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xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
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Error running test data #25

Closed jananiharan closed 3 years ago

jananiharan commented 4 years ago

I get the following error with the test data:

isescan.py --nthread 2 NC_012624.fna proteome hmm

isPredict begins at Fri Sep  4 14:57:49 2020
Traceback (most recent call last):
  File "/home/janani/anaconda3/bin/isescan.py", line 70, in <module>
    isPredictSingle(args4isPredictSingle)
  File "/home/janani/anaconda3/bin/isescan.py", line 24, in isPredictSingle
    args['nthread'])
  File "/home/janani/anaconda3/bin/isPredict.py", line 203, in isPredict
    dnaFiles = tools.rdDNAlist(dna_list)

I did a conda install and all paths seem to be OK. Thanks in advance!

xiezhq commented 4 years ago

Hi jananiharan,

I need more information from you to figure out what happened. Could you run the commands below and posted all contents (including the commands you are running) on your screen?

ls -lh NC_012624.fna
which python3
python3 /home/janani/anaconda3/bin/isescan.py NC_012624.fna proteome hmm --nthread 2

Thanks, Xie

jananiharan commented 4 years ago

Hi Xie,

Here it is:

$ ls -lh NC_012624.fna 
-rwxrwxr-x 1 janani janani 42K Sep  4 14:57 NC_012624.fna

$ which python3
/home/janani/anaconda3/bin/python3

$ python3 /home/janani/anaconda3/bin/isescan.py NC_012624.fna proteome hmm --nthread 2
isPredict begins at Sat Sep  5 22:52:23 2020
Traceback (most recent call last):
  File "/home/janani/anaconda3/bin/isescan.py", line 70, in <module>
    isPredictSingle(args4isPredictSingle)
  File "/home/janani/anaconda3/bin/isescan.py", line 24, in isPredictSingle
    args['nthread'])
  File "/home/janani/anaconda3/bin/isPredict.py", line 203, in isPredict
    dnaFiles = tools.rdDNAlist(dna_list)
AttributeError: module 'tools' has no attribute 'rdDNAlist'`
xiezhq commented 4 years ago

Could you run two commands and post the results?

which isescan.py
ls -lh /home/janani/anaconda3/bin/|grep tools.py
grep rdDNAlist /home/janani/anaconda3/bin/tools.py
jananiharan commented 4 years ago 
$ which isescan.py 
/home/janani/anaconda3/bin/isescan.py

$ ls -lh /home/janani/anaconda3/bin/|grep tools.py
-rwxrwxr-x 2 janani janani  77K Apr 20 12:11 tools.py

$ grep rdDNAlist /home/janani/anaconda3/bin/tools.py
def rdDNAlist(dnaListFile):
    dnaFiles = rdDNAlist(filelist)
xiezhq commented 4 years ago

It seems everything is there. Do you or your python3 have any module with same name as tools.py? Let's check it: Could you run the commands below?

which tools.py

and

python3 test.py > path.txt
echo $PYTHONPATH >> path.txt
for p in $(cat path.txt): do find "$p" -name "tools*"; done

The content of test.py is:

import sys
for p in sys.path:
    print(p)
jananiharan commented 4 years ago 
$ which tools.py
/home/janani/anaconda3/bin/tools.py

For the second block of code, I made one small correction:

python3 test.py > path.txt
echo $PYTHONPATH >> path.txt
for p in $(cat path.txt); do find "$p" -name "tools*"; done

.. which gave me


/home/janani/bin/tools
/home/janani/bin/tools/MaxBin-2.2.5/MaxBin-2.2.5/auxiliary/idba-1.1.1/src/tools
/home/janani/bin/tools/libiconv-1.15/tools
/home/janani/bin/tools/libiconv-1.15/libcharset/tools
/home/janani/bin/tools/antismash-5.1.1/antismash/detection/genefunctions/tools.py
/home/janani/bin/tools/MCR/v901/mcr/toolbox/matlab/toolstrip
/home/janani/bin/tools/MCR/v901/mcr/toolbox/matlab/uitools/toolsmenufcn.m
/home/janani/bin/tools/MCR/v901/mcr/toolbox/matlab/appdesigner/web/release/appdesigner/css-appdesigner/toolstrip.css
/home/janani/bin/tools/MCR/v901/mcr/toolbox/matlab/appdesigner/web/release/appdesigner/images/toolstrip
/home/janani/bin/tools/MCR/v901/mcr/toolbox/matlab/appdesigner/web/release/appdesigner/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/ui/install/installservicehandler/images/toolstrip
/home/janani/bin/tools/MCR/v901/ui/install/installservicehandler/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/resources/Simulink/en/tools.xml
/home/janani/bin/tools/MCR/v901/resources/Simulink/ja_JP/tools.xml
/home/janani/bin/tools/MCR/v901/resources/MATLAB/en/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/shared/configset/+configset/+dialog/web/release/images/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/shared/configset/+configset/+dialog/web/release/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/shared/dastudio/web/matlabeditor/release/matlabeditor/images/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/shared/dastudio/web/matlabeditor/release/matlabeditor/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/shared/dastudio/web/webmanager/release/webmanager/images/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/shared/dastudio/web/webmanager/release/webmanager/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/matlab/uitools/uifigureappjs/release/images/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/matlab/uitools/uifigureappjs/release/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/matlab/codetools/uicomponents/web/datatools/inspector/release/inspector/images/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/matlab/codetools/uicomponents/web/datatools/inspector/release/inspector/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/matlab/codetools/uicomponents/web/datatools/variableeditor/release/variableeditor/images/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/matlab/codetools/uicomponents/web/datatools/variableeditor/release/variableeditor/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/matlab/system/editor/analyzer/release/images/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/matlab/system/editor/analyzer/release/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/glee/web/release/images/toolstrip
/home/janani/bin/tools/MCR/v901/toolbox/glee/web/release/images/widgets/visualfamilies/toolstrip
/home/janani/bin/tools/MCR/v901/appdata/components/toolstrip_common 1452793619 8497975348203836217.xml
/home/janani/bin/tools/MCR/v901/appdata/files/toolstrip_common 1452793619_manifest.bin
/home/janani/bin/tools/MCR/v901/java/jar/toolstrip.jar
/home/janani/bin/tools/MCR/archives/toolstrip_common_1452793619.enc
/home/janani/bin/tools/MCR/archives/toolstrip_common_1452793619.xml
/home/janani/bin/tools/OrthoFinder-2.2.7/tools
/home/janani/bin/tools/autoconf-2.69/tests/tools.at
/home/janani/bin/tools/Roary-db170bf/build/bedtools2/docs/content/tools
/home/janani/bin/tools/OrthoFinder-2.2.6/tools
/home/janani/bin/tools/bin/macosx-intel/diamond-0.8.25/src/run/tools.h
/home/janani/bin/tools/bin/macosx-intel/diamond-0.8.25/src/run/tools.cpp
/home/janani/bin/tools/bbmap/pytools/tools
/home/janani/bin/tools/boost_1_67_0/libs/asio/tools
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/home/janani/bin/tools/boost_1_67_0/libs/predef/tools
/home/janani/bin/tools/boost_1_67_0/libs/heap/tools
/home/janani/bin/tools/boost_1_67_0/libs/test/test/writing-test-ts/tools-under-debugger-test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/test/test/writing-test-ts/tools-debuggable-test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/test/tools
/home/janani/bin/tools/boost_1_67_0/libs/test/doc/html/header/boost/test/tools
/home/janani/bin/tools/boost_1_67_0/libs/test/doc/html/boost_test/testing_tools/tools_assertion_severity_level.html
/home/janani/bin/tools/boost_1_67_0/libs/regex/tools
/home/janani/bin/tools/boost_1_67_0/libs/metaparse/tools
/home/janani/bin/tools/boost_1_67_0/libs/mpl/doc/src/docutils/tools
/home/janani/bin/tools/boost_1_67_0/libs/beast/tools
/home/janani/bin/tools/boost_1_67_0/libs/config/tools
/home/janani/bin/tools/boost_1_67_0/libs/typeof/tools
/home/janani/bin/tools/boost_1_67_0/libs/filesystem/tools
/home/janani/bin/tools/boost_1_67_0/libs/multiprecision/tools
/home/janani/bin/tools/boost_1_67_0/libs/convert/doc/tools.qbk
/home/janani/bin/tools/boost_1_67_0/libs/numeric/odeint/toolset.jam.patch
/home/janani/bin/tools/boost_1_67_0/libs/locale/tools
/home/janani/bin/tools/boost_1_67_0/libs/format/tools
/home/janani/bin/tools/boost_1_67_0/libs/geometry/doc/src/docutils/tools
/home/janani/bin/tools/boost_1_67_0/libs/xpressive/tools
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_series_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_tuple_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_solve_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_config_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_minima_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_fraction_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_test_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_test_data_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_toms748_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_polynomial_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_remez_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_rational_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_real_cast_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_precision_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_stats_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/test/compile_test/tools_roots_inc_test.cpp
/home/janani/bin/tools/boost_1_67_0/libs/math/tools
/home/janani/bin/tools/boost_1_67_0/libs/math/include_private/boost/math/tools
/home/janani/bin/tools/boost_1_67_0/tools
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset_gcc.py
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset_darwin.py
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset_intel_darwin.py
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset_clang_linux.py
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset-mock
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset_clang_vxworks.py
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset_requirements.py
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset_clang_darwin.py
/home/janani/bin/tools/boost_1_67_0/tools/build/test/toolset_defaults.py
/home/janani/bin/tools/boost_1_67_0/tools/build/doc/src/tools.adoc
/home/janani/bin/tools/boost_1_67_0/tools/build/src/build/toolset.jam
/home/janani/bin/tools/boost_1_67_0/tools/build/src/build/toolset.py
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/home/janani/bin/tools/boost_1_67_0/boost/math/tools
/home/janani/bin/tools/boost_1_67_0/doc/html/tools.html
/home/janani/bin/tools/get_homologues-x86_64-20190102/bin/macosx-intel/diamond-0.8.25/src/run/tools.h
/home/janani/bin/tools/get_homologues-x86_64-20190102/bin/macosx-intel/diamond-0.8.25/src/run/tools.cpp
/home/janani/bin/tools/R-3.5.1/tests/Examples/tools-Ex.Rout.save
/home/janani/bin/tools/R-3.5.1/tools
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/ko/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/ja/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/pt_BR/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/ru/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/en@quot/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/da/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/de/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/it/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/fr/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/pl/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/translations/inst/zh_CN/LC_MESSAGES/tools.mo
/home/janani/bin/tools/R-3.5.1/src/library/tools
/home/janani/bin/tools/R-3.5.1/src/library/tools/po/tools.pot
/home/janani/bin/tools/R-3.5.1/src/library/tools/R/tools-deprecated.R
/home/janani/bin/tools/R-3.5.1/src/library/tools/R/tools-defunct.R
/home/janani/bin/tools/R-3.5.1/src/library/tools/src/tools.h
/home/janani/bin/tools/R-3.5.1/src/library/tools/man/tools-deprecated.Rd
/home/janani/bin/tools/R-3.5.1/src/library/tools/man/tools-defunct.Rd
/home/janani/bin/tools/R-3.5.1/src/library/tools/man/tools-package.Rd
/home/janani/bin/tools/megahit/tools
/home/janani/anaconda3/lib/python3.7/site-packages/bokeh/models/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/bokeh/models/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/bokeh/server/static/js/lib/models/tools
/home/janani/anaconda3/lib/python3.7/site-packages/bokeh/server/static/js/types/models/tools
/home/janani/anaconda3/lib/python3.7/site-packages/nose/tools
/home/janani/anaconda3/lib/python3.7/site-packages/IPython/testing/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/IPython/testing/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/tools
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/tools/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/tools/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/sandbox/tools
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/sandbox/tools/tools_pca.py
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/sandbox/tools/__pycache__/tools_pca.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/sandbox/regression/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/sandbox/regression/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/tsa/arima/tools.py
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/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/tsa/statespace/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/statsmodels/tsa/statespace/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/notebook/bundler/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/notebook/bundler/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/sympy/strategies/branch/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/sympy/strategies/branch/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/sympy/strategies/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/sympy/strategies/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/pandas/tests/tools
/home/janani/anaconda3/lib/python3.7/site-packages/pandas/plotting/_matplotlib/tools.py
/home/janani/anaconda3/lib/python3.7/site-packages/pandas/plotting/_matplotlib/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/lib/python3.7/site-packages/pandas/core/tools
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/home/janani/anaconda3/pkgs/bokeh-2.2.1-py37hc8dfbb8_0/lib/python3.7/site-packages/bokeh/models/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/pkgs/bokeh-2.2.1-py37hc8dfbb8_0/lib/python3.7/site-packages/bokeh/server/static/js/lib/models/tools
/home/janani/anaconda3/pkgs/bokeh-2.2.1-py37hc8dfbb8_0/lib/python3.7/site-packages/bokeh/server/static/js/types/models/tools
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/home/janani/anaconda3/pkgs/pandas-1.1.1-py37h3340039_0/lib/python3.7/site-packages/pandas/plotting/_matplotlib/__pycache__/tools.cpython-37.pyc
/home/janani/anaconda3/pkgs/pandas-1.1.1-py37h3340039_0/lib/python3.7/site-packages/pandas/core/tools
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/home/janani/anaconda3/pkgs/libboost-1.67.0-h46d08c1_4/share/boost-build/src/tools
/home/janani/anaconda3/pkgs/libboost-1.67.0-h46d08c1_4/share/boost-build/src/tools/features/toolset-feature.jam
/home/janani/anaconda3/pkgs/libboost-1.67.0-h46d08c1_4/include/boost/test/tools
/home/janani/anaconda3/pkgs/libboost-1.67.0-h46d08c1_4/include/boost/msm/back/tools.hpp
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find: ‘/home/janani/anaconda3/lib/python37.zip’: No such file or directory
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/home/janani/anaconda3/lib/python3.7/site-packages/pandas/core/tools```
jananiharan commented 3 years ago

Hi! Checking in to see if you have any ideas on resolving this issue? Or is it something specific to my workspace that you haven't encountered before?

xiezhq commented 3 years ago

I am not sure of why it happened. It might be that your python3 import the tools module other than the tools.py shipped with ISEScan. Maybe you can rename the tools.py module shipped with ISEScan by doing the following:

cd /home/janani/anaconda3/bin/
mv tools.py isescantools.py
sed -i 's/itertools/itertool_s/g' is_analysis.py isPredict.py pred.py
sed -i 's/tools/isescantools/g' is_analysis.py isPredict.py pred.py
sed -i 's/itertool_s/itertools/g' is_analysis.py isPredict.py pred.py

Then run isescan as before to see if it solves your problem.

Xie

jananiharan commented 3 years ago

This fixes the problem! Thanks so much.