Biopython NCBIcommandline from PHP Hi, this is my first post. I am writing a web program in PHP and I want it to perform a python s... This issue is now closed. Join them; it only takes a minute: Sign up Windows can't find the file on subprocess.call() up vote 42 down vote favorite 10 I am getting the following error: WindowsError: [Error Trying To Extract Blast Results Into Xml Outfile From Larger Blast Xml File This is probably a fairly basic question, so I apologize in advance, but I can't seem to figure http://stackoverflow.com/questions/3022013/windows-cant-find-the-file-on-subprocess-call
Additionally, Linux does not suffer from this problem: $ python --version Python 2.7.3 $ cat test/script.sh #!/bin/sh echo "hello" $ PATH=$PATH:test script.sh hello $ PATH=$PATH:test python -c "from subprocess import call; But "subprocess.Popen(['foo.bar'])" will throw the following exception: Traceback (most recent call last): [...] File "C:\Python26\lib\subprocess.py", line 483, in check_call retcode = call(*popenargs, **kwargs) File "C:\Python26\lib\subprocess.py", line 470, in call return Popen(*popenargs, What crime would be illegal to uncover in medieval Europe? Messages (3) msg180520 - (view) Author: Pekka Klärck (pekka.klarck) Date: 2013-01-24 13:09 If you add a directory into PATH on Windows so that the directory is in quotes, subprocess does not
docs.python.org/2/library/… –nu everest Feb 13 at 15:18 1 @nueverest Only when the the command string is constructed from external input –Jirka-x1 Jul 22 at 16:59 add a comment| up vote When does TNG take place in relation to DS9? According to en.wikipedia.org/wiki/ComSpec the COMSPEC variable should only point to one path? Python Subprocess Windows Error 2 Smith (eric.smith) * Date: 2010-03-25 10:08 I agree with David that this is a Windows problem.
What legal documents are Italian citizens supposed to carry when traveling to Ireland? You are waiting for your subprocess to complete without reading away what it prints. They are found by the operating system, though, at least when run on the command prompt. http://stackoverflow.com/questions/20330385/cannot-find-the-file-specified-when-using-subprocess-calldir-shell-true-in Has anyone else had this problem/know how to fix it?
ADD COMMENT • link written 6.0 years ago by Istvan Albert ♦♦ 66k 1 6.0 years ago by Michael Schubert • 6.6k Cambridge, UK Michael Schubert • 6.6k wrote: I'm still Python The System Cannot Find The Path Specified Currently it sea... I wanted to simplify my question as much as possible so I only brought up the example with 'dir'. Ballpark salary equivalent today of "healthcare benefits" in the US?
python shell python-2.7 path subprocess share|improve this question edited Dec 3 '13 at 8:49 asked Dec 2 '13 at 14:14 Andreas 63116 3 dir is not an executable, it is Administration User List Committer List Help Tracker Documentation Tracker Development Report Tracker Problem Issue17023 classification Title: Subprocess does not find executable on Windows if it is PATH with quotes Type: behavior File Line 958, In _execute_child Startupinfo) The second example uses BLAST+ (the current version of NCBI BLAST), but has a problem: from Bio.Blast.Applications import NcbiblastpCommandline my_blast_db = r"C:\Niek\Test2.2.17\Worm\c_elegans.protein.WS200.fasta" my_blast_file = r"C:\Niek\Test2.2.17\Worm\worm-HD.fasta" blastp_cline = NcbiblastpCommandline(cmd='blastp', query=my_blast_file, db=my_blast_db, evalue=0.01, Python Subprocess.popen Cannot Find File msg101666 - (view) Author: STINNER Victor (haypo) * Date: 2010-03-25 01:48 This issue might be documentation is subprocess documentation.
What happens when a wizard tries to cast a cone of cold through a wall of fire? check my blog about • faq • rss Community Log In Sign Up Add New Post Question: Windows Cmd Not Responding With Python Blastall 2.2.17 0 6.0 years ago by Niek De Klein • No trouble to report with linux. share|improve this answer answered Jun 11 '10 at 10:42 Ryan Ginstrom 10.2k52948 Yes it is quoted properly. Pytesseract Filenotfounderror: [winerror 2] The System Cannot Find The File Specified
Is there anyway yo get the actual program to popup, as it does from the command prompt? –Parseltongue Nov 18 '13 at 8:09 @Parseltongue, Is there any message in Now, I would be surprised if your 2.7.8 makes the difference, but who knows. As a monk, can I use Deflect Missiles to protect my ally? http://rss4medics.com/cannot-find/python-subprocess-windows-cannot-find-the-file-specified.php When I do os.system("C:/Flow Check/Run Quick/Applications/Manipula.exe" "C:/Flow Check/Data Processing/BLAISE TO BLAISE.msu") nothing happens.
The only time you need to specify shell=True on Windows is when the command you wish to execute is built into the shell (e.g. Python Subprocess No Such File Or Directory Problem With Blastp Of Biopython: Returned Non-Zero Exit Status 1 I want to do a local BLAST using blastp from the Bio.Blast.Applications. Any idea what I can try.
Here is the ouput from the terminal. To reproduce: C:\>python --version Python 2.7.3 C:\>type test\script.bat @echo off echo hello C:\>set ORIG=%PATH% C:\>set PATH=%ORIG%;test C:\>script.bat hello C:\>python -c "from subprocess import call; call('script.bat')" hello C:\>set PATH=%ORIG%;"test" C:\>script.bat hello C:\>python Bhagavad Geeta 4.14 Boss sends a birthday message. Returned Non-zero Exit Status 1 All of the above is executed in the terminal started in Administrator mode.
Reload to refresh your session. How do I use the subprocess module with mswindows? Since the only thing this does is to run the process under cmd.exe I assume that cmd.exe itself adds some kind of PATH handling of its own. http://rss4medics.com/cannot-find/python-the-system-cannot-find-the-path-specified.php msg101647 - (view) Author: Sridhar Ratnakumar (srid) Date: 2010-03-24 18:26 Note that typing "foo.bar" in the Windows command line works, only subprocess is not able to find the executable.
dir or copy). Sign in to comment Contact GitHub API Training Shop Blog About © 2016 GitHub, Inc. I copied xcopy.exe into a local directory as xcopy.exe and xcopy.a.exe. Which one are you trying to build for again?
I copied the output from cygwin (64-bit), but I get the same error on Windows PowerShell (both are run as admin). Chromium and node.js do even support XP I think (as build target). I think os.listdir is more suitable for your case: >>> import os >>> os.listdir() ['1.txt', '2.txt', '3.txt', 'DLLs', 'Doc', 'e.txt', 'include', 'Lib', 'libs', 'LICENSE.txt', 'm.txt', 'msvcr100.dll', 'NEWS.txt', 'py.exe', 'python.exe', 'python33.dll', 'pythonw.exe', Oracle SQL - can I return the "before" state of a column value Performance difference in between Windows and Linux using intel compiler: looking at the assembly My cat sat on
share|improve this answer edited Dec 3 '13 at 9:04 answered Dec 2 '13 at 14:18 aIKid 11.7k31941 Actually I want to call an executable, but that does not work You signed in with another tab or window. Try our newsletter Sign up for our newsletter and get our top new questions delivered to your inbox (see an example). In any case, it looks to me like if there is a bug here it is in Windows.
It is the classical deadlock problem. When I add shell=True to subprocess.Popen a new error appears that there is no directory C:/Flow, I think because the shell has a hard time processing spaces... Is there still a way to prevent Trump from becoming president? Python automatically concatenates adjacent strings with nothing but whitespace in between: >>> "C:/Flow Check/Run Quick/Applications/Manipula.exe" "C:/Flow Check/Data Processing/BLAISE TO BLAISE.msu" 'C:/Flow Check/Run Quick/Applications/Manipula.exeC:/Flow Check/Data Processing/BLAISE TO BLAISE.msu' Note how there is
But the error remains the same. more stack exchange communities company blog Stack Exchange Inbox Reputation and Badges sign up log in tour help Tour Start here for a quick overview of the site Help Center Detailed How To Parse Psiblast Results Using Biopython And Blast-2.2.24+?