nosetests failed #34
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Hi blancaverag, Can you check the library Cheers, On 11/02/2016 10:36 PM, blancaverag wrote:
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Hi Tim, It does not exist. Blanca
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Thanks Blanca, There are possibly issues with using the --with-... flags. I will try to In the mean time, if you like you can try building without using the Cheers, On 12/02/2016 4:18 PM, blancaverag wrote:
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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 Automatically preparing build ... Warning: autoreconf failed Preparing build ... ERROR: aclocal failed 2016-02-12 9:14 GMT+01:00 timbalam notifications@github.com:
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Hi Blanca, I will try look into this soon. Have you tried running the nosetests Cheers, On 2/03/2016 2:39 AM, blancaverag wrote:
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Yes, I have tried and this is the result: ..Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/pkg_resources/init.py", File File File "build/bdist.linux-x86_64/egg/bamm/bamMaker.py", line 297, in subprocess.CalledProcessError: Command 'bwa mem -t 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 [E::hts_open_format] fail to open file [E::hts_open_format] fail to open file 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 If you don't have the installation logs then please try to reinstall BamM EERROR: test_bamParser.TestBamParser.test_A_makeTraceback (most recent call last): File "/home/programas/BamM/bamm/tests/test_bamParser.py", line 137, in File "/usr/local/lib/python2.7/subprocess.py", line 540, in check_call CalledProcessError: Command 'bamm make --silent -d ERROR: test_bamParser.TestBamParser.test_B_parseTraceback (most recent call last): ERROR: test suite for test_coverageStats.TestCoverageStatsTraceback (most recent call last): FAIL: test_bamParser.TestBamParser.test_C_extractTraceback (most recent call last): Ran 9 tests in 53.164s FAILED (errors=3, failures=1) 2016-03-02 9:06 GMT+01:00 timbalam notifications@github.com:
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Thanks, It does look like the bamm library build failed. I think that some of the errors might be due to using an incompatible Hopefully I'll have a chance to look into the build failure, possibly Tim On 2/03/2016 6:30 PM, blancaverag wrote:
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I have samtools version 1.2. Thanks! Blanca 2016-03-03 1:38 GMT+01:00 timbalam notifications@github.com:
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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
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Hi Josephine, |
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!!!
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