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Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
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Testing BamM using nosetests #16

Closed rdl88 closed 9 years ago

rdl88 commented 9 years ago

When running the nosetests command to test BamM I get this error message:

qiime@qiime-VirtualBox:~/GroopM/BamM$ nosetests .Traceback (most recent call last): File "/home/qiime/qiime_software/python-2.7.3-release/bin/bamm", line 583, in doWork(args) File "/home/qiime/qiime_software/python-2.7.3-release/bin/bamm", line 214, in doWork verbose=args.verbose) File "/home/qiime/GroopM/BamM/bamm/bamParser.py", line 384, in parseBams self.collapseBFIs(BFI_list) File "/home/qiime/GroopM/BamM/bamm/bamParser.py", line 484, in collapseBFIs self.BFI = BFI_list[baseBFI_index] File "", line 2, in getitem File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/managers.py", line 773, in _callmethod raise convert_to_error(kind, result) IndexError: list index out of range EWARNING: Could not find contig: [A] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.pe.1.bam]. WARNING: Could not find contig: [B] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.pe.1.bam]. WARNING: Could not find contig: [C] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.pe.1.bam]. WARNING: Could not find contig: [E] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.pe.1.bam]. WARNING: Could not find contig: [A] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.mp.bam]. WARNING: Could not find contig: [B] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.mp.bam]. WARNING: Could not find contig: [C] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.mp.bam]. WARNING: Could not find contig: [E] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.mp.bam]. WARNING: Could not find contig: [A] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.up.bam]. WARNING: Could not find contig: [B] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.up.bam]. WARNING: Could not find contig: [C] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.up.bam]. WARNING: Could not find contig: [E] in BAM: [/home/qiime/GroopM/BamM/bamm/tests/modelling/contigs.up.bam]. FNo file: /home/qiime/GroopM/BamM/bamm/tests/modelling/covs No file: /home/qiime/GroopM/BamM/bamm/tests/modelling/links

..........................................

ERROR: test_bamParser.TestBamParser.test_B_parse

Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/qiime/GroopM/BamM/bamm/tests/test_bamParser.py", line 154, in test_B_parse with open(covs_file) as c_fh: IOError: [Errno 2] No such file or directory: '/home/qiime/GroopM/BamM/bamm/tests/modelling/covs'

FAIL: test_bamParser.TestBamParser.test_C_extract

Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/qiime/GroopM/BamM/bamm/tests/test_bamParser.py", line 228, in test_C_extract assert_true(os.path.exists(full_path)) AssertionError: False is not true

Ran 45 tests in 0.948s

FAILED (errors=1, failures=1) qiime@qiime-VirtualBox:~/GroopM/BamM$

I looked at the managers.py script which seems to cause the error but I am not very experienced with Python scripts and have trouble understanding what the error means. Any help would be great.

Thank you

minillinim commented 9 years ago

Most likely this is caused by BamM not being installed properly before the tests have been run.

Can you try to reinstall BamM and let me know what the output is?

rdl88 commented 9 years ago

?Thank you for your response.

I had already itried reinstalling BamM and got the same error message, however so far I have been running BamM on a virtual box, since I do not have a Linux computer. Maybe that is the issue.

I will be getting a Linux computer soon, and I am hoping to not have any issues there. I will let you know if it is going to fix the error.

I appreciate your help.

Thank you

Daniel Lipus

PhD Student

Department of Civil and Environmental Engineering

University of Pittsburgh

Email: Dal124@pitt.edumailto:Dal124@pitt.edu

Phone: 914-482-8061

From: Michael Imelfort notifications@github.com Sent: Tuesday, January 6, 2015 9:11 PM To: minillinim/BamM Cc: Lipus, Daniel C Subject: Re: [BamM] Testing BamM using nosetests (#16)

Most likely this is caused by BamM not being installed properly before the tests have been run.

Can you try to reinstall BamM and let me know what the output is?

Reply to this email directly or view it on GitHubhttps://github.com/minillinim/BamM/issues/16#issuecomment-68969179.

minillinim commented 9 years ago

Hi,

Perhaps I should have been more clear. When you install BamM it prints a lot of stuff to the screen. If I look at what's written then I might be able to help you with your problem. BamM should run on a VM. If you have time and can try to re-run the install process and send me the contents of what's on the screen. I'll look into it for you.

Cheers,

Mike.

minillinim commented 9 years ago

Hi, I've uploaded a small script to the BamM web page called sysInfo.py. Could you please run that and post the output here. Thanks.

rdl88 commented 9 years ago

Hi Michael,

I hope I did it right. Here is the output:

Saving to: `sysInfo.py.gz'

100%[================================================>] 295 --.-K/s in 0s

2015-01-15 09:31:27 (27.4 MB/s) - `sysInfo.py.gz' saved [295/295]

qiime@qiime-VirtualBox:~/BamM$ gunzip sysInfo.py.gz qiime@qiime-VirtualBox:~/BamM$ chmod +x sysInfo.py qiime@qiime-VirtualBox:~/BamM$ ./sysInfo.py Error importing pytables Numpy version: 1.7.1 Location: /home/qiime/qiime_software/numpy-1.7.1-release/lib/python2.7/site-packages/numpy/init.pyc Error importing scipy MPL version: 1.3.1 Location: /home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/init.pyc Linux 3.2.0-57-generic 2.7.3 (default, Dec 19 2013, 03:13:59) [GCC 4.6.3] ['/home/qiime/BamM', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/nose-1.3.0-py2.7.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/pyparsing-2.0.1-py2.7.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/python_dateutil-2.2-py2.7.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/six-1.4.1-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/Sphinx-1.0.4-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/docutils-0.11-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/Jinja2-2.7.1-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/Pygments-1.6-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/MarkupSafe-0.18-py2.7-linux-x86_64.egg', '/home/qiime/qiime_software/pyqi-0.3.1-release/lib/python2.7/site-packages/pyqi-0.3.1-py2.7.egg', '/home/qiime/qiime_software/MySQL-python-1.2.3-release/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg', '/home/qiime/qiime_software/setuptools-0.6c11-release/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg', '/home/qiime/qiime_software/qiime-galaxy-0.0.1-repository-c2814c3c/lib', '/home/qiime/qiime_software/qiime-1.8.0-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/qiime-1.8.0-release/lib', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/ipython-latest-repository-e706d266/lib/python2.7/site-packages', '/home/qiime/qiime_software/tax2tree-1.0-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/biom-format-1.3.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pprospector-1.0.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pynast-1.2.2-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/emperor-0.9.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pyqi-0.3.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/MySQL-python-1.2.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/mpi4py-1.2.2-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/setuptools-0.6c11-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/gdata-2.0.17-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pysqlite-2.6.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/qcli-0.1.0-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/SQLAlchemy-0.7.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/tornado-3.1.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pyzmq-2.1.11-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/numpy-1.7.1-release/lib/python2.7/site-packages', '/home/qiime/BamM', '/home/qiime/qiime_software/python-2.7.3-release/lib/python27.zip', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/plat-linux2', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/lib-tk', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/lib-old', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/lib-dynload', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/qiime-1.8.0-release/lib/python2.7/site-packages']

I appreciate your help.

Thanks Daniel

Daniel Lipus

PhD Student

Department of Civil and Environmental Engineering

University of Pittsburgh

Email: Dal124@pitt.edumailto:Dal124@pitt.edu

Phone: 914-482-8061

From: Michael Imelfort notifications@github.com Sent: Thursday, January 15, 2015 12:45 AM To: minillinim/BamM Cc: Lipus, Daniel C Subject: Re: [BamM] Testing BamM using nosetests (#16)

Hi, I've uploaded a small script to the BamM web page called sysInfo.py. Could you please run that and post the output here. Thanks.

Reply to this email directly or view it on GitHubhttps://github.com/minillinim/BamM/issues/16#issuecomment-70042597.

minillinim commented 9 years ago

Not sure If I've caught this with 1.3.5

would you like to check now with the latest version

rdl88 commented 9 years ago

Michael,

?

Sorry, I am not sure, if I understand what you mean. Try it with the latest version of BamM? Is that 1.3.5?

Thanks

Daniel

Daniel Lipus

PhD Student

Department of Civil and Environmental Engineering

University of Pittsburgh

Email: Dal124@pitt.edumailto:Dal124@pitt.edu

Phone: 914-482-8061

From: Michael Imelfort notifications@github.com Sent: Friday, January 16, 2015 1:43 AM To: minillinim/BamM Cc: Lipus, Daniel C Subject: Re: [BamM] Testing BamM using nosetests (#16)

Not sure If I've caught this with 1.3.4

would you like to check now with the latest version

Reply to this email directly or view it on GitHubhttps://github.com/minillinim/BamM/issues/16#issuecomment-70214684.

minillinim commented 9 years ago

Yes,

I've been chasing three separate issues so the updates have been coming in fast.

rdl88 commented 9 years ago

I reinstalled BamM (version 1.3.6). here is the installation log:

qiime@qiime-VirtualBox:~/BamM$ python setup.py install --with-libhts-lib ../htslib --with-libhts-inc ../htslib --with-libcfu-inc ../libcfu-0.03/include --with-libcfu-lib ../libcfu-0.03/src checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 /home/qiime/libcfu-0.03/include... found checking for libcfu libraries in /home/qiime/libcfu-0.03/src... found checking for libhts headers in /home/qiime/htslib... found checking for libhts libraries in /home/qiime/htslib... found configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: config.h is unchanged rm -f bamParser rm -f bamExtractor rm -f *.o rm -f libBamM.a gcc -g -fPIC -pthread -O2 -Wall -I/home/qiime/htslib -I/home/qiime/libcfu-0.03/include -c -o bamExtractor.o bamExtractor.c gcc -g -fPIC -pthread -O2 -Wall -I/home/qiime/htslib -I/home/qiime/libcfu-0.03/include -c -o bamParser.o bamParser.c gcc -g -fPIC -pthread -O2 -Wall -I/home/qiime/htslib -I/home/qiime/libcfu-0.03/include -c -o pairedLink.o pairedLink.c gcc -g -fPIC -pthread -O2 -Wall -I/home/qiime/htslib -I/home/qiime/libcfu-0.03/include -c -o bamRead.o bamRead.c gcc -g -fPIC -pthread -O2 -Wall -I/home/qiime/htslib -I/home/qiime/libcfu-0.03/include -c -o coverageEstimators.o coverageEstimators.c gcc -g -fPIC -pthread -O2 -Wall -I/home/qiime/htslib -I/home/qiime/libcfu-0.03/include -static-libgcc -shared -Wl,-rpath,/home/qiime/htslib -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c -lm -L/home/qiime/libcfu-0.03/src -lcfu -L/home/qiime/htslib -lhts Building library /home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running install running build running build_py running build_scripts running install_lib running install_scripts changing mode of /home/qiime/qiime_software/python-2.7.3-release/bin/bamm to 775 changing mode of /home/qiime/qiime_software/python-2.7.3-release/bin/bamFlags to 775 running install_data copying c/libBamM.a -> /home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/site-packages/bamm/c/ running install_egg_info Writing /home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/site-packages/BamM-1.3.6-py2.7.egg-info

​But i got this error message, when I tried to run "nosetests"

qiime@qiime-VirtualBox:~/BamM$ nosetests .****

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.

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.

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.

Process Process-4: Traceback (most recent call last): File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap Process Process-3: Traceback (most recent call last): File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap Process Process-2: Traceback (most recent call last): File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() self.run() File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(_self._args, _self._kwargs) File "/home/qiime/BamM/bamm/bamParser.py", line 84, in externalParseWrapper File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(_self._args, _self._kwargs) File "/home/qiime/BamM/bamm/bamParser.py", line 84, in externalParseWrapper CW = CWrapper() CW = CWrapper() File "/home/qiime/BamM/bamm/cWrapper.py", line 463, in init self.run() File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(_self._args, *_self._kwargs) File "/home/qiime/BamM/bamm/bamParser.py", line 84, in externalParseWrapper CW = CWrapper() raise InvalidInstallationException File "/home/qiime/BamM/bamm/cWrapper.py", line 463, in init raise InvalidInstallationException InvalidInstallationException InvalidInstallationException File "/home/qiime/BamM/bamm/cWrapper.py", line 463, in init raise InvalidInstallationException InvalidInstallationException Traceback (most recent call last): File "/home/qiime/qiime_software/python-2.7.3-release/bin/bamm", line 583, in doWork(args) File "/home/qiime/qiime_software/python-2.7.3-release/bin/bamm", line 214, in doWork verbose=args.verbose) File "/home/qiime/BamM/bamm/bamParser.py", line 384, in parseBams self.collapseBFIs(BFI_list) File "/home/qiime/BamM/bamm/bamParser.py", line 484, in collapseBFIs self.BFI = BFI_list[baseBFI_index] File "", line 2, in getitem File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/managers.py", line 773, in _callmethod raise convert_to_error(kind, result) IndexError: list index out of range 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.

Process Process-3: Traceback (most recent call last): File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(_self._args, *_self._kwargs) File "/home/qiime/BamM/bamm/bamExtractor.py", line 151, in externalExtractWrapper CW = CWrapper() File "/home/qiime/BamM/bamm/cWrapper.py", line 463, in init raise InvalidInstallationException InvalidInstallationException FNo file: /home/qiime/BamM/bamm/tests/modelling/covs No file: /home/qiime/BamM/bamm/tests/modelling/links

..........................................

ERROR: test_bamParser.TestBamParser.test_B_parse

Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/qiime/BamM/bamm/tests/test_bamParser.py", line 154, in test_B_parse with open(covs_file) as c_fh: IOError: [Errno 2] No such file or directory: '/home/qiime/BamM/bamm/tests/modelling/covs'

FAIL: test_bamParser.TestBamParser.test_C_extract

Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/qiime/BamM/bamm/tests/test_bamParser.py", line 228, in test_C_extract assert_true(os.path.exists(full_path)) AssertionError: False is not true

Ran 45 tests in 2.460s

FAILED (errors=1, failures=1)

And when I ran sysInfo.py the error message looked like this:

qiime@qiime-VirtualBox:~$ ./sysInfo.py Error importing pytables Numpy version: 1.7.1 Location: /home/qiime/qiime_software/numpy-1.7.1-release/lib/python2.7/site-packages/numpy/init.pyc Error importing scipy MPL version: 1.3.1 Location: /home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/init.pyc Linux 3.2.0-57-generic 2.7.3 (default, Dec 19 2013, 03:13:59) [GCC 4.6.3] ['/home/qiime', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/nose-1.3.0-py2.7.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/pyparsing-2.0.1-py2.7.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/python_dateutil-2.2-py2.7.egg', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages/six-1.4.1-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/Sphinx-1.0.4-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/docutils-0.11-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/Jinja2-2.7.1-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/Pygments-1.6-py2.7.egg', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages/MarkupSafe-0.18-py2.7-linux-x86_64.egg', '/home/qiime/qiime_software/pyqi-0.3.1-release/lib/python2.7/site-packages/pyqi-0.3.1-py2.7.egg', '/home/qiime/qiime_software/MySQL-python-1.2.3-release/lib/python2.7/site-packages/MySQL_python-1.2.3-py2.7-linux-x86_64.egg', '/home/qiime/qiime_software/setuptools-0.6c11-release/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg', '/home/qiime/qiime_software/qiime-galaxy-0.0.1-repository-c2814c3c/lib', '/home/qiime/qiime_software/qiime-1.8.0-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/qiime-1.8.0-release/lib', '/home/qiime/qiime_software/matplotlib-1.3.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/ipython-latest-repository-e706d266/lib/python2.7/site-packages', '/home/qiime/qiime_software/tax2tree-1.0-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/biom-format-1.3.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pprospector-1.0.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pynast-1.2.2-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/emperor-0.9.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/sphinx-1.0.4-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pyqi-0.3.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/MySQL-python-1.2.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/mpi4py-1.2.2-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/setuptools-0.6c11-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/gdata-2.0.17-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pysqlite-2.6.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/qcli-0.1.0-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/SQLAlchemy-0.7.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/tornado-3.1.1-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/pyzmq-2.1.11-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/numpy-1.7.1-release/lib/python2.7/site-packages', '/home/qiime', '/home/qiime/qiime_software/python-2.7.3-release/lib/python27.zip', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/plat-linux2', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/lib-tk', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/lib-old', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/lib-dynload', '/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/site-packages', '/home/qiime/qiime_software/qiime-1.8.0-release/lib/python2.7/site-packages'] qiime@qiime-VirtualBox:~$

So to me it looks very similar to the previous error messages.

Thank you for your help!

Daniel Lipus

PhD Student

Department of Civil and Environmental Engineering

University of Pittsburgh

Email: Dal124@pitt.edumailto:Dal124@pitt.edu

Phone: 914-482-8061

From: Michael Imelfort notifications@github.com Sent: Sunday, January 18, 2015 8:14 AM To: minillinim/BamM Cc: Lipus, Daniel C Subject: Re: [BamM] Testing BamM using nosetests (#16)

Yes,

I've been chasing three separate issues so the updates have been coming in fast.

— Reply to this email directly or view it on GitHubhttps://github.com/minillinim/BamM/issues/16#issuecomment-70407833.

minillinim commented 9 years ago

The install worked, I think you're OK. I have an issue with Nosetests where it can fail spectacularly for weird reasons (My fault entirely)

If you have a bam file then try:

$ bamm parse

If it doesn't crash then you're good to go.

minillinim commented 9 years ago

Hi,

do you have bwa installed?

minillinim commented 9 years ago

Hi,

I think all the other errors may be cthe result of this one:

raise CalledProcessError(retcode, cmd) CalledProcessError: Command 'bwa bwasw -t 1 /home/julian/Downloads/BamM/bamm/tests/data/test_database.fna /home/julian/Downloads/BamM/bamm/tests/data/test_reads.1.fna /home/julian/Downloads/BamM/bamm/tests/data/test_reads.2.fna > /home/julian/Downloads/BamM/bamm/tests/data/test_results.test_database.test_reads.1.tam 2> /dev/null' returned non-zero exit status 134

Which is basically telling me that bwa crashed. Why? I don't know.

Could you try 3 things for me.

  1. Could you tell me the version of BWA you're running
  2. Could you try to run bwa on some data you have
  3. If this works, could you try to run bamm parse on the resulting bam file

Finally, could you keep track of the command line output for 2 and 3 and let me know what it says.

Mike.

minillinim commented 9 years ago

Ok

Thanks.

First, BWA 0.7.10 has some bugs that have been fixed in more recent versions. You should upgrade to the newest version. If you keep this version then bamm will fail the nosetests too as this version of bwa gives incorrect mappings.

I think you're problem is pretty simple. The bamm on your path does not seem to be the bamm GroopM and nosetests needs. When I run bamm I get this:

({{EREBUS}}:~)$ bamm

                           ...::: BamM :::...

                 Working with the BAM, not against it...

-------------------------------------------------------------------------
                               version: 1.3.7
-------------------------------------------------------------------------

 bamm make     ->  Make BAM/TAM files (sorted + indexed)
 bamm parse    ->  Get coverage profiles / linking reads / insert types
 bamm extract  ->  Extract reads / headers from BAM files

 USE: bamm OPTION -h to see detailed options

I would suspect that there is another program called bamm on your system. Perhaps: from http://bamm-project.org/? This is an unfortunate mistake on my part, I had no idea this program exited when I made bamm. I'm thinking out changing the name of my software.

In the meantime you can get past the nosetests issues by fixing your path variable.

$ export PATH=":$PATH" $ nosetests

Groopm doesn't need to have access to the bamm executable so it should work regardless of path problems

minillinim commented 9 years ago

Do this:

$ wget http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.12.tar.bz2 $ tar -xvf bwa-0.7.12.tar.bz2 $ cd bwa-0.7.12 $ make

Then you will have a file called bwa. you can run bwa from here. Generally, I'd uke the old version like this:

$ sudo cp bwa $(which bwa)

done!

minillinim commented 9 years ago

Ok

getting closer.

I need the full text of what the installer printed to the screen

minillinim commented 9 years ago

The problem is that gcc on your system is actually "clang"

The compiler is failing on specific gcc extensions that clang as some trouble with.

See here for how to get gcc on your system:

http://stackoverflow.com/questions/19535422/os-x-10-9-gcc-links-to-clang

minillinim commented 9 years ago

yes

minillinim commented 9 years ago

Try copying the file over to where it should be

minillinim commented 9 years ago

Ok.

After you install you have some issues with the location of libBamM.a -> copying the file will fix this It seems that your path is still pointing to the other bamm.

So...

fix your path make sure the libBamM.a is in the right place run nosetests

minillinim commented 9 years ago

try:

export PATH=/Users/Julian/BamM/bin:$PATH

minillinim commented 9 years ago

This is most likely because you are using clang instead of gcc.

Right now bamm needs gcc. You can use macports or brew to install gcc

minillinim commented 9 years ago

This line:

Looking for the c library at: /Users/Julian/BamM/bamm/c/libBamM.a

Have you copied the libBamM.a file to this location?

minillinim commented 9 years ago

What does : $ ls /Users/Julian/BamM/bamm/c/libBamM.a show?

Also, each time you close and reopen terminal it resets your path variable. Thus, you've gone back to the other bamm installation again.

I am getting ready to sign off for the day now. I probably won't get back to you again today.

People have reported issues installing BamM on OSX, it's something I'm working on, do you have access to a linux box to install this on?

minillinim commented 9 years ago

Hey, it worked!

Try run bamm parse on a bam file. If this works then groopm should work too

minillinim commented 9 years ago

type

$ PYTHONPATH

minillinim commented 9 years ago

Yes,

you need to add bamm to your pythonpath. Please see previous emails regarding instructions on how to do this

minillinim commented 9 years ago

Hi,

I appreciate that you're trying to contribute but I'm not in the position to accept money for this type of thing. A VM is something we're looking at doing but we're too busy right now to do that. I'm sorry I can't help with your issue, perhaps you could try another binning software like metabat.

wwood commented 8 years ago

Hi Julian,

1- What is the limitation of .bam files that I can add as the input for the tool?

Not sure I follow, what are you asking?

2- What is the running complexity of your tool?

We have not looked at this very comprehensively, I'm afraid.