Crontab无法运行Python脚本

Question

当我在命令行中执行我的Python脚本时，一切都很顺利，像这样：

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

但是当我尝试用crontab（定时任务）每天午夜运行这个脚本时，就出现了一系列错误：

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')'

我的脚本所在的目录如下：

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

crontab的内容是：

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

而我的Python脚本内容是：

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()

Answer 1

在你的脚本开头加上

#!/usr/bin/env python

这一行 - 现在它正在尝试把你的脚本当作bash来执行，而这一行的意思是“我是一个python脚本，请用正确的解释器来运行我”。这行也叫做哈希bang行，但它必须是你脚本的第一行。