BamM
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Ecogenomics
nosetests failed
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
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
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!!!
