Problem with apt-get and Source Lists

wiz@wiz-PC:/var/lib/apt$ file E:Problem with MergeList /var/lib/apt/lists/in.archive.ubuntu.com_ubuntu_dists_precise_main_binary-i386_Packages

E:Problem:                                                                               ERROR: cannot open `E:Problem' (No such file or directory)

with:                                                                                    ERROR: cannot open `with' (No such file or directory)

MergeList:                                                                               ERROR: cannot open `MergeList' (No such file or directory)

/var/lib/apt/lists/in.archive.ubuntu.com_ubuntu_dists_precise_main_binary-i386_Packages: HTML document, ASCII text, with CRLF line terminators

wiz@wiz-PC:/var/lib/apt$ file /var/lib/apt/lists/in.archive.ubuntu.com_ubuntu_dists_precise_main_binary-i386_Packages/var/lib/apt/lists/in.archive.ubuntu.com_ubuntu_dists_precise_main_binary-i386_Packages: HTML document, ASCII text, with CRLF line terminators

wiz@wiz-PC:/var/lib/apt$ file /var/lib/apt/lists/in.archive.ubuntu.com_ubuntu_dists_precise_main_binary-i386_Packages

/var/lib/apt/lists/in.archive.ubuntu.com_ubuntu_dists_precise_main_binary-i386_Packages: HTML document, ASCII text, with CRLF line terminators

wiz@wiz-PC:/var/lib/apt$ sudo rm /var/lib/apt/lists/in.archive.ubuntu.com_ubuntu_dists_precise_main_binary-i386_Packages

wiz@wiz-PC:/var/lib/apt$ sudo apt-get update

Ign http://archive.ubuntu.com precise InRelease

Ign http://in.archive.ubuntu.com precise InRelease                  

Ign http://in.archive.ubuntu.com precise-backports InRelease         

Ign http://in.archive.ubuntu.com precise-updates InRelease           

Ign http://extras.ubuntu.com precise InRelease                       

Ign http://security.ubuntu.com precise-security InRelease            

Get:1 http://archive.ubuntu.com precise Release.gpg [198 B]          

Get:2 http://in.archive.ubuntu.com precise Release.gpg [198 B]                                        

Get:3 http://in.archive.ubuntu.com precise-backports Release.gpg [198 B]                              

Get:4 http://extras.ubuntu.com precise Release.gpg [72 B]                                  

Get:5 http://security.ubuntu.com precise-security Release.gpg [198 B]                               

Hit http://archive.ubuntu.com precise Release                                                         

Get:6 http://in.archive.ubuntu.com precise-updates Release.gpg [198 B]                    

Ign http://archive.ubuntu.com precise Release                                                        

Hit http://extras.ubuntu.com precise Release                         

Get:7 http://security.ubuntu.com precise-security Release [49.6 kB]                       

Ign http://extras.ubuntu.com precise Release                                                      

Hit http://in.archive.ubuntu.com precise Release                                                  

Ign http://archive.ubuntu.com precise/main Sources/DiffIndex                                                              

Ign http://in.archive.ubuntu.com precise Release                                                                          

Ign http://extras.ubuntu.com precise/main Sources/DiffIndex                                          

Ign http://archive.ubuntu.com precise/restricted Sources/DiffIndex                                   

Ign http://extras.ubuntu.com precise/main i386 Packages/DiffIndex              

Ign http://extras.ubuntu.com precise/main TranslationIndex                                           

Hit http://archive.ubuntu.com precise/main Sources                                                   

Hit http://extras.ubuntu.com precise/main Sources                              

Hit http://archive.ubuntu.com precise/restricted Sources                                       

Hit http://extras.ubuntu.com precise/main i386 Packages               

Get:8 http://security.ubuntu.com precise-security/main Sources [58.4 kB]

Hit http://in.archive.ubuntu.com precise-backports Release                    

Get:9 http://in.archive.ubuntu.com precise-updates Release [49.6 kB]           

Ign http://in.archive.ubuntu.com precise-backports Release                                                    

Get:10 http://security.ubuntu.com precise-security/universe Sources [18.1 kB]                                 

Ign http://in.archive.ubuntu.com precise/main Sources/DiffIndex                          

Ign http://in.archive.ubuntu.com precise/universe Sources/DiffIndex                                      

Ign http://in.archive.ubuntu.com precise/restricted Sources/DiffIndex           

Ign http://in.archive.ubuntu.com precise/multiverse Sources/DiffIndex

Get:11 http://in.archive.ubuntu.com precise/main i386 Packages [1,274 kB]

Ign http://extras.ubuntu.com precise/main Translation-en_IN                               

Get:12 http://security.ubuntu.com precise-security/restricted Sources [1,950 B]                         

Get:13 http://security.ubuntu.com precise-security/multiverse Sources [1,392 B]             

Get:14 http://security.ubuntu.com precise-security/main i386 Packages [215 kB]                                   

Ign http://extras.ubuntu.com precise/main Translation-en                                                        

Get:15 http://security.ubuntu.com precise-security/universe i386 Packages [59.2 kB]

Get:16 http://security.ubuntu.com precise-security/restricted i386 Packages [3,968 B]

Get:17 http://security.ubuntu.com precise-security/multiverse i386 Packages [2,388 B]

Hit http://security.ubuntu.com precise-security/main TranslationIndex  

Hit http://security.ubuntu.com precise-security/multiverse TranslationIndex

Hit http://security.ubuntu.com precise-security/restricted TranslationIndex

Hit http://security.ubuntu.com precise-security/universe TranslationIndex

Hit http://security.ubuntu.com precise-security/main Translation-en    

Hit http://security.ubuntu.com precise-security/multiverse Translation-en

Hit http://security.ubuntu.com precise-security/restricted Translation-en

Hit http://security.ubuntu.com precise-security/universe Translation-en

Ign http://in.archive.ubuntu.com precise/universe i386 Packages/DiffIndex

Ign http://in.archive.ubuntu.com precise/restricted i386 Packages/DiffIndex

Ign http://in.archive.ubuntu.com precise/multiverse i386 Packages/DiffIndex

Hit http://in.archive.ubuntu.com precise/main TranslationIndex         

Hit http://in.archive.ubuntu.com precise/multiverse TranslationIndex   

Hit http://in.archive.ubuntu.com precise/restricted TranslationIndex   

Hit http://in.archive.ubuntu.com precise/universe TranslationIndex     

Ign http://in.archive.ubuntu.com precise-backports/main Sources/DiffIndex

Ign http://in.archive.ubuntu.com precise-backports/universe Sources/DiffIndex

Ign http://in.archive.ubuntu.com precise-backports/restricted Sources/DiffIndex

Ign http://in.archive.ubuntu.com precise-backports/multiverse Sources/DiffIndex

Ign http://in.archive.ubuntu.com precise-backports/main i386 Packages/DiffIndex

Ign http://in.archive.ubuntu.com precise-backports/universe i386 Packages/DiffIndex

Ign http://in.archive.ubuntu.com precise-backports/restricted i386 Packages/DiffIndex

Ign http://in.archive.ubuntu.com precise-backports/multiverse i386 Packages/DiffIndex

Hit http://in.archive.ubuntu.com precise-backports/main TranslationIndex

Hit http://in.archive.ubuntu.com precise-backports/multiverse TranslationIndex

Hit http://in.archive.ubuntu.com precise-backports/restricted TranslationIndex

Hit http://in.archive.ubuntu.com precise-backports/universe TranslationIndex

Hit http://in.archive.ubuntu.com precise/main Sources                  

Get:18 http://in.archive.ubuntu.com precise-updates/main Sources [195 kB]

Get:19 http://in.archive.ubuntu.com precise-updates/universe Sources [66.2 kB]

Get:20 http://in.archive.ubuntu.com precise-updates/restricted Sources [4,419 B]

Get:21 http://in.archive.ubuntu.com precise-updates/multiverse Sources [4,241 B]

Get:22 http://in.archive.ubuntu.com precise-updates/main i386 Packages [449 kB]

Get:23 http://in.archive.ubuntu.com precise-updates/universe i386 Packages [162 kB]

Get:24 http://in.archive.ubuntu.com precise-updates/restricted i386 Packages [8,374 B]

Get:25 http://in.archive.ubuntu.com precise-updates/multiverse i386 Packages [9,661 B]

Hit http://in.archive.ubuntu.com precise-updates/main TranslationIndex 

Hit http://in.archive.ubuntu.com precise-updates/multiverse TranslationIndex

Hit http://in.archive.ubuntu.com precise-updates/restricted TranslationIndex

Hit http://in.archive.ubuntu.com precise-updates/universe TranslationIndex

Hit http://in.archive.ubuntu.com precise/universe Sources              

Hit http://in.archive.ubuntu.com precise/restricted Sources            

Hit http://in.archive.ubuntu.com precise/multiverse Sources            

Hit http://in.archive.ubuntu.com precise/universe i386 Packages        

Hit http://in.archive.ubuntu.com precise/restricted i386 Packages      

Hit http://in.archive.ubuntu.com precise/multiverse i386 Packages      

Hit http://in.archive.ubuntu.com precise/main Translation-en           

Hit http://in.archive.ubuntu.com precise/multiverse Translation-en     

Hit http://in.archive.ubuntu.com precise/restricted Translation-en     

Hit http://in.archive.ubuntu.com precise/universe Translation-en       

Hit http://in.archive.ubuntu.com precise-backports/main Sources        

Hit http://in.archive.ubuntu.com precise-backports/universe Sources    

Hit http://in.archive.ubuntu.com precise-backports/restricted Sources  

Hit http://in.archive.ubuntu.com precise-backports/multiverse Sources  

Hit http://in.archive.ubuntu.com precise-backports/main i386 Packages  

Hit http://in.archive.ubuntu.com precise-backports/universe i386 Packages

Hit http://in.archive.ubuntu.com precise-backports/restricted i386 Packages

Hit http://in.archive.ubuntu.com precise-backports/multiverse i386 Packages

Hit http://in.archive.ubuntu.com precise-backports/main Translation-en 

Hit http://in.archive.ubuntu.com precise-backports/multiverse Translation-en

Hit http://in.archive.ubuntu.com precise-backports/restricted Translation-en

Hit http://in.archive.ubuntu.com precise-backports/universe Translation-en

Hit http://in.archive.ubuntu.com precise-updates/main Translation-en   

Hit http://in.archive.ubuntu.com precise-updates/multiverse Translation-en

Hit http://in.archive.ubuntu.com precise-updates/restricted Translation-en

Hit http://in.archive.ubuntu.com precise-updates/universe Translation-en

Fetched 2,633 kB in 50s (52.6 kB/s)                                    

Reading package lists... Error!

W: GPG error: http://archive.ubuntu.com precise Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>

W: GPG error: http://extras.ubuntu.com precise Release: The following signatures were invalid: BADSIG 16126D3A3E5C1192 Ubuntu Extras Archive Automatic Signing Key <ftpmaster@ubuntu.com>

W: GPG error: http://in.archive.ubuntu.com precise Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>

W: GPG error: http://in.archive.ubuntu.com precise-backports Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>

E: Encountered a section with no Package: header

E: Problem with MergeList /var/lib/apt/lists/in.archive.ubuntu.com_ubuntu_dists_precise_restricted_binary-i386_Packages

E: The package lists or status file could not be parsed or opened.

Here's what you need to do..

wiz@wiz-PC:/var/lib/apt$ sudo mv lists/ lists.old

wiz@wiz-PC:/var/lib/apt$ sudo mkdir -p lists/partial

wiz@wiz-PC:/var/lib/apt$ sudo apt-get update

You can now delete the lists.old. In case you require to generate a complete new Ubuntu source.lst file use the Ubuntu Sources List Generator

HTH
Wiz