assaron
commented
4 years ago It seems to be python 2 vs 3 related issue. quant3p was not yet properly upgraded to python3. You can try to run it inside conda python2 environment for now.
Open NitKV opened 4 years ago
assaron
commented
4 years ago It seems to be python 2 vs 3 related issue. quant3p was not yet properly upgraded to python3. You can try to run it inside conda python2 environment for now.
NitKV
commented
4 years ago Thank you so much for the reply. I tried to run it inside conda python2 environment, but got the following error:
running install
running bdist_egg
running egg_info
creating quant3p.egg-info
writing requirements to quant3p.egg-info/requires.txt
writing quant3p.egg-info/PKG-INFO
writing top-level names to quant3p.egg-info/top_level.txt
writing dependency_links to quant3p.egg-info/dependency_links.txt
writing entry points to quant3p.egg-info/entry_points.txt
writing manifest file 'quant3p.egg-info/SOURCES.txt'
reading manifest file 'quant3p.egg-info/SOURCES.txt'
writing manifest file 'quant3p.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/quant3p
copying quant3p/init.py -> build/lib/quant3p
copying quant3p/gtfextend.py -> build/lib/quant3p
copying quant3p/fixmm.py -> build/lib/quant3p
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/quant3p
copying build/lib/quant3p/init.py -> build/bdist.linux-x86_64/egg/quant3p
copying build/lib/quant3p/gtfextend.py -> build/bdist.linux-x86_64/egg/quant3p
copying build/lib/quant3p/fixmm.py -> build/bdist.linux-x86_64/egg/quant3p
byte-compiling build/bdist.linux-x86_64/egg/quant3p/init.py to init.pyc
byte-compiling build/bdist.linux-x86_64/egg/quant3p/gtfextend.py to gtfextend.pyc
byte-compiling build/bdist.linux-x86_64/egg/quant3p/fixmm.py to fixmm.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-2.7
copying bin/macs2-stranded -> build/scripts-2.7
copying bin/quant3p -> build/scripts-2.7
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/quant3p -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/macs2-stranded -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/quant3p to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/macs2-stranded to 755
copying quant3p.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating dist
creating 'dist/quant3p-0.1-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing quant3p-0.1-py2.7.egg
creating /home/WUR/derks047/.local/lib/python2.7/site-packages/quant3p-0.1-py2.7.egg
Extracting quant3p-0.1-py2.7.egg to /home/WUR/derks047/.local/lib/python2.7/site-packages
Adding quant3p 0.1 to easy-install.pth file
Installing macs2-stranded script to /home/WUR/derks047/.local/bin
Installing quant3p script to /home/WUR/derks047/.local/bin
Installing gtf-extend script to /home/WUR/derks047/.local/bin
Installing fix-mm script to /home/WUR/derks047/.local/bin
Installed /home/WUR/derks047/.local/lib/python2.7/site-packages/quant3p-0.1-py2.7.egg
Processing dependencies for quant3p==0.1
Searching for macs2>=2.1.0
Reading https://pypi.org/simple/macs2/
Best match: MACS2 2.2.5
Processing MACS2-2.2.5.tar.gz
Writing /tmp/easy_install-MsL_Au/MACS2-2.2.5/setup.cfg
Running MACS2-2.2.5/setup.py -q bdist_egg --dist-dir /tmp/easy_install-MsL_Au/MACS2-2.2.5/egg-dist-tmp-H98Wcn
CRITICAL: Python version must >= 3.5!
error: Setup script exited with 1
Could you help let me know what should be done? Many thanks
assaron
commented
4 years ago Macs2 should be 2.1.* before 2.2 which started to use python3
On Thu, Nov 28, 2019, 13:18 NitKV notifications@github.com wrote:
Thank you so much for the reply. I tried to run it inside conda python2 environment, but got the following error:
running install
running bdist_egg
running egg_info
creating quant3p.egg-info
writing requirements to quant3p.egg-info/requires.txt
writing quant3p.egg-info/PKG-INFO
writing top-level names to quant3p.egg-info/top_level.txt
writing dependency_links to quant3p.egg-info/dependency_links.txt
writing entry points to quant3p.egg-info/entry_points.txt
writing manifest file 'quant3p.egg-info/SOURCES.txt'
reading manifest file 'quant3p.egg-info/SOURCES.txt'
writing manifest file 'quant3p.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/quant3p
copying quant3p/init.py -> build/lib/quant3p
copying quant3p/gtfextend.py -> build/lib/quant3p
copying quant3p/fixmm.py -> build/lib/quant3p
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/quant3p
copying build/lib/quant3p/init.py -> build/bdist.linux-x86_64/egg/quant3p
copying build/lib/quant3p/gtfextend.py -> build/bdist.linux-x86_64/egg/quant3p
copying build/lib/quant3p/fixmm.py -> build/bdist.linux-x86_64/egg/quant3p
byte-compiling build/bdist.linux-x86_64/egg/quant3p/init.py to init .pyc
byte-compiling build/bdist.linux-x86_64/egg/quant3p/gtfextend.py to gtfextend.pyc
byte-compiling build/bdist.linux-x86_64/egg/quant3p/fixmm.py to fixmm.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-2.7
copying bin/macs2-stranded -> build/scripts-2.7
copying bin/quant3p -> build/scripts-2.7
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/quant3p -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/macs2-stranded -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/quant3p to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/macs2-stranded to 755
copying quant3p.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying quant3p.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating dist
creating 'dist/quant3p-0.1-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing quant3p-0.1-py2.7.egg
creating /home/WUR/derks047/.local/lib/python2.7/site-packages/quant3p-0.1-py2.7.egg
Extracting quant3p-0.1-py2.7.egg to /home/WUR/derks047/.local/lib/python2.7/site-packages
Adding quant3p 0.1 to easy-install.pth file
Installing macs2-stranded script to /home/WUR/derks047/.local/bin
Installing quant3p script to /home/WUR/derks047/.local/bin
Installing gtf-extend script to /home/WUR/derks047/.local/bin
Installing fix-mm script to /home/WUR/derks047/.local/bin
Installed /home/WUR/derks047/.local/lib/python2.7/site-packages/quant3p-0.1-py2.7.egg
Processing dependencies for quant3p==0.1
Searching for macs2>=2.1.0
Reading https://pypi.org/simple/macs2/
Best match: MACS2 2.2.5
Processing MACS2-2.2.5.tar.gz
Writing /tmp/easy_install-MsL_Au/MACS2-2.2.5/setup.cfg
Running MACS2-2.2.5/setup.py -q bdist_egg --dist-dir /tmp/easy_install-MsL_Au/MACS2-2.2.5/egg-dist-tmp-H98Wcn
CRITICAL: Python version must >= 3.5!
error: Setup script exited with 1
Could you help let me know what should be done? Many thanks
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ctlab/quant3p/issues/5?email_source=notifications&email_token=AAH56WPEOM7W6KPMK3BRMIDQV6LIBA5CNFSM4JRWIFT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFMEIRQ#issuecomment-559432774, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAH56WJYR72ZBJIKFMUVRTTQV6LIBANCNFSM4JRWIFTQ .
NitKV
commented
4 years ago Hi , I have unistalled the previus Macs2 and tried to reinstall with python2. But the for installing numpy it needs python3. So I am getting the following error:
/cm/shared/apps/python/2.7.11/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'long_description_content_type' warnings.warn(msg) running install running bdist_egg running egg_info writing requirements to MACS2.egg-info/requires.txt writing MACS2.egg-info/PKG-INFO writing top-level names to MACS2.egg-info/top_level.txt writing dependency_links to MACS2.egg-info/dependency_links.txt reading manifest file 'MACS2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'MACS2.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py running build_ext creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/Constants.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/OptValidator.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/OutputWriter.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/init.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/bdgbroadcall_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/bdgcmp_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/bdgdiff_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/bdgopt_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/bdgpeakcall_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/callpeak_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/cmbreps_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/diffpeak_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/filterdup_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/pileup_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/predictd_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/randsample_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/refinepeak_cmd.py -> build/bdist.linux-x86_64/egg/MACS2 creating build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/init.py -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/Parser.so -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/PeakIO.so -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/BedGraphIO.so -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/FixWidthTrack.so -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/PairedEndTrack.so -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/BedGraph.so -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/ScoreTrack.so -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/IO/CallPeakUnit.so -> build/bdist.linux-x86_64/egg/MACS2/IO copying build/lib.linux-x86_64-2.7/MACS2/Prob.so -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/Pileup.so -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/PeakModel.so -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/PeakDetect.so -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/Signal.so -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/hashtable.so -> build/bdist.linux-x86_64/egg/MACS2 copying build/lib.linux-x86_64-2.7/MACS2/Statistics.so -> build/bdist.linux-x86_64/egg/MACS2 byte-compiling build/bdist.linux-x86_64/egg/MACS2/Constants.py to Constants.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/OptValidator.py to OptValidator.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/OutputWriter.py to OutputWriter.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/bdgbroadcall_cmd.py to bdgbroadcall_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/bdgcmp_cmd.py to bdgcmp_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/bdgdiff_cmd.py to bdgdiff_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/bdgopt_cmd.py to bdgopt_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/bdgpeakcall_cmd.py to bdgpeakcall_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py to callpeak_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/cmbreps_cmd.py to cmbreps_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/diffpeak_cmd.py to diffpeak_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/filterdup_cmd.py to filterdup_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/pileup_cmd.py to pileup_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/predictd_cmd.py to predictd_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/randsample_cmd.py to randsample_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/refinepeak_cmd.py to refinepeak_cmd.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/init.py to init.pyc creating stub loader for MACS2/Prob.so creating stub loader for MACS2/IO/Parser.so creating stub loader for MACS2/Pileup.so creating stub loader for MACS2/PeakModel.so creating stub loader for MACS2/PeakDetect.so creating stub loader for MACS2/Signal.so creating stub loader for MACS2/IO/PeakIO.so creating stub loader for MACS2/IO/BedGraphIO.so creating stub loader for MACS2/IO/FixWidthTrack.so creating stub loader for MACS2/IO/PairedEndTrack.so creating stub loader for MACS2/IO/BedGraph.so creating stub loader for MACS2/IO/ScoreTrack.so creating stub loader for MACS2/IO/CallPeakUnit.so creating stub loader for MACS2/hashtable.so creating stub loader for MACS2/Statistics.so byte-compiling build/bdist.linux-x86_64/egg/MACS2/Prob.py to Prob.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/Parser.py to Parser.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/Pileup.py to Pileup.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/PeakModel.py to PeakModel.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/PeakDetect.py to PeakDetect.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/Signal.py to Signal.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/PeakIO.py to PeakIO.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/BedGraphIO.py to BedGraphIO.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/FixWidthTrack.py to FixWidthTrack.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/PairedEndTrack.py to PairedEndTrack.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/BedGraph.py to BedGraph.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/ScoreTrack.py to ScoreTrack.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/IO/CallPeakUnit.py to CallPeakUnit.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/hashtable.py to hashtable.pyc byte-compiling build/bdist.linux-x86_64/egg/MACS2/Statistics.py to Statistics.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/macs2 -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/macs2 to 775 copying MACS2.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying MACS2.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MACS2.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MACS2.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MACS2.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt zip_safe flag not set; analyzing archive contents... creating 'dist/MACS2-2.1.4-py2.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing MACS2-2.1.4-py2.7-linux-x86_64.egg Removing /home/WUR/veetil01/.local/lib/python2.7/site-packages/MACS2-2.1.4-py2.7-linux-x86_64.egg Copying MACS2-2.1.4-py2.7-linux-x86_64.egg to /home/WUR/veetil01/.local/lib/python2.7/site-packages MACS2 2.1.4 is already the active version in easy-install.pth Installing macs2 script to /home/WUR/veetil01/.local/bin
Installed /home/WUR/veetil01/.local/lib/python2.7/site-packages/MACS2-2.1.4-py2.7-linux-x86_64.egg
Processing dependencies for MACS2==2.1.4
Searching for numpy>=1.16
Reading https://pypi.python.org/simple/numpy/
Best match: numpy 1.17.4
Downloading https://files.pythonhosted.org/packages/ff/59/d3f6d46aa1fd220d020bdd61e76ca51f6548c6ad6d24ddb614f4037cf49d/numpy-1.17.4.zip#sha256=f58913e9227400f1395c7b800503ebfdb0772f1c33ff8cb4d6451c06cabdf316
Processing numpy-1.17.4.zip
Writing /tmp/easy_install-EZz_Ik/numpy-1.17.4/setup.cfg
Running numpy-1.17.4/setup.py -q bdist_egg --dist-dir /tmp/easy_install-EZz_Ik/numpy-1.17.4/egg-dist-tmp-ZAPA2N
Traceback (most recent call last):
File "setup.py", line 112, in
File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 621, in easy_install
File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 672, in install_item
File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 717, in process_distribution
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 826, in resolve File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1071, in best_match File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1083, in obtain File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 640, in easy_install
File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 670, in install_item
File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 850, in install_eggs
File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 1078, in build_and_install
File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 1064, in run_setup
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 246, in run_setup
File "/cm/shared/apps/python/2.7.11/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 195, in setup_context
File "/cm/shared/apps/python/2.7.11/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 166, in save_modules
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 141, in resume
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 154, in save_modules
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 195, in setup_context
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 243, in run_setup
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 273, in run
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 242, in runner
File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 46, in _execfile
File "/tmp/easy_install-EZz_Ik/numpy-1.17.4/setup.py", line 31, in
assaron
commented
4 years ago OK, i've upgraded the code, should work with the latest versions of masc2, htseq and other programs. Please, check
NitKV
commented
4 years ago Hi, Now I am able ti install quant3p, but when I try to run the example in the manual :
quant3p -n example -g example/mm10.slice.gtf example/bam/*.bam
I get the following error:
[veetil01@login0 quant3p]$ quant3p -n example -g example/mm10.slice.gtf example/bam/2h_rep1.bam Calling peaks... Calling peaks
Usage: samtools view [options]
Options: -b output BAM -h print header for the SAM output -H print header only (no alignments) -S input is SAM -u uncompressed BAM output (force -b) -1 fast compression (force -b) -x output FLAG in HEX (samtools-C specific) -X output FLAG in string (samtools-C specific) -c print only the count of matching records -B collapse the backward CIGAR operation -@ INT number of BAM compression threads [0] -L FILE output alignments overlapping the input BED FILE [null] -t FILE list of reference names and lengths (force -S) [null] -T FILE reference sequence file (force -S) [null] -o FILE output file name [stdout] -R FILE list of read groups to be outputted [null] -f INT required flag, 0 for unset [0] -F INT filtering flag, 0 for unset [0] -q INT minimum mapping quality [0] -l STR only output reads in library STR [null] -r STR only output reads in read group STR [null] -s FLOAT fraction of templates to subsample; integer part as seed [-1] -? longer help
/home/WUR/veetil01/.local/bin/macs2-stranded: line 95: 0 / 0 :
division by 0 (error token is "0 ")
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
usage: macs2 callpeak [-h] -t TFILE [TFILE ...] [-c [CFILE [CFILE ...]]]
[-f
{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
[-g GSIZE] [-s TSIZE] [--keep-dup KEEPDUPLICATES]
[--outdir OUTDIR] [-n NAME] [-B] [--verbose VERBOSE]
[--trackline] [--SPMR] [--nomodel] [--shift SHIFT]
[--extsize EXTSIZE] [--bw BW] [--d-min D_MIN]
[-m MFOLD MFOLD] [--fix-bimodal] [-q QVALUE | -p PVALUE]
[--scale-to {large,small}] [--ratio RATIO]
[--down-sample] [--seed SEED] [--tempdir TEMPDIR]
[--nolambda] [--slocal SMALLLOCAL] [--llocal LARGELOCAL]
[--max-gap MAXGAP] [--min-length MINLEN] [--broad]
[--broad-cutoff BROADCUTOFF] [--cutoff-analysis]
[--call-summits] [--fe-cutoff FECUTOFF]
[--buffer-size BUFFER_SIZE] [--to-large]
usage: macs2 callpeak [-h] -t TFILE [TFILE ...] [-c [CFILE [CFILE ...]]]
[-f
{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
[-g GSIZE] [-s TSIZE] [--keep-dup KEEPDUPLICATES]
[--outdir OUTDIR] [-n NAME] [-B] [--verbose VERBOSE]
[--trackline] [--SPMR] [--nomodel] [--shift SHIFT]
[--extsize EXTSIZE] [--bw BW] [--d-min D_MIN]
[-m MFOLD MFOLD] [--fix-bimodal] [-q QVALUE | -p PVALUE]
[--scale-to {large,small}] [--ratio RATIO]
[--down-sample] [--seed SEED] [--tempdir TEMPDIR]
[--nolambda] [--slocal SMALLLOCAL] [--llocal LARGELOCAL]
[--max-gap MAXGAP] [--min-length MINLEN] [--broad]
[--broad-cutoff BROADCUTOFF] [--cutoff-analysis]
[--call-summits] [--fe-cutoff FECUTOFF]
[--buffer-size BUFFER_SIZE] [--to-large]
macs2 callpeak: error: argument -s/--tsize: expected one argument
macs2 callpeak: error: argument -s/--tsize: expected one argument
macs2-stranded: Error on or near line 104; exiting with status 1
Extending annotaion...
Traceback (most recent call last):
File "/home/WUR/veetil01/.local/bin/gtf-extend", line 11, in
On Mon, Dec 2, 2019 at 6:33 PM Alexey Sergushichev notifications@github.com wrote:
OK, i've upgraded the code, should work with the latest versions of masc2, htseq and other programs. Please, check
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ctlab/quant3p/issues/5?email_source=notifications&email_token=ANY7IU7J5ZW2Y4UUIKMCOCTQWVBGTA5CNFSM4JRWIFT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFUIL2A#issuecomment-560498152, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANY7IU4W6WOSIDXAFLGSJ23QWVBGTANCNFSM4JRWIFTQ .
-- Thanks and regards, Nithya
assaron
commented
4 years ago From the logs I see that it uses python2.7 installation (actually, mixed one with both 2.7 and 3.7). You can try to reinstall it from scratch.
NitKV
commented
4 years ago Hi , I have reinstalled quant3p, but again getting the following error:
[veetil01@login0 quant3p]$ quant3p -n example -g example/mm10.slice.gtf example/bam/*.bam Calling peaks... Calling peaks
Usage: samtools view [options]
Options: -b output BAM -h print header for the SAM output -H print header only (no alignments) -S input is SAM -u uncompressed BAM output (force -b) -1 fast compression (force -b) -x output FLAG in HEX (samtools-C specific) -X output FLAG in string (samtools-C specific) -c print only the count of matching records -B collapse the backward CIGAR operation -@ INT number of BAM compression threads [0] -L FILE output alignments overlapping the input BED FILE [null] -t FILE list of reference names and lengths (force -S) [null] -T FILE reference sequence file (force -S) [null] -o FILE output file name [stdout] -R FILE list of read groups to be outputted [null] -f INT required flag, 0 for unset [0] -F INT filtering flag, 0 for unset [0] -q INT minimum mapping quality [0] -l STR only output reads in library STR [null] -r STR only output reads in read group STR [null] -s FLOAT fraction of templates to subsample; integer part as seed [-1] -? longer help
/home/WUR/veetil01/.local/bin/macs2-stranded: line 95: 0 / 0 : division by
0 (error token is "0 ")
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
usage: macs2 callpeak [-h] -t TFILE [TFILE ...] [-c [CFILE [CFILE ...]]]
[-f
{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
[-g GSIZE] [-s TSIZE] [--keep-dup KEEPDUPLICATES]
[--outdir OUTDIR] [-n NAME] [-B] [--verbose VERBOSE]
[--trackline] [--SPMR] [--nomodel] [--shift SHIFT]
[--extsize EXTSIZE] [--bw BW] [--d-min D_MIN]
[-m MFOLD MFOLD] [--fix-bimodal] [-q QVALUE | -p
PVALUE]
[--scale-to {large,small}] [--ratio RATIO]
[--down-sample] [--seed SEED] [--tempdir TEMPDIR]
[--nolambda] [--slocal SMALLLOCAL] [--llocal
LARGELOCAL]
[--max-gap MAXGAP] [--min-length MINLEN] [--broad]
[--broad-cutoff BROADCUTOFF] [--cutoff-analysis]
[--call-summits] [--fe-cutoff FECUTOFF]
[--buffer-size BUFFER_SIZE] [--to-large]
macs2 callpeak: error: argument -s/--tsize: expected one argument
usage: macs2 callpeak [-h] -t TFILE [TFILE ...] [-c [CFILE [CFILE ...]]]
[-f
{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
[-g GSIZE] [-s TSIZE] [--keep-dup KEEPDUPLICATES]
[--outdir OUTDIR] [-n NAME] [-B] [--verbose VERBOSE]
[--trackline] [--SPMR] [--nomodel] [--shift SHIFT]
[--extsize EXTSIZE] [--bw BW] [--d-min D_MIN]
[-m MFOLD MFOLD] [--fix-bimodal] [-q QVALUE | -p
PVALUE]
[--scale-to {large,small}] [--ratio RATIO]
[--down-sample] [--seed SEED] [--tempdir TEMPDIR]
[--nolambda] [--slocal SMALLLOCAL] [--llocal
LARGELOCAL]
[--max-gap MAXGAP] [--min-length MINLEN] [--broad]
[--broad-cutoff BROADCUTOFF] [--cutoff-analysis]
[--call-summits] [--fe-cutoff FECUTOFF]
[--buffer-size BUFFER_SIZE] [--to-large]
macs2 callpeak: error: argument -s/--tsize: expected one argument
macs2-stranded: Error on or near line 104; exiting with status 1
Extending annotaion...
Traceback (most recent call last):
File "/home/WUR/veetil01/.local/bin/gtf-extend", line 11, in
On Tue, Dec 3, 2019 at 11:33 AM Alexey Sergushichev < notifications@github.com> wrote:
From the logs I see that it uses python2.7 installation (actually, mixed one with both 2.7 and 3.7). You can try to reinstall it from scratch.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ctlab/quant3p/issues/5?email_source=notifications&email_token=ANY7IUYIUP5UVXB4274X4UTQWYYW3A5CNFSM4JRWIFT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFY4U4Y#issuecomment-561105523, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANY7IU7A4E4TX6AJVOZOWJLQWYYW3ANCNFSM4JRWIFTQ .
-- Thanks and regards, Nithya
assaron
commented
4 years ago It seems you are running it not from conda environment, no? What is your version of samtools?
Hi , I am trying to run quant3p for the example file inside the tool. But I am getting the following error:
Calling peaks... Calling peaks INFO @ Tue, 26 Nov 2019 12:01:15:
Command line: callpeak -t /dev/fd/63 --outdir trial.neg.macs -s 26 --nomodel -f SAM -g 3e9 -n trial.neg -q 0.01
ARGUMENTS LIST:
name = trial.neg
format = SAM
ChIP-seq file = ['/dev/fd/63']
control file = None
effective genome size = 3.00e+09
band width = 300
model fold = [5, 50]
qvalue cutoff = 1.00e-02
The maximum gap between significant sites is assigned as the read length/tag size.
The minimum length of peaks is assigned as the predicted fragment length "d".
Larger dataset will be scaled towards smaller dataset.
Range for calculating regional lambda is: 10000 bps
Broad region calling is off
Paired-End mode is off
INFO @ Tue, 26 Nov 2019 12:01:15: #1 read tag files... INFO @ Tue, 26 Nov 2019 12:01:15: #1 read treatment tags... Traceback (most recent call last): File "/home/WUR/veetil01/.local/bin/macs2", line 4, in
import('pkg_resources').run_script('MACS2==2.2.5', 'macs2')
File "/cm/shared/apps/python/3.7.1/lib/python3.7/site-packages/pkg_resources/init.py", line 658, in run_script
INFO @ Tue, 26 Nov 2019 12:01:15:
Command line: callpeak -t /dev/fd/63 --outdir trial.pos.macs -s 26 --nomodel -f SAM -g 3e9 -n trial.pos -q 0.01
ARGUMENTS LIST:
name = trial.pos
format = SAM
ChIP-seq file = ['/dev/fd/63']
control file = None
effective genome size = 3.00e+09
band width = 300
model fold = [5, 50]
qvalue cutoff = 1.00e-02
The maximum gap between significant sites is assigned as the read length/tag size.
The minimum length of peaks is assigned as the predicted fragment length "d".
Larger dataset will be scaled towards smaller dataset.
Range for calculating regional lambda is: 10000 bps
Broad region calling is off
Paired-End mode is off
File "/cm/shared/apps/python/3.7.1/lib/python3.7/site-packages/pkg_resources/init.py", line 1438, in run_script INFO @ Tue, 26 Nov 2019 12:01:15: #1 read tag files... INFO @ Tue, 26 Nov 2019 12:01:15: #1 read treatment tags... exec(code, namespace, namespace) File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/MACS2-2.2.5-py3.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 652, in
main()
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/MACS2-2.2.5-py3.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 51, in main
run( args )
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/MACS2-2.2.5-py3.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 65, in run
else: (treat, control) = load_tag_files_options (options)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/MACS2-2.2.5-py3.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 391, in load_tag_files_options
treat = tp.build_fwtrack()
File "MACS2/IO/Parser.pyx", line 187, in MACS2.IO.Parser.GenericParser.build_fwtrack
File "MACS2/IO/Parser.pyx", line 202, in MACS2.IO.Parser.GenericParser.build_fwtrack
File "MACS2/IO/Parser.pyx", line 696, in MACS2.IO.Parser.SAMParser.fw_parse_line
IndexError: list index out of range
INFO @ Tue, 26 Nov 2019 12:01:15: #1 tag size is determined as 26 bps
INFO @ Tue, 26 Nov 2019 12:01:15: #1 tag size = 26.0
INFO @ Tue, 26 Nov 2019 12:01:15: #1 total tags in treatment: 9214
INFO @ Tue, 26 Nov 2019 12:01:15: #1 user defined the maximum tags...
INFO @ Tue, 26 Nov 2019 12:01:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
INFO @ Tue, 26 Nov 2019 12:01:15: #1 tags after filtering in treatment: 1984
INFO @ Tue, 26 Nov 2019 12:01:15: #1 Redundant rate of treatment: 0.78
INFO @ Tue, 26 Nov 2019 12:01:15: #1 finished!
INFO @ Tue, 26 Nov 2019 12:01:15: #2 Build Peak Model...
INFO @ Tue, 26 Nov 2019 12:01:15: #2 Skipped...
INFO @ Tue, 26 Nov 2019 12:01:15: #2 Use 200 as fragment length
INFO @ Tue, 26 Nov 2019 12:01:15: #3 Call peaks...
INFO @ Tue, 26 Nov 2019 12:01:15: #3 Pre-compute pvalue-qvalue table...
INFO @ Tue, 26 Nov 2019 12:01:15: #3 Call peaks for each chromosome...
INFO @ Tue, 26 Nov 2019 12:01:15: #4 Write output xls file... trial.pos.macs/trial.pos_peaks.xls
INFO @ Tue, 26 Nov 2019 12:01:15: #4 Write peak in narrowPeak format file... trial.pos.macs/trial.pos_peaks.narrowPeak
INFO @ Tue, 26 Nov 2019 12:01:15: #4 Write summits bed file... trial.pos.macs/trial.pos_summits.bed
INFO @ Tue, 26 Nov 2019 12:01:15: Done!
macs2-stranded: Error on or near line 105; exiting with status 1
Extending annotaion...
Traceback (most recent call last):
File "/home/WUR/veetil01/.local/bin/gtf-extend", line 11, in
load_entry_point('quant3p==0.1', 'console_scripts', 'gtf-extend')()
File "/cm/shared/apps/python/3.7.1/lib/python3.7/site-packages/pkg_resources/init.py", line 480, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/cm/shared/apps/python/3.7.1/lib/python3.7/site-packages/pkg_resources/init.py", line 2693, in load_entry_point
return ep.load()
File "/cm/shared/apps/python/3.7.1/lib/python3.7/site-packages/pkg_resources/ init.py", line 2324, in load
return self.resolve()
File "/cm/shared/apps/python/3.7.1/lib/python3.7/site-packages/pkg_resources/init.py", line 2330, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/gtfextend.py", line 27
print "Loading peaks..."
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Loading peaks...")?
Error occured when processing GFF file (line 1 of file trial.mm10.slice.fixed.gtf):
Error occured when processing GFF file (line 1 of file trial.mm10.slice.fixed.gtf):
[Errno 2] No such file or directory: 'trial.mm10.slice.fixed.gtf'
[Errno 2] No such file or directory: 'trial.mm10.slice.fixed.gtf'
[Exception type: FileNotFoundError, raised in init.py:47]
[Exception type: FileNotFoundError, raised in init.py:47]
2019-11-26 12:01:16,409 - INFO: Finding exonic multimappers...
2019-11-26 12:01:16,412 - INFO: Finding exonic multimappers...
Traceback (most recent call last):
File "/home/WUR/veetil01/.local/bin/fix-mm", line 11, in
load_entry_point('quant3p==0.1', 'console_scripts', 'fix-mm')()
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/fixmm.py", line 95, in main
exonicBam = bamTool.intersect(xgtf, split=True, s=True, nonamecheck=True)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 840, in decorated
result = method(self, args, kwargs)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 308, in wrapped
cmds, tmp, stdin = self.handle_kwargs(prog=prog, kwargs)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1412, in handle_kwargs
kwargs[inarg2] = self._collapse(instream2)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1300, in _collapse
for i in iterable:
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/fixmm.py", line 64, in extended_exons
Traceback (most recent call last):
File "/home/WUR/veetil01/.local/bin/fix-mm", line 11, in
for exon in last_exons.itervalues():
AttributeError: 'dict' object has no attribute 'itervalues'
load_entry_point('quant3p==0.1', 'console_scripts', 'fix-mm')()
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/fixmm.py", line 95, in main
exonicBam = bamTool.intersect(xgtf, split=True, s=True, nonamecheck=True)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 840, in decorated
result = method(self, args, kwargs)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 308, in wrapped
cmds, tmp, stdin = self.handle_kwargs(prog=prog, kwargs)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1412, in handle_kwargs
kwargs[inarg2] = self._collapse(instream2)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1300, in _collapse
for i in iterable:
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/fixmm.py", line 64, in extended_exons
for exon in last_exons.itervalues():
AttributeError: 'dict' object has no attribute 'itervalues'
Error occured when processing GFF file (line 1 of file trial.mm10.slice.fixed.gtf):
[Errno 2] No such file or directory: 'trial.mm10.slice.fixed.gtf'
[Exception type: FileNotFoundError, raised in init.py:47]
Error occured when processing GFF file (line 1 of file trial.mm10.slice.fixed.gtf):
[Errno 2] No such file or directory: 'trial.mm10.slice.fixed.gtf'
[Exception type: FileNotFoundError, raised in init__.py:47]
2019-11-26 12:01:17,390 - INFO: Finding exonic multimappers...
Traceback (most recent call last):
File "/home/WUR/veetil01/.local/bin/fix-mm", line 11, in
load_entry_point('quant3p==0.1', 'console_scripts', 'fix-mm')()
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/fixmm.py", line 95, in main
exonicBam = bamTool.intersect(xgtf, split=True, s=True, nonamecheck=True)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 840, in decorated
result = method(self, args, kwargs)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 308, in wrapped
2019-11-26 12:01:17,397 - INFO: Finding exonic multimappers...
cmds, tmp, stdin = self.handle_kwargs(prog=prog, kwargs)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1412, in handle_kwargs
kwargs[inarg2] = self._collapse(instream2)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1300, in _collapse
for i in iterable:
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/fixmm.py", line 64, in extended_exons
for exon in last_exons.itervalues():
AttributeError: 'dict' object has no attribute 'itervalues'
Traceback (most recent call last):
File "/home/WUR/veetil01/.local/bin/fix-mm", line 11, in
load_entry_point('quant3p==0.1', 'console_scripts', 'fix-mm')()
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/fixmm.py", line 95, in main
exonicBam = bamTool.intersect(xgtf, split=True, s=True, nonamecheck=True)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 840, in decorated
result = method(self, args, kwargs)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 308, in wrapped
cmds, tmp, stdin = self.handle_kwargs(prog=prog, kwargs)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1412, in handle_kwargs
kwargs[inarg2] = self._collapse(instream2)
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/pybedtools-0.8.0-py3.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1300, in _collapse
for i in iterable:
File "/home/WUR/veetil01/.local/lib/python3.7/site-packages/quant3p-0.1-py3.7.egg/quant3p/fixmm.py", line 64, in extended_exons
for exon in last_exons.itervalues():
AttributeError: 'dict' object has no attribute 'itervalues'
quant3p: Error on or near line 121; exiting with status 1
Could someone please help me to find the solution. I am in need to run it for my sample sets. Many thanks in advance.