asked 2 years ago viewed 13834 times active 1 year ago Upcoming Events 2016 Community Moderator Election ends Nov 22 Linked 2 Traceback error when using subprocess in Python 1 How You are waiting for your subprocess to complete without reading away what it prints. Mar 19 '06 #4 This discussion thread is closed Start new discussion Replies have been disabled for this discussion. Extracting Accession Numbers With Ncbixml.Parse Greetings; I am a first time python user, and am stumped. http://amigasuperbit.com/cannot-find/python-subprocess-windows-the-system-cannot-find-the-file-specified.html
option, but blastp is the default anyway. How to reply? share|improve this answer edited Jan 6 '13 at 4:28 Tian He 9711 answered Jan 6 '11 at 16:00 Douglas Macdonald 77463 8 That's because there's no executable called dir.exe while Why is (a % 256) different than (a & 0xFF)? http://stackoverflow.com/questions/3022013/windows-cant-find-the-file-on-subprocess-call
Bhagavad Geeta 4.14 Boss sends a birthday message. What legal documents are Italian citizens supposed to carry when traveling to Ireland? WScript.CreateObject("WScript.Shell").Run "xcopy", 1, true WScript.CreateObject("WScript.Shell").Run "xcopy.a", 1, true I only tested on XP. All of the above is executed in the terminal started in Administrator mode.
Do humans have an ethical obligation to prevent animal on animal violence? On which point(s) in a jet engine does the reaction force act? msg101666 - (view) Author: STINNER Victor (haypo) * Date: 2010-03-25 01:48 This issue might be documentation is subprocess documentation. Python Subprocess Windows Error 2 Why not use os.listdir() instead? –Martijn Pieters♦ Dec 2 '13 at 14:17 strange, the code works for me on ubuntu, rhel, win xp, win 7 –alko Dec 2 '13
Register Lostyourlogin? Python Filenotfounderror: [winerror 2] The System Cannot Find The File Specified Changing it to a structure that first writes the file then reads it gives you more control and insight into what is actually happening. As a matter of fact, passing shell=True will produce the desired effect. http://stackoverflow.com/questions/20330385/cannot-find-the-file-specified-when-using-subprocess-calldir-shell-true-in Already have an account?
share|improve this answer answered Sep 13 at 15:51 Sam Inverso 414 add a comment| Your Answer draft saved draft discarded Sign up or log in Sign up using Google Sign Python The System Cannot Find The Path Specified Wikipedia's knowledge would seem to be outdated. –zigg Dec 6 '13 at 15:14 For me , the values is already os.environ['COMSPEC'] 'C:\\Windows\\system32\\cmd.exe'..............and i am running this on jenkins.......Not working Why is (a % 256) different than (a & 0xFF)? 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 do not need shell=True to run a batch file or console-based executable. Has someone Windows where the bootstrap script doesn't fail and can check his Python version? File Line 958, In _execute_child Startupinfo) Thanks, Niek Edit: I used blast 2.2.17 in command line directly (using same commands as used above) to create an xml file and read that in as result_handle. Python Subprocess.popen Cannot Find File E.g.
This issue is now closed. check my blog Is it possible for an diesel engine computer to detect (and prevent) a runaway condition? 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... Pytesseract Filenotfounderror: [winerror 2] The System Cannot Find The File Specified
How to define a "final slide" in a beamer template? Try our newsletter Sign up for our newsletter and get our top new questions delivered to your inbox (see an example). Python 3.x latest, stable. http://amigasuperbit.com/cannot-find/python-subprocess-windows-cannot-find-the-file-specified.html Powered by Biostar version 2.3.0 Traffic: 1325 users visited in the last hour 418,791 Members | 2,149 Online Join Now login Ask Question Home Questions Articles Browse Topics Latest
History Date User Action Args 2010-03-2510:08:29eric.smithsetstatus: open -> closednosy: + eric.smithmessages: + msg101688resolution: not a bugstage: test needed -> resolved 2010-03-2502:06:06r.david.murraysetmessages: + msg101669 2010-03-2501:49:30hayposetmessages: + msg101667 2010-03-2501:48:54hayposetnosy: + haypomessages: + msg101666 Python Subprocess No Such File Or Directory current community chat Stack Overflow Meta Stack Overflow your communities Sign up or log in to customize your list. How To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
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 Any ideas? Maybe someone could update the docs with a troubleshooting hint? @nexon How did you figure it out? @batjko Thanks, I tried many different versions of Python with no effect. Returned Non-zero Exit Status 1 David Murray (r.david.murray) * Date: 2010-03-24 20:08 Note that it works with shell=True.
C:\Python27)?If so, can you find the files it mentions: C:\Python27\lib\subprocess.py and probably more importantly: C:\Users\Martin\Source\Repos\atom-shell\script\lib\util.py? I'm trying to run a PSIBlast program which selects certain sequences out at every round before it... Is adding the ‘tbl’ prefix to table names really a problem? have a peek at these guys Basic Geometric intuition, context is undergraduate mathematics What crime would be illegal to uncover in medieval Europe?
asked 6 years ago viewed 29569 times active 1 month ago Upcoming Events 2016 Community Moderator Election ends Nov 22 Linked 1 Can't make django less work on Windows 0 Error 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... If I run it from the command line, Manipula will run for three seconds, do the necessary processing, and end itself. –Parseltongue Nov 18 '13 at 8:17 | show 7 more Browse other questions tagged python path python-3.x or ask your own question.
Which one are you trying to build for again? Are there still systems around with a /bin/sh binary? from Bio.Blast import NCBIStandalone from Bio.Blast import NCBIXML 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" my_blast_exe = r"C:\Niek\blast-2.2.17\bin\blastall.exe" result_handle, error_handle = NCBIStandalone.blastall(my_blast_exe, "blastp", my_blast_db, my_blast_file, matrix="BLOSUM62") blast_records = NCBIXML.parse(result_handle) y = 0 And of course, you escaped backslashes properly, or used slashes, right?
When running this VBScript, the first line runs, the second gives me an error 0x8007002, "The system could not find the file specified". Start a coup online without the government intervening How much time would it take for a planet scale Miller-Urey experiment to generate intelligent life Drawing a torso with a head (using Ballpark salary equivalent today of "healthcare benefits" in the US? Can Trump undo the UN climate change agreement?
The problem you see here is that the Windows API function CreateProcess, used by subprocess under the hood, doesn't auto-resolve other executable extensions than .exe. How do pilots identify the taxi path to the runway? I tried the following script that I found in... I have updated my question... –Andreas Dec 2 '13 at 14:37 add a comment| up vote 1 down vote In case anyone else besides me doesn't see this in the (3.4)
Biopython Import Error Hi everybody! I just don't know what's going on. What is this line of counties voting for the Democratic party in the 2016 elections? how to parse blast in biopython Hi all, I have been trying to write a program to search for specific proteins in an organisms gen...
The statement p = subprocess.call('dir', shell=True) works fine on another machine and I think that it is related. Mimsy were the Borogoves - why is "mimsy" an adjective? 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.