assembly graph process is more or less
identical to the approaches used in the FALCON assembler
developed by Jason Chin and others in Pacific Biosciences, Inc.

Usage:
  pg_run.py asm <reads.lst> <index_nchunk> <index_nproc>
                            <ovlp_nchunk> <ovlp_nproc>
                            <mapping_nchunk> <mapping_nproc>
                            <cns_nchunk> <cns_nproc>
                            <sort_nproc>
                            [--with-consensus]
                            [--with-alt]
                            [--with-L0-index]
                            [--output <output>]
                            [--shimmer-k <shimmer_k>]
                            [--shimmer-w <shimmer_w>]
                            [--shimmer-r <shimmer_r>]
                            [--shimmer-l <shimmer_l>]
                            [--best_n_ovlp <n_ovlp>]
                            [--mc_lower <mc_lower>]
                            [--mc_upper <mc_upper>]
                            [--aln_bw <aln_bw>]
                            [--ovlp_upper <ovlp_upper>]
                            [--min_len <min_len>]
                            [--min_idt <min_idt>]
  pg_run.py (-h | --help)
  pg_run.py --verison

Options:
  -h --help                   Show this help
  --version                   Show version
  --with-consensus            Generate consensus after getting the draft contigs
  --with-alt                  Generate alt contigs
  --with-L0-index             Keep level-0 index
  --output <output>           Set output directory (will be created if not exist) [default: ./wd]
  --shimmer-k <shimmer_k>     Level 0 k-mer size [default: 16]
  --shimmer-w <shimmer_w>     Level 0 window size [default: 80]
  --shimmer-r <shimmer_r>     Reduction factore for high level SHIMMER [default: 6]
  --shimmer-l <shimmer_l>     number of level of shimmer used, the value should be 1 or 2 [default: 2]
  --best_n_ovlp <n_ovlp>      Find best n_ovlp overlap [default: 4]
  --mc_lower <mc_lower>       Does not cosider SHIMMER with count less than mc_low [default: 2]
  --mc_upper <mc_upper>       Does not cosider SHIMMER with count greater than mc_upper [default: 240]
  --aln_bw <aln_bw>           Max off-diagonal gap allow during overlap confirmation [default: 100]
  --ovlp_upper <ovlp_upper>   Ignore cluster with overlap count greater ovlp_upper [default: 120]
  --min_len <min_len>         Minimum overlap length for assembly graph construction [default: 4000]
  --min_idt <min_idt>         Minimum identity for considering two reads that are properly overlaps [default: 96]

Licenses:

Peregrine Assembler and SHIMMER Genome Assembly Toolkit
Copyright (c) 2019- by Jason, Chen-Shan, Chin

Peregrine Assembler and  SHIMMER Genome Assembly Toolkit
is licensed under a Creative Commons
Attribution-NonCommercial-ShareAlike 4.0 International
License.

You should have received a copy of the license along with
this work. If not, see
<http://creativecommons.org/licenses/by-nc-sa/4.0/>.

************************************************************
If you want to use it for any commericial purposes
(including promotion activity for a commerical product),
please contact Jason Chin for a commericial license.
************************************************************

This software uses the following libraray from Heng Li's
Minimap2 codebase under MIT License:

mm_sketch.c kvec.h kseq.h khash.h kalloc.h kalloc.c

The MIT License

Copyright (c) 2018-     Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

License for code from FALCON

#################################################################################$$
# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted (subject to the limitations in the
# disclaimer below) provided that the following conditions are met:
#
#  * Redistributions of source code must retain the above copyright
#  notice, this list of conditions and the following disclaimer.
#
#  * Redistributions in binary form must reproduce the above
#  copyright notice, this list of conditions and the following
#  disclaimer in the documentation and/or other materials provided
#  with the distribution.
#
#  * Neither the name of Pacific Biosciences nor the names of its
#  contributors may be used to endorse or promote products derived
#  from this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
# GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
# BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
# USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
# OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
# SUCH DAMAGE.
#################################################################################

Thanks indeed.

Yedomon

Yedomon commented 3 years ago

Hello Dear Jason.

I run the peregrine assembly using the following command:


$ find ~/datafile/001.i.bat./03.pacbio.hifi.reads/ -name "*.fastq" | sort > ibat-seqdata.lst 

$ conda activate peregrine

$ pg_run.py asm ~/analysis/02_assembly_by_peregrine_using_pacbio_hifi_reads/ibat-seqdata.lst --output ~/analysis/02_assembly_by_peregrine_using_pacbio_hifi_reads

I got this message:


Peregrine Assembler & SHIMMER ASMKit(1.6.3+3.g008082a.dirty)
pypeflow 2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476

Peregrine
=========

Peregrine is a fast genome assembler for accurate long
reads (length > 10kb, accuraccy > 99%). It can assemble
a human genome from 30x reads within 20 cpu hours from
reads to polished consensus. It uses Sparse HIereachical
MimiMizER (SHIMMER) for fast read-to-read overlaps without
explicitly quadratic comparisions used in other OLC
assemblers.

Peregrine Assembler and SHIMMER Genome Assembly Toolkit
Copyright (c) 2019- by Jason, Chen-Shan, Chin

Peregrine Assembler and  SHIMMER Genome Assembly Toolkit
is licensed under a Creative Commons
Attribution-NonCommercial-ShareAlike 4.0 International
License.

You should have received a copy of the license along with
this work. If not, see
<http://creativecommons.org/licenses/by-nc-sa/4.0/>.

************************************************************
If you want to use it for any commericial purposes
(including promotion activity for a commerical product),
please contact Jason Chin for a commericial license.
************************************************************

run `pg_run.py -h` for help and other license information

using pypeflow 2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476

This is a pre-release, please do not re-distribute without permission.

I agree that I am not using this software for any commericial purposes (yes/no):

I typed yes. The assembly process did not start. Do I need a license? Please let me know how can I deal with this situation.

Yedomon

bgruening commented 3 years ago

Does anyone want to provide a Bioconda package for Peregrine and solve this problem once and for all? :)

cschin commented 3 years ago

at this moment, we don't have bandwidth to work on providing a bioconda package. For non-commercial use, you may change the source code to bypass the agreement.

@Yedomon I think you might need to check your input files to make sure all the data file paths are correct.