Closed dstern closed 3 years ago
Hello, Thank you for your interest in JustOrthologs. I have previously encountered this error when the required python libraries are not installed. From README_WRAPPER, Python libraries that must be installed include:
If biopython is not installed, then one of the files is not created and cannot be removed by os.remove. Thank you for letting me know that you had this issue. Please let me know if installing the libraries (with pip install) solves the issue for you. Then I'll add some error checking in the wrapper script to ensure all python libraries are properly installed so other people don't have the same issue.
Hey @ridgelab ,
I ran into the same issue as dstern.
With the command
bash run_multiple_species.sh -i smallTest/wrapperTest/ -o outputDir/ -e output_ortholog_groups -f .fasta.gz -g .gff3
(all scripts adjusted to call python2 instead of just python), I got the following output:
Traceback (most recent call last): File "wrapper.py", line 240, in
os.remove(extract1) OSError: [Errno 2] No such file or directory: '.extract_1_2113848' Traceback (most recent call last): File "wrapper.py", line 240, in os.remove(extract1) OSError: [Errno 2] No such file or directory: '.extract_1_1597833' Traceback (most recent call last): File "wrapper.py", line 240, in os.remove(extract1) OSError: [Errno 2] No such file or directory: '.extract_1_1589643' Traceback (most recent call last): File "wrapper.py", line 240, in os.remove(extract1) OSError: [Errno 2] No such file or directory: '.extract_1_5593029' Traceback (most recent call last): File "wrapper.py", line 240, in os.remove(extract1) OSError: [Errno 2] No such file or directory: '.extract_1_3831114' Traceback (most recent call last): File "wrapper.py", line 240, in os.remove(extract1) OSError: [Errno 2] No such file or directory: '.extract_1_1896815'
All required python modules are installed (see list below). To double check, I also tried every import
function from your scripts on the python2.7 console and they worked. I tried just the wrapper as well but it throws the same error.
I am not sure what the error could be but I would love to resolve it. Your software seems to be the perfect fit to analyse my data. Do you have an idea what else I could try/look at to troubleshoot?
Best, Merle
Python 2.7.15+ (default, Nov 27 2018, 23:36:35)
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> help ("modules")
Please wait a moment while I gather a list of all available modules...
/usr/lib/python2.7/dist-packages/Bio/GA/__init__.py:14: BiopythonDeprecationWarning: Bio.GA has been deprecated, and we intend to remove it in a future release of Biopython. Please consider using DEAP instead. If you would like to continue using Bio.GA, please contact the Biopython developers via the mailing list or GitHub.
BiopythonDeprecationWarning)
/usr/lib/python2.7/dist-packages/Bio/NeuralNetwork/__init__.py:14: BiopythonDeprecationWarning: Bio.NeuralNetwork has been deprecated, and we intend to remove it in a future release of Biopython. Please consider using scikit-learn or TensorFlow instead. If you would like to continue using Bio.SomeModule, please contact the Biopython developers via the mailing list or GitHub.
BiopythonDeprecationWarning)
INFO:rdflib:RDFLib Version: 4.2.1
/usr/lib/python2.7/dist-packages/Bio/SearchIO/__init__.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.
BiopythonExperimentalWarning)
/usr/lib/python2.7/dist-packages/Bio/codonalign/__init__.py:27: BiopythonExperimentalWarning: Bio.codonalign is an experimental module which may undergo significant changes prior to its future official release.
BiopythonExperimentalWarning)
/usr/lib/python2.7/dist-packages/Bio/phenotype/__init__.py:101: BiopythonExperimentalWarning: Bio.phenotype is an experimental submodule which may undergo significant changes prior to its future official release.
BiopythonExperimentalWarning)
INFO:keyring.backend:Loading Windows (alt)
INFO:keyring.backend:Loading pyfs
INFO:keyring.backend:Loading multi
INFO:keyring.backend:Loading Google
INFO:keyring.backend:Loading Gnome
INFO:keyring.backend:Loading keyczar
INFO:keyring.backend:Loading file
/usr/lib/python2.7/dist-packages/matplotlib/cbook/deprecation.py:106: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
/usr/lib/python2.7/dist-packages/statsmodels/compat/pandas.py:56: FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead.
from pandas.core import datetools
BaseHTTPServer _threading_local hotshot repr
Bastion _tkinter html5lib requests
Bio _warnings htmlentitydefs resource
CDROM _weakref htmllib rexec
CGIHTTPServer _weakrefset httplib rfc822
Canvas abc idna rlcompleter
ConfigParser aifc ihooks robotparser
Cookie antigravity imaplib ruamel
Crypto antlr imgfuncs runpy
Cython anydbm imghdr sampletau
DLFCN argparse imp sched
DbgPlugInDiggers array importlib schema_salad
Dialog asn1crypto imputil scipy
DocXMLRPCServer ast indicator_keyboard scour
FileDialog asynchat inspect seaborn
FixTk asyncore io secretstorage
HTMLParser atexit ipaddress select
IN atk isodate sets
MimeWriter attr itertools setuptools
OpenSSL audiodev jdcal sgmllib
PIL audioop joblib sha
PyQt4 avro json shellescape
Queue backports keyring shelve
SPARQLWrapper base64 keyrings shlex
ScrolledText bdb keyword shutil
SimpleDialog binascii lib2to3 signal
SimpleHTTPServer binhex libexiv2python simplejson
SimpleXMLRPCServer bisect libvboxjxpcom sip
SocketServer bs4 linecache sipconfig
StringIO bsddb linuxaudiodev sipconfig_nd
TYPES bz2 locale site
Tix cPickle lockfile sitecustomize
Tkconstants cProfile logging six
Tkdnd cStringIO lsb_release smtpd
Tkinter cachecontrol lxml smtplib
UserDict cairo macpath sndhdr
UserList calendar macurl2path socket
UserString certifi mailbox spwd
VBoxAuth cgi mailcap sqlite3
VBoxAuthSimple cgitb markupbase sre
VBoxDD chardet marshal sre_compile
VBoxDD2 checkm math sre_constants
VBoxDDU chunk matplotlib sre_parse
VBoxDbg cmath md5 ssl
VBoxDragAndDropSvc cmd mhlib stat
VBoxGlobal code mimetools statsmodels
VBoxGuestControlSvc codecs mimetypes statvfs
VBoxGuestPropSvc codeop mimify string
VBoxHeadless collections mirage stringold
VBoxHostChannel colorsys mistune stringprep
VBoxKeyboard commands mlt strop
VBoxNetDHCP compileall mmap struct
VBoxNetNAT compiler mock subprocess
VBoxOGLhostcrutil contextlib modulefinder subprocess32
VBoxOGLhosterrorspu cookielib monotonic sunau
VBoxOGLrenderspu copy mpl_toolkits sunaudio
VBoxPython copy_reg multifile symbol
VBoxPython2_7 crypt multiprocessing symtable
VBoxREM cryptography mutex sys
VBoxRT csv netrc sysconfig
VBoxSDL ctypes new syslog
VBoxSVGA3D curses nis tables
VBoxSharedClipboard cvxopt nntplib tabnanny
VBoxSharedCrOpenGL cwltool ntpath talloc
VBoxSharedFolders cycler nturl2path tarfile
VBoxVMM cython numbers telnetlib
VBoxXPCOM datetime numexpr tempfile
VBoxXPCOMC dateutil numpy termios
VirtualBoxVM dbhash olefile test
_LWPCookieJar dbm opcode textwrap
_MozillaCookieJar dbus openpyxl this
__builtin__ decimal operator thread
__future__ decorator optparse threading
_abcoll dendropy os time
_ast desman os2emxpath timeit
_bisect difflib ossaudiodev tkColorChooser
_bsddb dircache pandas tkCommonDialog
_cffi_backend dis pango tkFileDialog
_codecs distutils pangocairo tkFont
_codecs_cn doctest parser tkMessageBox
_codecs_hk dsextras patsy tkSimpleDialog
_codecs_iso2022 dumbdbm pbr toaiff
_codecs_jp dummy_thread pdb token
_codecs_kr dummy_threading pickle tokenize
_codecs_tw duplicity pickletools trace
_collections easy_install pip traceback
_csv email pipes ttk
_ctypes enchant pkg_resources tty
_ctypes_test encodings pkgutil turtle
_curses ensurepip platform types
_curses_panel enum plistlib typing
_dbus_bindings errno pluggy unicodedata
_dbus_glib_bindings et_xmlfile popen2 unittest
_elementtree ete3 poplib urllib
_functools exceptions posix urllib2
_hashlib fasteners posixfile urllib3
_heapq fcntl posixpath urlparse
_hotshot filecmp pprint user
_io fileinput profile uu
_json fnmatch pstats uuid
_locale formatter pty vboxapi
_lsprof fpformat pwd vboxshell
_md5 fractions py warnings
_mlt ftplib py_compile wave
_multibytecodec funcsigs pyclbr weakref
_multiprocessing functools pydoc webbrowser
_osx_support future_builtins pydoc_data webencodings
_posixsubprocess gc pyexiv2 wheel
_pyio genericpath pyexpat whichdb
_pytest getopt pygtk wsgiref
_random getpass pygtkcompat xdg
_ruamel_yaml gettext pylab xdrlib
_sha gi pylocales xlrd
_sha256 gio pyparsing xlwt
_sha512 glib pysam xml
_socket glob pytest xmllib
_sqlite3 gobject pytz xmlrpclib
_sre grp pyximport xmouse
_ssl gtk quopri xxsubtype
_strptime gtkspellcheck random zim
_struct gtkunixprint rdflib zipfile
_symtable gzip rdflib_jsonld zipimport
_sysconfigdata hashlib re zlib
_sysconfigdata_nd heapq readline
_testcapi hmac reportlab
Hello Merle, Thank you for your interest in JustOrthologs. Which operating system are you using? If you are using Windows, then it is possible that the multiprocessing module isn't working correctly. We recently ran into that issue on a different software package that we have, and we developed a fix for that software package. We are working on implementing the fix for JustOrthologs as well, although we haven't pushed it yet.
If you aren't on Windows, try running the following command:
python2 gff3_parser.py -g smallTest/wrapperTest/small_human.gff3 -f smallTest/wrapperTest/small_human.fasta.gz -o output.fasta
A similar command is called by both the wrapper and run_multiple_species.sh to create the extracted file that is later removed. My guess is that something is happening there (maybe permission denied for writing?). Please let me know what happens because I cannot replicate the error on my side.
Thanks.
Hi, thanks for the quick reply. I am using Ubuntu 18.04. I ran the command and it ran without any error message.
Ok. Thanks for the update. The wrapper simply takes the individual programs and runs them. So, each of the programs listed in README_OTHER_PROGRAMS and README are run. If those commands run without error on your system, then the wrapper should also run without error. Obviously that is not occurring, though. Would you mind checking those individual commands and seeing if any of those commands throw an error? If we're not able to find where the error is occurring, I would be happy to check the files that you want to run through JustOrthologs. You can email me at jmiller@byu.edu with the files, and I'll see if they're formatted correctly for JustOrthologs to run.
Hi,
I'm having the exact same error. Did you find a solution to the problem?
I have installed JustOrthologs from github and tried to run the wrapper with recommended command from inside JustOrthologs folder. Throws error from line 240. I have tried this on two machines with independent installs of python 2.7 and get same error.
JustOrthologs sternd$ python2.7 wrapper.py -g1 smallTest/wrapperTest/small_pan.gff3 -g2 smallTest/wrapperTest/small_human.gff3 -r1 smallTest/wrapperTest/small_pan.fasta.gz -r2 smallTest/wrapperTest/small_human.fasta.gz -all -o output Traceback (most recent call last): File "wrapper.py", line 240, in
os.remove(extract1)
OSError: [Errno 2] No such file or directory: '.extract_1_1605371'