Analysis of the project failed after upgrading to SonarQube 5.0

We perform SonarQube analysis for Java Java projects using Jenkins Plugin, everything works fine with SonarQube version 4.0, but after upgrading to 5.0 I see the following messages on the console output:

16:07:06 16:07:05.662 INFO  - Sensor ScmStatsSensor done: 576 ms
16:07:06 16:07:05.662 INFO  - Sensor InitialOpenIssuesSensor...
16:07:06 16:07:05.948 INFO  - Sensor InitialOpenIssuesSensor done: 286 ms
16:07:06 16:07:05.948 INFO  - Sensor ProjectLinksSensor...
16:07:06 16:07:06.095 INFO  - Sensor ProjectLinksSensor done: 147 ms
16:07:06 16:07:06.165 INFO  - Sensor VersionEventsSensor...
16:07:07 16:07:06.447 INFO  - Sensor VersionEventsSensor done: 282 ms
16:07:07 16:07:06.447 INFO  - Sensor FileHashSensor...
16:07:07 16:07:06.465 INFO  - Sensor FileHashSensor done: 18 ms
16:07:07 16:07:06.465 INFO  - Sensor SCM Sensor...
16:07:07 16:07:06.485 INFO  - SCM provider for this project is: git
16:07:07 16:07:06.485 INFO  - Retrieve SCM blame information...
16:07:07 16:07:06.493 INFO  - 175 files to be analyzed
16:07:10 16:07:09.710 INFO  - Retrieve SCM blame information done: 3225 ms
16:07:10 16:07:09.710 INFO  - Sensor SCM Sensor done: 3245 ms
16:07:10 16:07:09.710 INFO  - Sensor CPD Sensor...
16:07:10 16:07:09.710 INFO  - 175/175 files analyzed
16:07:10 16:07:09.711 INFO  - JavaCpdEngine is used for java
16:07:10 16:07:09.722 INFO  - Cross-project analysis disabled
16:07:11 16:07:10.365 INFO  - Sensor CPD Sensor done: 655 ms
16:07:11 16:07:10.610 INFO  - Execute decorators...
16:07:29 16:07:28.875 INFO  - Store results in database
16:08:10 16:08:09.762 WARN  - Unexpected exception on closing transaction.  Cause: java.sql.SQLException: Already closed.
16:08:10 16:08:09.772 WARN  - Unexpected exception on closing transaction.  Cause: java.sql.SQLException: Already closed.
16:08:10 INFO: ------------------------------------------------------------------------
16:08:10 INFO: EXECUTION FAILURE
16:08:10 INFO: ------------------------------------------------------------------------
16:08:10 Total time: 5:08.498s
16:08:11 Final Memory: 89M/834M
16:08:11 INFO: ------------------------------------------------------------------------
16:08:11 ERROR: Error during Sonar runner execution
16:08:11 ERROR: Unable to execute Sonar
16:08:11 ERROR: Caused by: Unable to save file sources
16:08:11 ERROR: Caused by: 
16:08:11 ### Error committing transaction.  Cause: org.postgresql.util.PSQLException: An I/O error occurred while sending to the backend.
16:08:11 ### Cause: org.postgresql.util.PSQLException: An I/O error occurred while sending to the backend.
16:08:11 ERROR: Caused by: An I/O error occurred while sending to the backend.
16:08:11 ERROR: 
16:08:11 ERROR: To see the full stack trace of the errors, re-run SonarQube Runner with the -e switch.
16:08:11 ERROR: Re-run SonarQube Runner using the -X switch to enable full debug logging.
16:08:11 Build step 'Invoke Standalone Sonar Analysis' marked build as failure
16:08:11 [locks-and-latches] Releasing all the locks
16:08:11 [locks-and-latches] All the locks released
16:08:11 Finished: FAILURE

Another Android Project event log is slightly different:

18:30:22.646 INFO  - Load module settings
18:30:35.302 INFO  - Language is forced to java
18:30:35.306 INFO  - Loading rules...
18:30:37.220 INFO  - Loading rules done: 1914 ms
18:30:37.253 INFO  - Configure Maven plugins
18:30:37.616 INFO  - No quality gate is configured.
18:30:38.168 INFO  - Base dir: <base dir path>
18:30:38.168 INFO  - Working dir:<working dir path>
18:30:38.169 INFO  - Source paths: app/src/main
18:30:38.169 INFO  - Source encoding: UTF-8, default locale: en_US
18:30:38.170 INFO  - Index files
18:30:40.158 INFO  - 525 files indexed
18:31:01.142 WARN  - SQL Error: 0, SQLState: 08006
18:31:01.143 ERROR - An I/O error occurred while sending to the backend.
18:31:01.459 WARN  - Unexpected exception on closing transaction.  Cause: java.sql.SQLException: Already closed.
INFO: ------------------------------------------------------------------------
INFO: EXECUTION FAILURE
INFO: ------------------------------------------------------------------------
Total time: 1:40.863s
Final Memory: 51M/648M
INFO: ------------------------------------------------------------------------
ERROR: Error during Sonar runner execution
ERROR: Unable to execute Sonar
ERROR: Caused by: org.hibernate.exception.JDBCConnectionException: could not execute query
ERROR: Caused by: could not execute query
ERROR: Caused by: An I/O error occurred while sending to the backend.
ERROR: 
ERROR: To see the full stack trace of the errors, re-run SonarQube Runner with the -e switch.
ERROR: Re-run SonarQube Runner using the -X switch to enable full debug logging.
Build step 'Invoke Standalone Sonar Analysis' marked build as failure
An attempt to send an e-mail to empty list of recipients, ignored.
Finished: FAILURE

We use PostgreSQL 9.3.6 on the SonarQube server. Any suggestions on how to fix this problem would be greatly appreciated!

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