Crontab wont run python script

Question

When I execute my python script from the command line I have no problems like so:

[rv@med240-183 db]$ python formatdb.py
[rv@med240-183 db]$

When I try to use crontab to run the script every midnight I get a series of errors:

import: unable to open X server `' @ import.c/ImportImageCommand/367.
/home/rv/ncbi-blast-2.2.23+/db/formatdb.py: line 2: from: command not found
/home/rv/ncbi-blast-2.2.23+/db/formatdb.py: line 3: from: command not found
import: unable to open X server `' @ import.c/ImportImageCommand/367.
/home/rv/ncbi-blast-2.2.23+/db/formatdb.py: line 6: syntax error near
unexpected token `('
/home/rv/ncbi-blast-2.2.23+/db/formatdb.py: line 6: `conx = MySQLdb.connect
(user = 'root', passwd = '******', db = 'vaxijen_antigens')'

The directory of my script is as follows:

/home/rv/ncbi-blast-2.2.23+/db/

Crontab looks like:

SHELL=/bin/bash
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/bin/python/:/home/rv/ncbi-blast-2.2.23+/database_backup:/home/rv/ncbi-blast-2.2.23+/db/
MAILTO="******"
HOME=/

# For details see man 4 crontabs

# Example of job definition:
# .---------------- minute (0 - 59)
# |  .------------- hour (0 - 23)
# |  |  .---------- day of month (1 - 31)
# |  |  |  .------- month (1 - 12) OR jan,feb,mar,apr ...
# |  |  |  |  .---- day of week (0 - 6) (Sunday=0 or 7) OR sun,mon,tue,wed,thu,fri,sat
# |  |  |  |  |
# *  *  *  *  *  command to be executed
0 0 * * * root /home/rv/ncbi-blast-2.2.23+/database_backup/backup.py
0 0 * * * root /home/rv/ncbi-blast-2.2.23+/db/formatdb.py

and my python script looks like:

import MySQLdb
from subprocess import call
from subprocess import Popen
import re

conx = MySQLdb.connect (user = 'root', passwd = '******', db = 'vaxijen_antigens')

cursor = conx.cursor()
cursor.execute('select * from sequence')
row = cursor.fetchall()

f = open('vdatabase.fasta', 'w')

for i in row:
    f.write('>'+i[0].strip()+'\n')
    #f.write(i[1].strip().replace(' ','')+'\n')
    s = re.sub(r'[^\w]','',str(i[1]))
    s = ''.join(s)
    for k in range(0, len(s), 60):
        f.write('%s\n' % (s[k:k+60]))
    f.write('\n')

f.close

Popen(["formatdb", "-p", "T", "-i", "vdatabase.fasta"]).wait()

What operating system do you have? Where are some similar bugs in gentoo, try to use for example this answer to solve your problem schwobeseggl.de/2009/08/04/gentoo-portage-python. Your problem is that when you are running it manually - you starting it from X enviroment, but cron works without X server... — Mikhail Chernykh
– Mikhail Chernykh, Commented Jul 26, 2010 at 17:17

Wayne Werner · Accepted Answer · 2010-07-26 17:14:35Z

28

Add

#!/usr/bin/env python

to the beginning of your script - right now it's trying to execute your script as a bash, that line says "I'm a python script, please use the right interpreter". It's also called a hash-bang line, but it needs to be the first line in your script.

answered Jul 26, 2010 at 17:14

Wayne Werner

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2 Comments

Wayne Werner Over a year ago

That's happened to me a few times - and like you I couldn't see the obvious, whoops >.< sometimes another pair of eyes is invaluable.

Helen Neely Over a year ago

Awesome stuff - just adding that shebang line saved me a whole day of hair pulling. Thanks :)

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