In this post I am sharing, the troubleshooting step of the error which we found on using linux yum command.Error: database disk image is malformed, we found this problem running the command yum update

To resolve this issue run the below given command

yum clean dbcache

If still issue persist,run below given command

yum clean all

As per man page of yum :

yum clean dbcache
Eliminate the sqlite cache used for faster access to metadata. Using this option will force yum to download the sqlite metadata the next time it is run, or recreate the sqlite metadata if using an older repo

Given below is the reference from our system:

[root@localhost ~]# yum update
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: centos.excellmedia.net
 * epel: epel.mirror.net.in
 * extras: centos.excellmedia.net
 * updates: centos.excellmedia.net
Error: database disk image is malformed
[root@localhost ~]# yum update
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: centos.excellmedia.net
 * epel: epel.mirror.net.in
 * extras: centos.excellmedia.net
 * updates: centos.excellmedia.net
Error: database disk image is malformed
[root@localhost ~]#
[root@localhost ~]# yum update
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: centos.excellmedia.net
 * epel: epel.mirror.net.in
 * extras: centos.excellmedia.net
 * updates: centos.excellmedia.net
Error: database disk image is malformed
[root@localhost ~]# yum clean dbcache
Loaded plugins: fastestmirror
Cleaning repos: base epel extras updates
5 sqlite files removed
[root@localhost ~]#
[root@localhost ~]# yum update
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: centos.excellmedia.net
 * epel: epel.mirror.net.in
 * extras: centos.excellmedia.net
 * updates: centos.excellmedia.net
base/primary_db                                                                                                                         | 3.5 MB     00:00    
epel/primary_db                                                                                                                         | 4.8 MB     00:01    
extras/primary_db                                                                                                                       |  18 kB     00:00    
updates/primary_db                                                                                                                      | 1.3 MB     00:00    
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package ca-certificates.noarch 0:2013.1.94-65.0.el6 will be updated
---> Package ca-certificates.noarch 0:2013.1.95-65.1.el6_5 will be an update
---> Package ethtool.i686 2:3.5-1.el6 will be updated
---> Package ethtool.i686 2:3.5-1.2.el6_5 will be an update
---> Package kernel.i686 0:2.6.32-431.3.1.el6 will be installed
---> Package kernel-firmware.noarch 0:2.6.32-431.1.2.0.1.el6 will be updated
---> Package kernel-firmware.noarch 0:2.6.32-431.3.1.el6 will be an update
---> Package nss.i686 0:3.15.3-2.el6_5 will be updated
---> Package nss.i686 0:3.15.3-3.el6_5 will be an update
---> Package nss-sysinit.i686 0:3.15.3-2.el6_5 will be updated
---> Package nss-sysinit.i686 0:3.15.3-3.el6_5 will be an update
---> Package nss-tools.i686 0:3.15.3-2.el6_5 will be updated
---> Package nss-tools.i686 0:3.15.3-3.el6_5 will be an update
---> Package openssl.i686 0:1.0.1e-16.el6_5 will be updated
---> Package openssl.i686 0:1.0.1e-16.el6_5.4 will be an update
---> Package tzdata.noarch 0:2013g-1.el6 will be updated
---> Package tzdata.noarch 0:2013i-1.el6 will be an update
---> Package yum.noarch 0:3.2.29-40.el6.centos will be updated
---> Package yum.noarch 0:3.2.29-43.el6.centos will be an update
--> Finished Dependency Resolution

Dependencies Resolved

===============================================================================================================================================================
 Package                                  Arch                            Version                                       Repository                        Size
===============================================================================================================================================================
Installing:
 kernel                                   i686                            2.6.32-431.3.1.el6                            updates                           26 M
Updating:
 ca-certificates                          noarch                          2013.1.95-65.1.el6_5                          updates                          1.1 M
 ethtool                                  i686                            2:3.5-1.2.el6_5                               updates                           97 k
 kernel-firmware                          noarch                          2.6.32-431.3.1.el6                            updates                           13 M
 nss                                      i686                            3.15.3-3.el6_5                                updates                          825 k
 nss-sysinit                              i686                            3.15.3-3.el6_5                                updates                           40 k
 nss-tools                                i686                            3.15.3-3.el6_5                                updates                          367 k
 openssl                                  i686                            1.0.1e-16.el6_5.4                             updates                          1.5 M
 tzdata                                   noarch                          2013i-1.el6                                   updates                          447 k
 yum                                      noarch                          3.2.29-43.el6.centos                          updates                          996 k

Transaction Summary
===============================================================================================================================================================
Install       1 Package(s)
Upgrade       9 Package(s)

Total download size: 44 M
Is this ok [y/N]: y