Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
16 stars 7 forks source link

nosetests failed #34

Open blancaverag opened 8 years ago

blancaverag commented 8 years ago

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self._dlltype(name) File "/usr/lib64/python2.6/ctypes/init.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self._dlltype(name) File "/usr/lib64/python2.6/ctypes/init.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz <type 'exceptions.AttributeError'> Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute 'exit' E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna > /home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam 2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self._dlltype(name) File "/usr/lib64/python2.6/ctypes/init.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

timbalam commented 8 years ago

Hi blancaverag,

Can you check the library libbamM.a exists at the location /usr/lib/python2.6/site-packages/bamm/libBamM.a?

Cheers, Tim

On 11/02/2016 10:36 PM, blancaverag wrote:

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self./handle = /dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute '__exit//' E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna > /home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam 2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34.

blancaverag commented 8 years ago

Hi Tim,

It does not exist.

Blanca El 12/02/2016 01:27, "timbalam" notifications@github.com escribió:

Hi blancaverag,

Can you check the library libbamM.a exists at the location /usr/lib/python2.6/site-packages/bamm/libBamM.a?

Cheers, Tim

On 11/02/2016 10:36 PM, blancaverag wrote:

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory

E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self./handle = /dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute '__exit//'

E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna >

/home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam 2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183124068.

timbalam commented 8 years ago

Thanks Blanca,

There are possibly issues with using the --with-... flags. I will try to work it out next week.

In the mean time, if you like you can try building without using the external htslib and libcfu libraries.

Cheers, Tim

On 12/02/2016 4:18 PM, blancaverag wrote:

Hi Tim,

It does not exist.

Blanca El 12/02/2016 01:27, "timbalam" notifications@github.com escribió:

Hi blancaverag,

Can you check the library libbamM.a exists at the location /usr/lib/python2.6/site-packages/bamm/libBamM.a?

Cheers, Tim

On 11/02/2016 10:36 PM, blancaverag wrote:

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory

E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self./handle = /dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute '__exit//'

E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna >

/home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam

2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183124068.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183195920.

blancaverag commented 8 years ago

Hi Tim,

I run the installation without the --with.. flags. This is the error now:

Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... ERROR: aclocal failed checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include... found checking for libhts libraries in /usr/local/lib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/lib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/lib -lhts Building BamM library /usr/local/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/bamMaker.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/version.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFilter.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFile.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/init.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamParser.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamExtractor.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/libBamM.a -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamLink.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamRead.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bammExceptions.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/cWrapper.py -> /usr/local/lib/python2.7/site-packages/bamm byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamMaker.py to bamMaker.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/version.py to version.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFilter.py to bamFilter.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFile.py to bamFile.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/init.py to init.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamParser.py to bamParser.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamExtractor.py to bamExtractor.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamLink.py to bamLink.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamRead.py to bamRead.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bammExceptions.py to bammExceptions.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/cWrapper.py to cWrapper.pyc running install_scripts changing mode of /usr/local/bin/bamFlags to 755 changing mode of /usr/local/bin/bamm to 755 running install_egg_info Removing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info Writing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info

2016-02-12 9:14 GMT+01:00 timbalam notifications@github.com:

Thanks Blanca,

There are possibly issues with using the --with-... flags. I will try to work it out next week.

In the mean time, if you like you can try building without using the external htslib and libcfu libraries.

Cheers, Tim

On 12/02/2016 4:18 PM, blancaverag wrote:

Hi Tim,

It does not exist.

Blanca El 12/02/2016 01:27, "timbalam" notifications@github.com escribió:

Hi blancaverag,

Can you check the library libbamM.a exists at the location /usr/lib/python2.6/site-packages/bamm/libBamM.a?

Cheers, Tim

On 11/02/2016 10:36 PM, blancaverag wrote:

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory

E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self./handle = /dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute '__exit//'

E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna >

/home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam

2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183124068.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183195920.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183224319.

timbalam commented 8 years ago

Hi Blanca,

I will try look into this soon. Have you tried running the nosetests with this installation? Is the libBamM.a file missing again?

Cheers, Tim

On 2/03/2016 2:39 AM, blancaverag wrote:

Hi Tim,

I run the installation without the --with.. flags. This is the error now:

Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... ERROR: aclocal failed checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include... found checking for libhts libraries in /usr/local/lib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/lib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/lib -lhts Building BamM library /usr/local/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/bamMaker.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/version.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFilter.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFile.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/init.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamParser.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamExtractor.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/libBamM.a -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamLink.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamRead.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bammExceptions.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/cWrapper.py -> /usr/local/lib/python2.7/site-packages/bamm byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamMaker.py to bamMaker.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/version.py to version.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFilter.py to bamFilter.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFile.py to bamFile.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/init.py to init.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamParser.py to bamParser.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamExtractor.py to bamExtractor.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamLink.py to bamLink.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamRead.py to bamRead.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bammExceptions.py to bammExceptions.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/cWrapper.py to cWrapper.pyc running install_scripts changing mode of /usr/local/bin/bamFlags to 755 changing mode of /usr/local/bin/bamm to 755 running install_egg_info Removing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info Writing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info

2016-02-12 9:14 GMT+01:00 timbalam notifications@github.com:

Thanks Blanca,

There are possibly issues with using the --with-... flags. I will try to work it out next week.

In the mean time, if you like you can try building without using the external htslib and libcfu libraries.

Cheers, Tim

On 12/02/2016 4:18 PM, blancaverag wrote:

Hi Tim,

It does not exist.

Blanca El 12/02/2016 01:27, "timbalam" notifications@github.com escribió:

Hi blancaverag,

Can you check the library libbamM.a exists at the location /usr/lib/python2.6/site-packages/bamm/libBamM.a?

Cheers, Tim

On 11/02/2016 10:36 PM, blancaverag wrote:

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory

E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self./handle = /dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute '__exit//'

E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna >

/home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam

2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183124068.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183195920.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183224319.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-190801990.

blancaverag commented 8 years ago

Yes, I have tried and this is the result:

..Traceback (most recent call last): File "/usr/local/bin/bamm", line 4, in import('pkg_resources').run_script('BamM==1.7.0', 'bamm') File "/usr/local/lib/python2.7/site-packages/pkg_resources/init.py", line 726, in run_script self.require(requires)[0].run_script(script_name, ns)

File "/usr/local/lib/python2.7/site-packages/pkg_resources/init.py", line 1491, in run_script exec(script_code, namespace, namespace)

File "/usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/EGG-INFO/scripts/bamm", line 660, in

File "/usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/EGG-INFO/scripts/bamm", line 155, in doWork

File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 297, in makeBams File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 628, in makeBam File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 856, in mem_to_sorted_indexed_bam File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 677, in _sam_to_sorted_and_run File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 684, in _run_cmd File "/usr/local/lib/python2.7/subprocess.py", line 540, in check_call

raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'bwa mem -t 1 /home/programas/BamM/bamm/tests/modeling/contigs.fa 2> /dev/null /home/programas/BamM/bamm/tests/modeling/pe.1.fa /home/programas/BamM/bamm/tests/modeling/pe.2.fa | samtools view -SubhF 4 - 2> /dev/null | samtools sort -m 2G -@ 1 -o /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam 2> /dev/null' returned non-zero exit status 1

E****

ERROR:

BAM file /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam not found


For further usage details:

bamm parse -h

E[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam" for reading.

[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.mp.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.mp.bam" for reading.

[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.up.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.up.bam" for reading.

FNo file: /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/contigs.mp.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.mp.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/contigs.up.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.up.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/covs

No file: /home/programas/BamM/bamm/tests/modeling/links

....****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details.

If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/bamm/libBamM.a


E

ERROR: test_bamParser.TestBamParser.test_A_make

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg)

File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 137, in test_A_make subprocess.check_call(cmd, shell=True)

File "/usr/local/lib/python2.7/subprocess.py", line 540, in check_call

raise CalledProcessError(retcode, cmd)

CalledProcessError: Command 'bamm make --silent -d /home/programas/BamM/bamm/tests/modeling/contigs.fa -i /home/programas/BamM/bamm/tests/modeling/mp.fa -c /home/programas/BamM/bamm/tests/modeling/pe.1.fa /home/programas/BamM/bamm/tests/modeling/pe.2.fa -s /home/programas/BamM/bamm/tests/modeling/up.fa -o /home/programas/BamM/bamm/tests/modeling' returned non-zero exit status 1

ERROR: test_bamParser.TestBamParser.test_B_parse

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 172, in test_B_parse with open(covs_file) as c_fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/covs'

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 209, in run self.setUp() File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp self.setupContext(ancestor) File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext try_run(context, names) File "/usr/local/lib/python2.7/site-packages/nose/util.py", line 470, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/local/lib/python2.7/ctypes/init.py", line 443, in LoadLibrary return self._dlltype(name) File "/usr/local/lib/python2.7/ctypes/init.py", line 365, in init self._handle = _dlopen(self._name, mode) OSError: /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/bamm/libBamM.a: cannot open shared object file: Not a directory

FAIL: test_bamParser.TestBamParser.test_C_extract

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 246, in test_C_extract assert_true(os.path.exists(full_path)) AssertionError: False is not true


Ran 9 tests in 53.164s

FAILED (errors=3, failures=1)

2016-03-02 9:06 GMT+01:00 timbalam notifications@github.com:

Hi Blanca,

I will try look into this soon. Have you tried running the nosetests with this installation? Is the libBamM.a file missing again?

Cheers, Tim

On 2/03/2016 2:39 AM, blancaverag wrote:

Hi Tim,

I run the installation without the --with.. flags. This is the error now:

Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... ERROR: aclocal failed checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include... found checking for libhts libraries in /usr/local/lib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/lib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/lib -lhts Building BamM library /usr/local/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/bamMaker.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/version.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFilter.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFile.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/init.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamParser.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamExtractor.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/libBamM.a -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamLink.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamRead.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bammExceptions.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/cWrapper.py -> /usr/local/lib/python2.7/site-packages/bamm byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamMaker.py to bamMaker.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/version.py to version.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFilter.py to bamFilter.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFile.py to bamFile.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/init.py to init.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamParser.py to bamParser.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamExtractor.py to bamExtractor.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamLink.py to bamLink.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamRead.py to bamRead.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bammExceptions.py to bammExceptions.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/cWrapper.py to cWrapper.pyc running install_scripts changing mode of /usr/local/bin/bamFlags to 755 changing mode of /usr/local/bin/bamm to 755 running install_egg_info Removing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info Writing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info

2016-02-12 9:14 GMT+01:00 timbalam notifications@github.com:

Thanks Blanca,

There are possibly issues with using the --with-... flags. I will try to work it out next week.

In the mean time, if you like you can try building without using the external htslib and libcfu libraries.

Cheers, Tim

On 12/02/2016 4:18 PM, blancaverag wrote:

Hi Tim,

It does not exist.

Blanca El 12/02/2016 01:27, "timbalam" notifications@github.com escribió:

Hi blancaverag,

Can you check the library libbamM.a exists at the location /usr/lib/python2.6/site-packages/bamm/libBamM.a?

Cheers, Tim

On 11/02/2016 10:36 PM, blancaverag wrote:

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory

E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self./handle = /dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute '__exit//'

E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna >

/home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam

2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34.

— Reply to this email directly or view it on GitHub < https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183124068>.

— Reply to this email directly or view it on GitHub <https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183195920 .

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183224319.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-190801990.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-191119795.

timbalam commented 8 years ago

Thanks,

It does look like the bamm library build failed.

I think that some of the errors might be due to using an incompatible version of Samtools. Can you check which version of Samtools you are using? You'll need 1.*.

Hopefully I'll have a chance to look into the build failure, possibly next week.

Tim

On 2/03/2016 6:30 PM, blancaverag wrote:

Yes, I have tried and this is the result:

..Traceback (most recent call last): File "/usr/local/bin/bamm", line 4, in import('pkg_resources').run_script('BamM==1.7.0', 'bamm') File "/usr/local/lib/python2.7/site-packages/pkg_resources/init.py", line 726, in run_script self.require(requires)[0].run_script(script_name, ns)

File "/usr/local/lib/python2.7/site-packages/pkg_resources/init.py", line 1491, in run_script exec(script_code, namespace, namespace)

File "/usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/EGG-INFO/scripts/bamm", line 660, in

File "/usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/EGG-INFO/scripts/bamm", line 155, in doWork

File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 297, in makeBams File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 628, in makeBam File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 856, in mem_to_sorted_indexed_bam File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 677, in _sam_to_sorted_and_run File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 684, in _run_cmd File "/usr/local/lib/python2.7/subprocess.py", line 540, in check_call

raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'bwa mem -t 1 /home/programas/BamM/bamm/tests/modeling/contigs.fa 2> /dev/null /home/programas/BamM/bamm/tests/modeling/pe.1.fa /home/programas/BamM/bamm/tests/modeling/pe.2.fa | samtools view -SubhF 4 - 2> /dev/null | samtools sort -m 2G -@ 1 -o /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam 2> /dev/null' returned non-zero exit status 1

E****

ERROR:

BAM file /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam not found


For further usage details:

bamm parse -h

E[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam" for reading.

[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.mp.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.mp.bam" for reading.

[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.up.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.up.bam" for reading.

FNo file: /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/contigs.mp.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.mp.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/contigs.up.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.up.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/covs

No file: /home/programas/BamM/bamm/tests/modeling/links

....****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details.

If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/bamm/libBamM.a


E

ERROR: test_bamParser.TestBamParser.test_A_make

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg)

File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 137, in test_A_make subprocess.check_call(cmd, shell=True)

File "/usr/local/lib/python2.7/subprocess.py", line 540, in check_call

raise CalledProcessError(retcode, cmd)

CalledProcessError: Command 'bamm make --silent -d /home/programas/BamM/bamm/tests/modeling/contigs.fa -i /home/programas/BamM/bamm/tests/modeling/mp.fa -c /home/programas/BamM/bamm/tests/modeling/pe.1.fa /home/programas/BamM/bamm/tests/modeling/pe.2.fa -s /home/programas/BamM/bamm/tests/modeling/up.fa -o /home/programas/BamM/bamm/tests/modeling' returned non-zero exit status 1

ERROR: test_bamParser.TestBamParser.test_B_parse

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 172, in test_B_parse with open(covs_file) as c_fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/covs'

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 209, in run self.setUp() File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp self.setupContext(ancestor) File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext try_run(context, names) File "/usr/local/lib/python2.7/site-packages/nose/util.py", line 470, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/local/lib/python2.7/ctypes/init.py", line 443, in LoadLibrary return self._dlltype(name) File "/usr/local/lib/python2.7/ctypes/init.py", line 365, in init self._handle = _dlopen(self._name, mode) OSError: /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/bamm/libBamM.a: cannot open shared object file: Not a directory

FAIL: test_bamParser.TestBamParser.test_C_extract

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 246, in test_C_extract assert_true(os.path.exists(full_path)) AssertionError: False is not true


Ran 9 tests in 53.164s

FAILED (errors=3, failures=1)

2016-03-02 9:06 GMT+01:00 timbalam notifications@github.com:

Hi Blanca,

I will try look into this soon. Have you tried running the nosetests with this installation? Is the libBamM.a file missing again?

Cheers, Tim

On 2/03/2016 2:39 AM, blancaverag wrote:

Hi Tim,

I run the installation without the --with.. flags. This is the error now:

Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... ERROR: aclocal failed checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include... found checking for libhts libraries in /usr/local/lib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/lib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/lib -lhts Building BamM library /usr/local/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/bamMaker.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/version.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFilter.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFile.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/init.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamParser.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamExtractor.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/libBamM.a -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamLink.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamRead.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bammExceptions.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/cWrapper.py -> /usr/local/lib/python2.7/site-packages/bamm byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamMaker.py to bamMaker.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/version.py to version.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFilter.py to bamFilter.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFile.py to bamFile.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/init.py to init.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamParser.py to bamParser.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamExtractor.py to bamExtractor.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamLink.py to bamLink.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamRead.py to bamRead.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bammExceptions.py to bammExceptions.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/cWrapper.py to cWrapper.pyc running install_scripts changing mode of /usr/local/bin/bamFlags to 755 changing mode of /usr/local/bin/bamm to 755 running install_egg_info Removing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info Writing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info

2016-02-12 9:14 GMT+01:00 timbalam notifications@github.com:

Thanks Blanca,

There are possibly issues with using the --with-... flags. I will try to work it out next week.

In the mean time, if you like you can try building without using the external htslib and libcfu libraries.

Cheers, Tim

On 12/02/2016 4:18 PM, blancaverag wrote:

Hi Tim,

It does not exist.

Blanca El 12/02/2016 01:27, "timbalam" notifications@github.com escribió:

Hi blancaverag,

Can you check the library libbamM.a exists at the location /usr/lib/python2.6/site-packages/bamm/libBamM.a?

Cheers, Tim

On 11/02/2016 10:36 PM, blancaverag wrote:

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory

E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self./handle = /dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute '__exit//'

E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna >

/home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam

2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34.

— Reply to this email directly or view it on GitHub < https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183124068>.

— Reply to this email directly or view it on GitHub <https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183195920 .

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183224319.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-190801990.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-191119795.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-191126550.

blancaverag commented 8 years ago

I have samtools version 1.2.

Thanks!

Blanca

2016-03-03 1:38 GMT+01:00 timbalam notifications@github.com:

Thanks,

It does look like the bamm library build failed.

I think that some of the errors might be due to using an incompatible version of Samtools. Can you check which version of Samtools you are using? You'll need 1.*.

Hopefully I'll have a chance to look into the build failure, possibly next week.

Tim

On 2/03/2016 6:30 PM, blancaverag wrote:

Yes, I have tried and this is the result:

..Traceback (most recent call last): File "/usr/local/bin/bamm", line 4, in import('pkg_resources').run_script('BamM==1.7.0', 'bamm') File "/usr/local/lib/python2.7/site-packages/pkg_resources/init.py", line 726, in run_script self.require(requires)[0].run_script(script_name, ns)

File "/usr/local/lib/python2.7/site-packages/pkg_resources/init.py", line 1491, in run_script exec(script_code, namespace, namespace)

File

"/usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/EGG-INFO/scripts/bamm", line 660, in

File

"/usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/EGG-INFO/scripts/bamm", line 155, in doWork

File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 297, in makeBams File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 628, in makeBam File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 856, in mem_to_sorted_indexed_bam File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 677, in _sam_to_sorted_and_run File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 684, in _run_cmd File "/usr/local/lib/python2.7/subprocess.py", line 540, in check_call

raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'bwa mem -t 1 /home/programas/BamM/bamm/tests/modeling/contigs.fa 2> /dev/null /home/programas/BamM/bamm/tests/modeling/pe.1.fa /home/programas/BamM/bamm/tests/modeling/pe.2.fa | samtools view -SubhF 4 - 2> /dev/null | samtools sort -m 2G -@ 1 -o /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam 2> /dev/null' returned non-zero exit status 1

E****

ERROR:

BAM file /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam not found


For further usage details:

bamm parse -h

E[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam" for reading.

[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.mp.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.mp.bam" for reading.

[E::hts_open_format] fail to open file '/home/programas/BamM/bamm/tests/modeling/contigs.up.bam' ERROR: Failed to open "/home/programas/BamM/bamm/tests/modeling/contigs.up.bam" for reading.

FNo file: /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.pe.1.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/contigs.mp.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.mp.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/contigs.up.bam

No file: /home/programas/BamM/bamm/tests/modeling/contigs.up.bam.bai

No file: /home/programas/BamM/bamm/tests/modeling/covs

No file: /home/programas/BamM/bamm/tests/modeling/links

....****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details.

If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at:

/usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/bamm/libBamM.a


E

ERROR: test_bamParser.TestBamParser.test_A_make

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg)

File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 137, in test_A_make subprocess.check_call(cmd, shell=True)

File "/usr/local/lib/python2.7/subprocess.py", line 540, in check_call

raise CalledProcessError(retcode, cmd)

CalledProcessError: Command 'bamm make --silent -d /home/programas/BamM/bamm/tests/modeling/contigs.fa -i /home/programas/BamM/bamm/tests/modeling/mp.fa -c /home/programas/BamM/bamm/tests/modeling/pe.1.fa /home/programas/BamM/bamm/tests/modeling/pe.2.fa -s /home/programas/BamM/bamm/tests/modeling/up.fa -o /home/programas/BamM/bamm/tests/modeling' returned non-zero exit status 1

ERROR: test_bamParser.TestBamParser.test_B_parse

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 172, in test_B_parse with open(covs_file) as c_fh: IOError: [Errno 2] No such file or directory: '/home/programas/BamM/bamm/tests/modeling/covs'

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 209, in run self.setUp() File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp self.setupContext(ancestor) File "/usr/local/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext try_run(context, names) File "/usr/local/lib/python2.7/site-packages/nose/util.py", line 470, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/local/lib/python2.7/ctypes/init.py", line 443, in LoadLibrary return self._dlltype(name) File "/usr/local/lib/python2.7/ctypes/init.py", line 365, in init self._handle = _dlopen(self._name, mode) OSError:

/usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg/bamm/libBamM.a: cannot open shared object file: Not a directory

FAIL: test_bamParser.TestBamParser.test_C_extract

Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 246, in test_C_extract assert_true(os.path.exists(full_path)) AssertionError: False is not true


Ran 9 tests in 53.164s

FAILED (errors=3, failures=1)

2016-03-02 9:06 GMT+01:00 timbalam notifications@github.com:

Hi Blanca,

I will try look into this soon. Have you tried running the nosetests with this installation? Is the libBamM.a file missing again?

Cheers, Tim

On 2/03/2016 2:39 AM, blancaverag wrote:

Hi Tim,

I run the installation without the --with.. flags. This is the error now:

Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... ERROR: aclocal failed checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include... found checking for libhts libraries in /usr/local/lib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/lib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/lib -lhts Building BamM library /usr/local/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/bamMaker.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/version.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFilter.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamFile.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/init.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamParser.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamExtractor.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/libBamM.a -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamLink.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bamRead.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/bammExceptions.py -> /usr/local/lib/python2.7/site-packages/bamm copying build/lib/bamm/cWrapper.py -> /usr/local/lib/python2.7/site-packages/bamm byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamMaker.py to bamMaker.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/version.py to version.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFilter.py to bamFilter.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamFile.py to bamFile.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/init.py to init.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamParser.py to bamParser.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamExtractor.py to bamExtractor.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamLink.py to bamLink.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bamRead.py to bamRead.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/bammExceptions.py to bammExceptions.pyc byte-compiling /usr/local/lib/python2.7/site-packages/bamm/cWrapper.py to cWrapper.pyc running install_scripts changing mode of /usr/local/bin/bamFlags to 755 changing mode of /usr/local/bin/bamm to 755 running install_egg_info Removing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info Writing /usr/local/lib/python2.7/site-packages/BamM-1.7.0-py2.7.egg-info

2016-02-12 9:14 GMT+01:00 timbalam notifications@github.com:

Thanks Blanca,

There are possibly issues with using the --with-... flags. I will try to work it out next week.

In the mean time, if you like you can try building without using the external htslib and libcfu libraries.

Cheers, Tim

On 12/02/2016 4:18 PM, blancaverag wrote:

Hi Tim,

It does not exist.

Blanca El 12/02/2016 01:27, "timbalam" notifications@github.com escribió:

Hi blancaverag,

Can you check the library libbamM.a exists at the location /usr/lib/python2.6/site-packages/bamm/libBamM.a?

Cheers, Tim

On 11/02/2016 10:36 PM, blancaverag wrote:

Hi,

I have been trying to install BamM. I am giving it the paths for libraries I needed to install manually. I get this results in the installation process:

sudo python setup.py install --with-libhts-lib /usr/local/include/htslib/ --with-libhts-inc /usr/local/include/htslib/ Preparing the BamM build system...please wait

Found GNU Autoconf version 2.63 Found GNU Automake version 1.11.1 Found GNU Libtool version 2.2.6b

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... automake: no `Makefile.am' found for any configure output ERROR: automake failed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for lgamma,log,exp in -lm... yes checking for libcfu headers in /usr/local/include... found checking for libcfu libraries in /usr/local/lib... found checking for libhts headers in /usr/local/include/htslib... found checking for libhts libraries in /usr/local/include/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands === configuring in libcfu-0.03 (/home/programas/BamM/c/libcfu-0.03) configure: WARNING: no configuration information is in libcfu-0.03 === configuring in htslib-1.2.1 (/home/programas/BamM/c/htslib-1.2.1) configure: WARNING: no configuration information is in htslib-1.2.1 rm -f *.o rm -f libBamM.a gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamParser.o bamParser.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamRead.o bamRead.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o stats.o stats.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/include/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/include/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/usr/local/lib -lcfu -L/usr/local/include/htslib -lhts Building BamM library /usr/lib64/python2.6/distutils/dist.py:266: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py copying bamm/libBamM.a -> build/lib/bamm running build_scripts running install_lib copying build/lib/bamm/libBamM.a -> /usr/lib/python2.6/site-packages/bamm running install_scripts changing mode of /usr/bin/bamFlags to 755 changing mode of /usr/bin/bamm to 755 running install_egg_info Removing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info Writing /usr/lib/python2.6/site-packages/BamM-1.7.0-py2.6.egg-info

Although reconf and automake failed, it outputs no more errors, so I run nosetests with the following errors:


ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory

E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


Traceback (most recent call last): File "/usr/bin/bamm", line 660, in doWork(args) File "/usr/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/usr/lib/python2.6/site-packages/bamm/bamFilter.py", line 152, in filter CW = CWrapper() File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self./handle = /dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory ENo file: /home/programas/BamM/bamm/tests/filter_test_data/1_filtered.bam No file: /home/programas/BamM/bamm/tests/filter_test_data/2_filtered.bam Error opening file: /home/programas/BamM/bamm/tests/modeling/data/MG1655.fna.gz Traceback (most recent call last): File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 510, in doWork(args) File "/home/programas/BamM/bamm/tests/modeling/makeTestData.py", line 175, in doWork with all_open(args.fasta, "r") as fh: AttributeError: GzipFile instance has no attribute '__exit//'

E...E****

ERROR:

Problem importing the BamM c library. This typically means that BamM is not installed correctly. Please check the installation logs for more details. If you don't have the installation logs then please try to reinstall BamM and look at the output. Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a


E

ERROR: test_bamFilter.TestBamFilter.testFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 210, in testFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0 --percentage_id 0' returned non-zero exit status 1

ERROR: test_bamFilter.TestBamFilter.testInverseFilter

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 220, in testInverseFilter self.generate_bam(bamName, args) File "/home/programas/BamM/bamm/tests/test_bamFilter.py", line 120, in generate_bam subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bamm filter -b /home/programas/BamM/bamm/tests/filter_test_data/1.bam -o /home/programas/BamM/bamm/tests/filter_test_data --use_secondary --use_supplementary --percentage_aln 0.9 --percentage_id 0 -v' returned non-zero exit status 1

ERROR: test suite for test_bamParser.TestBamParser

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 73, in setup_class with open(os.path.join(self.model_dir, self.poFile), "r") as fh: IOError: [Errno 2] No such file or directory:

'/home/programas/BamM/bamm/tests/modeling/predicted_outputs.json'

ERROR: Test creation of TAM file with output prefix.

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/programas/BamM/bamm/tests/test_cli.py", line 144, in testOutputTam bs.makeBams() File "/home/programas/BamM/bamm/bamMaker.py", line 297, in makeBams BM.makeBam() File "/home/programas/BamM/bamm/bamMaker.py", line 597, in makeBam self.bwasw() File "/home/programas/BamM/bamm/bamMaker.py", line 894, in bwasw self._run_cmd(cmd) File "/home/programas/BamM/bamm/bamMaker.py", line 684, in _run_cmd subprocess.check_call(cmd, shell=True) File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/programas/BamM/bamm/tests/cli_test_data/test_database.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.1.fna /home/programas/BamM/bamm/tests/cli_test_data/test_reads.2.fna >

/home/programas/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam

2> /dev/null' returned non-zero exit status 127

ERROR: test suite for test_coverageStats.TestCoverageStats

Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/suite.py", line 154, in run self.setUp() File "/usr/lib/python2.6/site-packages/nose/suite.py", line 202, in setUp self.setupContext(ancestor) File "/usr/lib/python2.6/site-packages/nose/suite.py", line 225, in setupContext try_run(context, names) File "/usr/lib/python2.6/site-packages/nose/util.py", line 453, in try_run return func() File "/home/programas/BamM/bamm/tests/test_coverageStats.py", line 81, in setup_class self.CW = CWrapper(UT=True) File "/home/programas/BamM/bamm/cWrapper.py", line 464, in init self.libPMBam = c.cdll.LoadLibrary(c_lib) File "/usr/lib64/python2.6/ctypes/init.py", line 431, in LoadLibrary return self./dlltype(name) File "/usr/lib64/python2.6/ctypes/_init/.py", line 353, in init self._handle = _dlopen(self._name, mode) OSError: libhts.so.1: cannot open shared object file: No such file or directory


Ran 6 tests in 1.126s

FAILED (errors=5)

Would appreciate some help! Thanks!!!

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34.

— Reply to this email directly or view it on GitHub < https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183124068>.

— Reply to this email directly or view it on GitHub < https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183195920 .

— Reply to this email directly or view it on GitHub < https://github.com/Ecogenomics/BamM/issues/34#issuecomment-183224319>.

— Reply to this email directly or view it on GitHub <https://github.com/Ecogenomics/BamM/issues/34#issuecomment-190801990 .

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-191119795.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-191126550.

— Reply to this email directly or view it on GitHub https://github.com/Ecogenomics/BamM/issues/34#issuecomment-191510044.

jzrapp commented 7 years ago

Dear @timbalam,

we're trying to install BamM for two days now. Finally the nosetests is running, but it still doesn't run smoothly:

jrapp@aphros:/opt/bio/dset/BamM$ nosetests .....Traceback (most recent call last): File "/usr/local/bin/bamm", line 660, in doWork(args) File "/usr/local/bin/bamm", line 155, in doWork BS.makeBams() File "/usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py", line 298, in makeBams BM.makeBam() File "/usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py", line 632, in makeBam BV.validate_bam("%s.bam" % self.outFileName) File "/usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py", line 1037, in validate_bam 'Found duplicates:\n' %sortedBamFile) + outstr bamm.bammExceptions.DuplicateSequenceNameException: Duplicate reference sequence names found in bam file '/opt/bio/dset/BamM/bamm/tests/modeling/contigs_bad.up.bam'. Please check that reference sequence names used to generate bam file are unique. Found duplicates: 4 AA ....[E::hts_open_format] fail to open file '/opt/bio/dset/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam.bam' samtools view: failed to open "/opt/bio/dset/BamM/bamm/tests/cli_test_data/test_results.test_database.test_reads.1.tam.bam" for reading: No such file or directory ..........................................

Ran 51 tests in 35.534s

OK

Could you help with that? We're using samtools v1.3

Thanks a lot! Josephine

wwood commented 7 years ago

Hi Josephine, That error when running nosetests is a false alarm - don't worry yourself. It appears you have a working installation now. ben