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How do I resolve 500 errors received while re-indexing?

How do I resolve 500 errors received while re-indexing?

Getting this error when trying to do a re-index:

Technical details
Log's referral number: 966feac7-fe16-4006-b6ac-7f8f2d8b27d4

Cause
Referer URL: http://sundown.swpayroll.local:8080/secure/admin/jira/IndexProgress.jspa?taskId=12901

java.lang.NullPointerException
java.lang.NullPointerException
at com.atlassian.jira.web.action.admin.index.IndexAdminImpl.doProgress(IndexAdminImpl.java:395)
at sun.reflect.GeneratedMethodAccessor34399.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at webwork.util.InjectionUtils$DefaultInjectionImpl.invoke(InjectionUtils.java:70)
at webwork.util.InjectionUtils.invoke(InjectionUtils.java:56)
at webwork.action.ActionSupport.invokeCommand(ActionSupport.java:438)
at webwork.action.ActionSupport.execute(ActionSupport.java:157)
at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:88)
at webwork.interceptor.DefaultInterceptorChain.proceed(DefaultInterceptorChain.java:39)
at webwork.interceptor.NestedInterceptorChain.proceed(NestedInterceptorChain.java:31)
at webwork.interceptor.ChainedInterceptor.intercept(ChainedInterceptor.java:16)
at webwork.interceptor.DefaultInterceptorChain.proceed(DefaultInterceptorChain.java:35)
at webwork.dispatcher.GenericDispatcher.executeAction(GenericDispatcher.java:225)
at webwork.dispatcher.GenericDispatcher.executeAction(GenericDispatcher.java:154)
at com.atlassian.jira.web.dispatcher.JiraWebworkActionDispatcher.service(JiraWebworkActionDispatcher.java:152)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:87)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.atlassian.jira.web.filters.XContentTypeOptionsNoSniffFilter.doFilter(XContentTypeOptionsNoSniffFilter.java:22)
at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.atlassian.core.filters.HeaderSanitisingFilter.doFilter(HeaderSanitisingFilter.java:44)
...

2 answers

1 accepted

0 votes

Answer accepted

That's a lot to parse through, but I think the important bit is this:

2018-06-13 19:50:17,058 IssueIndexer:thread-2 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lc.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
com.atlassian.jira.util.RuntimeIOException: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lc.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)

Which indicates to me, there is some other application on this system (most likely an antivirus product like mcafee or symantec) that is messing up your indexes that Jira is trying to create. Since there is a java.io.FileNotFoundException, that part tells us that something on the system has quarantined or removed this file. I am inclined to believe this is a false positive on the part of the antivirus product.

Please see the KB: Anti-Virus in JIRA applications

We know that running these kinds of application can directly interfere with Jira's operations. Some more so than others. If you can't completely remove the antivirus from this system, then I would strongly suggest that you at least exclude the $JIRAHOME and $JIRAINSTALL directories on your system so that Jira can continue to operate without encountering this particular error.

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Comment

That did the trick...Thanks for the help...I've passed the information along to our Information Security department

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Comment

1 vote

Sorry this error does not provide a clear source of this problem yet. I'd recommend trying to follow the steps in this KB: Unable to rebuild JIRA application indexes

Stop JIRA
Make a backup of the following directory and all its sub-directories:
$JIRA_HOME/caches/indexes
Remove that directory and all its sub-directories:
$JIRA_HOME/caches/indexes
This will be rebuilt when JIRA is re-indexed
Start JIRA

Perform a locked/full re-index of JIRA

These steps should be enough to let Jira recreate these indexes fresh if the indexes themselves are corrupted. Try these steps, and if you are still seeing problem with recreating the indexes, I would want to see more information from your logs to better understand what might cause this.

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Comment

Performed the above steps and on completion of step 5, received a similar error (see snippet below):

Technical details

Log's referral number: 387d05c4-25e1-4b71-b743-539e4d965793

Cause

Referer URL: http://sundown.swpayroll.local:8080/secure/admin/jira/IndexProgress.jspa?taskId=13000

java.lang.NullPointerException

java.lang.NullPointerException
 at com.atlassian.jira.web.action.admin.index.IndexAdminImpl.doProgress(IndexAdminImpl.java:395)
 at sun.reflect.GeneratedMethodAccessor691.invoke(Unknown Source)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
 at java.lang.reflect.Method.invoke(Method.java:498)
 at webwork.util.InjectionUtils$DefaultInjectionImpl.invoke(InjectionUtils.java:70)
 at webwork.util.InjectionUtils.invoke(InjectionUtils.java:56)
 at webwork.action.ActionSupport.invokeCommand(ActionSupport.java:438)
 at webwork.action.ActionSupport.execute(ActionSupport.java:157)
 at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:88)
 at webwork.interceptor.DefaultInterceptorChain.proceed(DefaultInterceptorChain.java:39)
 at webwork.interceptor.NestedInterceptorChain.proceed(NestedInterceptorChain.java:31)
 at webwork.interceptor.ChainedInterceptor.intercept(ChainedInterceptor.java:16)
 at webwork.interceptor.DefaultInterceptorChain.proceed(DefaultInterceptorChain.java:35)
 at webwork.dispatcher.GenericDispatcher.executeAction(GenericDispatcher.java:225)
 at webwork.dispatcher.GenericDispatcher.executeAction(GenericDispatcher.java:154)
 at com.atlassian.jira.web.dispatcher.JiraWebworkActionDispatcher.service(JiraWebworkActionDispatcher.java:152)
 at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
 at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
 at com.atlassian.jira.web.filters.steps.ChainedFilterStepRunner.doFilter(ChainedFilterStepRunner.java:87)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
 at com.atlassian.jira.web.filters.XContentTypeOptionsNoSniffFilter.doFilter(XContentTypeOptionsNoSniffFilter.java:22)
 at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
 at com.atlassian.core.filters.HeaderSanitisingFilter.doFilter(HeaderSanitisingFilter.java:44)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:70)
 at com.atlassian.jira.onboarding.postsetup.ui.PostSetupAnnouncementsFilter.doFilter(PostSetupAnnouncementsFilter.java:61)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:78)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:70)
 at com.atlassian.jira.tzdetect.IncludeResourcesFilter.doFilter(IncludeResourcesFilter.java:40)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:78)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:70)
 at com.atlassian.jira.baseurl.IncludeResourcesFilter.doFilter(IncludeResourcesFilter.java:38)
 at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:78)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:70)
 at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:25)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:78)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:70)
 at com.atlassian.servicedesk.internal.web.RedirectExternalCustomerToPortalFilter.doFilter(RedirectExternalCustomerToPortalFilter.scala:18)
 at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)

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Comment

Rather than just focusing on that specific stacktrace, I'd like to see what is in the rest of the $JIRAHOME/log/atlassian-jira.log file at this time and just before. This should help us understand more about this problem and what might be causing this.

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Comment

See below (part 1):

2018-06-13 19:43:06,636 localhost-startStop-1 INFO [jira.upgrade.util.BuildNumberDao] Setting current version to 6.4.8
2018-06-13 19:43:06,646 localhost-startStop-1 INFO [jira.upgrade.util.BuildNumberDao] Setting downgrade version to 6.3.12
2018-06-13 19:43:06,671 localhost-startStop-1 INFO [jira.whatsnew.listeners.WhatsNewUpgradeFinishedListenerImpl] Enabling show-whats-new-flag for all users
2018-06-13 19:43:06,701 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.atlassian.jira.welcome.jira-welcome-plugin:show-whats-new-flag' was null. Not enabling.
2018-06-13 19:43:07,361 UpmScheduler:thread-1 WARN anonymous [atlassian.jira.security.GlobalPermissionsCache] Could not add permission Global Permission: [group=administrators][permissionKey=ADMINISTER] - it already existed?
2018-06-13 19:43:07,386 UpmScheduler:thread-1 WARN anonymous [atlassian.jira.security.GlobalPermissionsCache] Could not add permission Global Permission: [group=administrators][permissionKey=ADMINISTER] - it already existed?
2018-06-13 19:43:07,401 UpmScheduler:thread-1 WARN anonymous [atlassian.jira.security.GlobalPermissionsCache] Could not add permission Global Permission: [group=confluence-administrators][permissionKey=SYSTEM_ADMIN] - it already existed?
2018-06-13 19:43:08,521 localhost-startStop-1 INFO [timedpromise.internal.bootstrap.TimedPromiseLauncher] Timed Promises is initializing...
2018-06-13 19:43:08,626 localhost-startStop-1 INFO [timedpromise.internal.bootstrap.TimedPromiseLauncher] Timed Promises is initialized.
2018-06-13 19:43:08,757 UpmScheduler:thread-1 WARN anonymous [atlassian.upm.pac.PacClientImpl] Update check request may take longer because of the number of add-ons
2018-06-13 19:43:19,987 Modification Check:thread-1 INFO [atlassian.jira.startup.JiraStartupLogger]

___ Modifications ___________________________

Modified Files : jira-application.properties, seraph-config.xml
Removed Files : None

2018-06-13 19:43:25,017 localhost-startStop-1 INFO [plugins.hipchat.service.HipChatPluginLauncher] HipChat Plugin launched successfully
2018-06-13 19:43:29,098 localhost-startStop-1 INFO [ext.bamboo.service.PlanStatusUpdateServiceImpl] Job 'com.atlassian.jira.plugin.ext.bamboo.service.PlanStatusUpdateServiceImpl:job' scheduled to run every 60000ms
2018-06-13 19:43:29,133 localhost-startStop-1 INFO [automation.internal.bootstrap.AutomationPluginLauncher] Service Desk Automation Plugin is starting...
2018-06-13 19:43:35,098 localhost-startStop-1 INFO [automation.internal.bootstrap.AutomationPluginLauncher] Service Desk Automation Plugin is started.
2018-06-13 19:43:35,108 localhost-startStop-1 INFO [plugins.dvcs.scheduler.DvcsScheduler] DvcsScheduler job handler registered
2018-06-13 19:43:35,143 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle]

*********************************************************************************
JIRA ServiceDesk v2.5.9 #DevVersion built 2015-10-13T00:54:57.908-05:00 - Starting initialisation...
*********************************************************************************

2018-06-13 19:43:35,148 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Checking licensing...
2018-06-13 19:43:35,148 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Checking for add on downgrade...
2018-06-13 19:43:35,153 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Initialising ActiveObjects support and running AO upgrade tasks...
2018-06-13 19:43:35,158 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Running add on upgrade tasks...
2018-06-13 19:43:35,208 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle]

*********************************************************************************
JIRA ServiceDesk v2.5.9 #DevVersion built 2015-10-13T00:54:57.908-05:00 -
Description : JIRA Service Desk (Server) 3 Agents: Starter License
Type : COMMERCIAL
Valid : true
Maintenance Expiry : 02-08-2018
Maximum Users : 3
Organisation : Netchex
SEN : SEN-5509673
*********************************************************************************

2018-06-13 19:43:35,218 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Loading dynamic modules...
2018-06-13 19:43:44,994 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Registering event listeners...
2018-06-13 19:43:44,999 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Adding customer fields support...
2018-06-13 19:43:45,161 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Adding Service Desk Request Participants custom field...
2018-06-13 19:43:45,299 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Invalidating look and feel cache...
2018-06-13 19:43:45,334 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Adding auto watch handler...
2018-06-13 19:43:45,339 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Adding security type...
2018-06-13 19:43:45,394 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Adding project roles...
2018-06-13 19:43:45,874 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Attempt to register timed promise task runners...
2018-06-13 19:43:52,074 localhost-startStop-1 INFO [atlassian.servicedesk.bootstrap.lifecycle] Registering async upgrade tasks...
2018-06-13 19:43:52,179 localhost-startStop-1 INFO [servicedesk.bootstrap.lifecycle.TenantAwareneODMailInitialiser] Initialize configuration on tenant ready...
2018-06-13 19:43:52,224 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle] Registering Service Desk async job runner
2018-06-13 19:43:52,239 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle] Registered Service Desk async job runner successfully
2018-06-13 19:43:52,239 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle] Service Desk Async upgrade tasks set to run at Wed Jun 13 21:32:58 CDT 2018 (in 01:49:05 from current date of Wed Jun 13 19:43:52 CDT 2018)
2018-06-13 19:43:52,269 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle] Successfully scheduled jobId=sd.async.upgrade.tasks.job.runner
2018-06-13 19:43:52,269 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle]

*********************************************************************************
JIRA ServiceDesk v2.5.9 #DevVersion built 2015-10-13T00:54:57.908-05:00 - Finished initialisation.
*********************************************************************************

2018-06-13 19:43:52,284 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle]

JIRA ServiceDesk Run History

*JIRA ServiceDesk v2.3-OD-08-002-D20150218T054701 (DevVersion) started at 01 Mar 2015 02:40

2018-06-13 19:43:52,324 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle]

The following JIRA ServiceDesk upgrade tasks have been run on this system

UpgradeTask AO-1 started at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion)
UpgradeTask AO-1 ended at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion) and took 1107 ms
UpgradeTask AO-201 started at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion)
UpgradeTask AO-201 ended at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion) and took 432 ms
UpgradeTask AO-300 started at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion)
UpgradeTask AO-300 ended at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion) and took 536 ms
UpgradeTask AO-400 started at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion)
UpgradeTask AO-400 ended at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion) and took 676 ms
UpgradeTask AO-501 started at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion)
UpgradeTask AO-501 ended at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion) and took 1338 ms
UpgradeTask UPG-1 started at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion)
UpgradeTask UPG-1 ended at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion) and took 0 ms
UpgradeTask UPG-2 started at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion)
UpgradeTask UPG-2 ended at 01 Mar 2015 02:39 within v2.3-OD-08-002-D20150218T054701 (DevVersion) and took 13 ms

2018-06-13 19:43:52,334 localhost-startStop-1 INFO [atlassian.servicedesk.lifecycle]

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Comment

See below (part 2):

*********************************************************************************
JIRA ServiceDesk v2.5.9 #DevVersion built 2015-10-13T00:54:57.908-05:00 - started. How can we help you?
*********************************************************************************

2018-06-13 19:43:52,364 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-agile-shortcut' was null. Not enabling.
2018-06-13 19:43:52,369 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-taskboard-shortcut' was null. Not enabling.
2018-06-13 19:43:52,369 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-chartboard-shortcut' was null. Not enabling.
2018-06-13 19:43:52,369 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-releasedboard-shortcut' was null. Not enabling.
2018-06-13 19:43:52,369 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-boardsearch-shortcut' was null. Not enabling.
2018-06-13 19:43:52,369 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-nextcolumn-shortcut' was null. Not enabling.
2018-06-13 19:43:52,374 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-prevcolumn-shortcut' was null. Not enabling.
2018-06-13 19:43:52,389 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-toggledetailview-shortcut' was null. Not enabling.
2018-06-13 19:43:52,389 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-priority-shortcut' was null. Not enabling.
2018-06-13 19:43:52,389 localhost-startStop-1 INFO [atlassian.plugin.manager.DefaultPluginManager] Returned module for key 'com.pyxis.greenhopper.jira:greenhopper-delete-shortcut' was null. Not enabling.
2018-06-13 19:43:52,389 localhost-startStop-1 INFO [greenhopper.plugin.sampledata.JiraImportersPluginInstallerImpl] Checking if jira-importers-plugin is present and at version 4.4 or higher
2018-06-13 19:43:52,394 localhost-startStop-1 INFO [greenhopper.plugin.sampledata.JiraImportersPluginInstallerImpl] jira-importers-plugin already at 7.0.12.
2018-06-13 19:43:52,849 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10022'.
2018-06-13 19:43:52,879 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10000'.
2018-06-13 19:43:52,879 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10001'.
2018-06-13 19:43:52,884 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10002'.
2018-06-13 19:43:52,939 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10013'.
2018-06-13 19:43:52,944 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10014'.
2018-06-13 19:43:52,944 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10015'.
2018-06-13 19:43:52,949 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10020'.
2018-06-13 19:43:52,949 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10021'.
2018-06-13 19:43:52,949 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10023'.
2018-06-13 19:43:52,954 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10024'.
2018-06-13 19:43:52,984 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10016'.
2018-06-13 19:43:52,989 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10017'.
2018-06-13 19:43:52,994 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10018'.
2018-06-13 19:43:52,994 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10019'.
2018-06-13 19:43:53,054 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10028'.
2018-06-13 19:43:53,059 localhost-startStop-1 INFO [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10029'.
2018-06-13 19:43:56,714 localhost-startStop-1 INFO [greenhopper.service.logging.LogSupport]

Managed Issue Types
Epic id=10005 name=Epic
Story id=10100 name=Story

Managed Custom Fields
Epic Colour id=customfield_10011 name=Epic Color type=com.pyxis.greenhopper.jira:gh-epic-color
Epic Link id=customfield_10008 name=Epic Link type=com.pyxis.greenhopper.jira:gh-epic-link
Epic Name id=customfield_10009 name=Epic Name type=com.pyxis.greenhopper.jira:gh-epic-label
Epic Status id=customfield_10010 name=Epic Status type=com.pyxis.greenhopper.jira:gh-epic-status
Default Global Rank id=customfield_10012 name=Rank type=com.pyxis.greenhopper.jira:gh-lexo-rank
Sprint id=customfield_10007 name=Sprint type=com.pyxis.greenhopper.jira:gh-sprint
Story Points id=customfield_10005 name=Story Points type=com.atlassian.jira.plugin.system.customfieldtypes:float

Managed Issue Link Types
Epic Link Issue Link Type id=10200 name=Epic-Story Link

2018-06-13 19:43:57,219 localhost-startStop-1 INFO [atlassian.jira.scheduler.JiraSchedulerLauncher] Starting the JIRA Scheduler....
2018-06-13 19:43:57,314 localhost-startStop-1 INFO [atlassian.jira.scheduler.JiraSchedulerLauncher] JIRA Scheduler started.
2018-06-13 19:43:57,984 localhost-startStop-1 INFO [atlassian.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 322 MiB. Committed: 392 MiB. Max: 742 MiB
Non-heap memory : Used: 123 MiB. Committed: 128 MiB. Max: 32 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 445 MiB. Committed: 520 MiB. Max: 774 MiB
---------------------------------------------------------------------------------

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See below (part 3):

2018-06-13 19:44:59,048 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10022'.
2018-06-13 19:44:59,058 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10000'.
2018-06-13 19:44:59,058 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10001'.
2018-06-13 19:44:59,058 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10002'.
2018-06-13 19:44:59,063 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10013'.
2018-06-13 19:44:59,063 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10014'.
2018-06-13 19:44:59,063 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10015'.
2018-06-13 19:44:59,063 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10020'.
2018-06-13 19:44:59,063 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10021'.
2018-06-13 19:44:59,063 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10023'.
2018-06-13 19:44:59,068 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10024'.
2018-06-13 19:44:59,083 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10016'.
2018-06-13 19:44:59,083 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10017'.
2018-06-13 19:44:59,083 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10018'.
2018-06-13 19:44:59,088 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10019'.
2018-06-13 19:44:59,088 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10028'.
2018-06-13 19:44:59,088 http-bio-8080-exec-3 INFO jschock 1184x35x2 cwe81y 10.10.10.5 /rest/gadget/1.0/issueTable/jql [fields.layout.field.AbstractFieldLayoutManager] Field layout contains non-orderable field with id 'customfield_10029'.
2018-06-13 19:45:09,854 http-bio-8080-exec-21 WARN jschock 1184x127x4 cwe81y 10.10.10.5 /plugins/servlet/streams [atlassian.streams.internal.StreamsCompletionService] Registering failure for stream provider Bitbucket Connector due to cancellation (timeout)
2018-06-13 19:45:09,874 http-bio-8080-exec-21 WARN jschock 1184x127x4 cwe81y 10.10.10.5 /plugins/servlet/streams [atlassian.streams.internal.StreamsCompletionService] Registering failure for stream provider Bitbucket Connector due to error timeout
2018-06-13 19:45:09,879 http-bio-8080-exec-21 WARN jschock 1184x127x4 cwe81y 10.10.10.5 /plugins/servlet/streams [atlassian.streams.internal.StreamsCompletionService] Registering failure for stream provider JIRA due to cancellation (timeout)
2018-06-13 19:45:09,879 http-bio-8080-exec-21 WARN jschock 1184x127x4 cwe81y 10.10.10.5 /plugins/servlet/streams [atlassian.streams.internal.StreamsCompletionService] Registering failure for stream provider JIRA due to error timeout
2018-06-13 19:45:09,884 http-bio-8080-exec-21 WARN jschock 1184x127x4 cwe81y 10.10.10.5 /plugins/servlet/streams [atlassian.streams.internal.StreamsCompletionService] Registering failure for stream provider Confluence due to cancellation (timeout)
2018-06-13 19:45:09,884 http-bio-8080-exec-21 WARN jschock 1184x127x4 cwe81y 10.10.10.5 /plugins/servlet/streams [atlassian.streams.internal.StreamsCompletionService] Registering failure for stream provider Confluence due to error timeout
2018-06-13 19:45:09,884 http-bio-8080-exec-21 WARN jschock 1184x127x4 cwe81y 10.10.10.5 /plugins/servlet/streams [atlassian.streams.internal.StreamsCompletionService] Registering failure for stream provider Confluence - 2 due to cancellation (timeout)
2018-06-13 19:45:09,884 http-bio-8080-exec-21 WARN jschock 1184x127x4 cwe81y 10.10.10.5 /plugins/servlet/streams [atlassian.streams.internal.StreamsCompletionService] Registering failure for stream provider Confluence - 2 due to error timeout
2018-06-13 19:45:18,904 http-bio-8080-exec-5 WARN jschock 1185x182x1 cwe81y 10.10.10.5 /secure/admin/IndexAdmin.jspa [jira.issue.index.IndexConsistencyUtils] Index consistency check failed for index 'Issue': expectedCount=6859; actualCount=0
2018-06-13 19:45:34,945 JiraTaskExectionThread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing started
2018-06-13 19:45:34,955 JiraTaskExectionThread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [jira.util.index.CompositeIndexLifecycleManager] Reindex All starting...
2018-06-13 19:45:34,960 JiraTaskExectionThread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 0% complete. Current index: Issue
2018-06-13 19:45:34,975 JiraTaskExectionThread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [jira.issue.index.DefaultIndexManager] Reindexing: {indexIssues=true, indexChangeHistory=true, indexComments=true, indexWorklogs=true}
2018-06-13 19:45:41,610 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 1% complete. Current index: Issue
2018-06-13 19:45:46,526 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 2% complete. Current index: Issue
2018-06-13 19:45:52,266 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 3% complete. Current index: Issue
2018-06-13 19:45:58,351 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 4% complete. Current index: Issue
2018-06-13 19:46:04,422 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 5% complete. Current index: Issue
2018-06-13 19:46:09,812 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 6% complete. Current index: Issue
2018-06-13 19:46:15,903 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 7% complete. Current index: Issue
2018-06-13 19:46:21,783 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 8% complete. Current index: Issue
2018-06-13 19:46:27,768 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 9% complete. Current index: Issue
2018-06-13 19:46:33,214 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 10% complete. Current index: Issue
2018-06-13 19:46:38,934 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 11% complete. Current index: Issue
2018-06-13 19:46:44,929 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 12% complete. Current index: Issue
2018-06-13 19:46:50,810 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 13% complete. Current index: Issue
2018-06-13 19:46:56,145 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 14% complete. Current index: Issue
2018-06-13 19:47:01,867 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 15% complete. Current index: Issue
2018-06-13 19:47:07,747 IssueIndexer:thread-9 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 16% complete. Current index: Issue
2018-06-13 19:47:13,329 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 17% complete. Current index: Issue
2018-06-13 19:47:19,019 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 18% complete. Current index: Issue
2018-06-13 19:47:24,812 IssueIndexer:thread-7 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 19% complete. Current index: Issue
2018-06-13 19:47:30,294 IssueIndexer:thread-7 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 20% complete. Current index: Issue
2018-06-13 19:47:35,829 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 21% complete. Current index: Issue
2018-06-13 19:47:41,432 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 22% complete. Current index: Issue
2018-06-13 19:47:48,124 IssueIndexer:thread-9 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 23% complete. Current index: Issue
2018-06-13 19:47:53,979 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 24% complete. Current index: Issue
2018-06-13 19:48:00,015 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 25% complete. Current index: Issue
2018-06-13 19:48:05,065 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 26% complete. Current index: Issue
2018-06-13 19:48:12,115 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 27% complete. Current index: Issue
2018-06-13 19:48:18,436 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 28% complete. Current index: Issue
2018-06-13 19:48:24,666 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 29% complete. Current index: Issue
2018-06-13 19:48:30,771 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 30% complete. Current index: Issue
2018-06-13 19:48:37,262 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 31% complete. Current index: Issue
2018-06-13 19:48:43,592 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 32% complete. Current index: Issue
2018-06-13 19:48:50,193 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 33% complete. Current index: Issue
2018-06-13 19:48:56,483 IssueIndexer:thread-10 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 34% complete. Current index: Issue
2018-06-13 19:49:02,973 IssueIndexer:thread-7 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 35% complete. Current index: Issue
2018-06-13 19:49:09,664 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 36% complete. Current index: Issue
2018-06-13 19:49:15,559 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 37% complete. Current index: Issue
2018-06-13 19:49:21,909 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 38% complete. Current index: Issue
2018-06-13 19:49:28,525 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 39% complete. Current index: Issue
2018-06-13 19:49:35,080 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 40% complete. Current index: Issue
2018-06-13 19:49:41,126 IssueIndexer:thread-10 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 41% complete. Current index: Issue
2018-06-13 19:49:47,816 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 42% complete. Current index: Issue
2018-06-13 19:49:53,516 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 43% complete. Current index: Issue
2018-06-13 19:50:00,387 IssueIndexer:thread-7 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 44% complete. Current index: Issue
2018-06-13 19:50:06,452 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 45% complete. Current index: Issue
2018-06-13 19:50:11,762 IssueIndexer:thread-9 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 46% complete. Current index: Issue
2018-06-13 19:50:17,058 IssueIndexer:thread-2 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16979'

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Comment

See below (part 4):

2018-06-13 19:50:17,058 IssueIndexer:thread-2 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lc.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
com.atlassian.jira.util.RuntimeIOException: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lc.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:147)
at com.atlassian.jira.index.DefaultIndexEngine$WriterReference.commit(DefaultIndexEngine.java:285)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy$2.commit(DefaultIndexEngine.java:78)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy.perform(DefaultIndexEngine.java:148)
at com.atlassian.jira.index.DefaultIndexEngine.write(DefaultIndexEngine.java:217)
at com.atlassian.jira.index.DefaultIndex.perform(DefaultIndex.java:36)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:431)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:412)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:334)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:330)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:9)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:38)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:35)
at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:85)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lc.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput$Descriptor.<init>(SimpleFSDirectory.java:69)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput.<init>(SimpleFSDirectory.java:90)
at org.apache.lucene.store.FSDirectory.openInput(FSDirectory.java:345)
at org.apache.lucene.index.CompoundFileWriter.copyFile(CompoundFileWriter.java:231)
at org.apache.lucene.index.CompoundFileWriter.close(CompoundFileWriter.java:201)
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:604)
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3543)
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3508)
at org.apache.lucene.index.IndexWriter.prepareCommit(IndexWriter.java:3371)
at org.apache.lucene.index.IndexWriter.commitInternal(IndexWriter.java:3444)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3426)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3410)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:143)
... 18 more
2018-06-13 19:50:17,293 IssueIndexer:thread-9 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16978'
2018-06-13 19:50:17,298 IssueIndexer:thread-9 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1ld.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
com.atlassian.jira.util.RuntimeIOException: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1ld.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:147)
at com.atlassian.jira.index.DefaultIndexEngine$WriterReference.commit(DefaultIndexEngine.java:285)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy$2.commit(DefaultIndexEngine.java:78)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy.perform(DefaultIndexEngine.java:148)
at com.atlassian.jira.index.DefaultIndexEngine.write(DefaultIndexEngine.java:217)
at com.atlassian.jira.index.DefaultIndex.perform(DefaultIndex.java:36)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:431)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:412)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:334)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:330)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:9)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:38)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:35)
at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:85)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1ld.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput$Descriptor.<init>(SimpleFSDirectory.java:69)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput.<init>(SimpleFSDirectory.java:90)
at org.apache.lucene.store.FSDirectory.openInput(FSDirectory.java:345)
at org.apache.lucene.index.CompoundFileWriter.copyFile(CompoundFileWriter.java:231)
at org.apache.lucene.index.CompoundFileWriter.close(CompoundFileWriter.java:201)
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:604)
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3543)
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3508)
at org.apache.lucene.index.IndexWriter.prepareCommit(IndexWriter.java:3371)
at org.apache.lucene.index.IndexWriter.commitInternal(IndexWriter.java:3444)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3426)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3410)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:143)
... 18 more

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See below (part 5):

2018-06-13 19:50:17,468 IssueIndexer:thread-8 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16977'
2018-06-13 19:50:17,468 IssueIndexer:thread-8 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1le.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
com.atlassian.jira.util.RuntimeIOException: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1le.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:147)
at com.atlassian.jira.index.DefaultIndexEngine$WriterReference.commit(DefaultIndexEngine.java:285)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy$2.commit(DefaultIndexEngine.java:78)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy.perform(DefaultIndexEngine.java:148)
at com.atlassian.jira.index.DefaultIndexEngine.write(DefaultIndexEngine.java:217)
at com.atlassian.jira.index.DefaultIndex.perform(DefaultIndex.java:36)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:431)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:412)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:334)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:330)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:9)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:38)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:35)
at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:85)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1le.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput$Descriptor.<init>(SimpleFSDirectory.java:69)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput.<init>(SimpleFSDirectory.java:90)
at org.apache.lucene.store.FSDirectory.openInput(FSDirectory.java:345)
at org.apache.lucene.index.CompoundFileWriter.copyFile(CompoundFileWriter.java:231)
at org.apache.lucene.index.CompoundFileWriter.close(CompoundFileWriter.java:201)
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:604)
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3543)
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3508)
at org.apache.lucene.index.IndexWriter.prepareCommit(IndexWriter.java:3371)
at org.apache.lucene.index.IndexWriter.commitInternal(IndexWriter.java:3444)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3426)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3410)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:143)
... 18 more
2018-06-13 19:50:17,693 IssueIndexer:thread-4 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16974'
2018-06-13 19:50:17,693 IssueIndexer:thread-4 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lf.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
com.atlassian.jira.util.RuntimeIOException: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lf.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:147)
at com.atlassian.jira.index.DefaultIndexEngine$WriterReference.commit(DefaultIndexEngine.java:285)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy$2.commit(DefaultIndexEngine.java:78)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy.perform(DefaultIndexEngine.java:148)
at com.atlassian.jira.index.DefaultIndexEngine.write(DefaultIndexEngine.java:217)
at com.atlassian.jira.index.DefaultIndex.perform(DefaultIndex.java:36)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:431)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:412)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:334)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:330)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:9)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:38)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:35)
at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:85)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lf.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput$Descriptor.<init>(SimpleFSDirectory.java:69)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput.<init>(SimpleFSDirectory.java:90)
at org.apache.lucene.store.FSDirectory.openInput(FSDirectory.java:345)
at org.apache.lucene.index.CompoundFileWriter.copyFile(CompoundFileWriter.java:231)
at org.apache.lucene.index.CompoundFileWriter.close(CompoundFileWriter.java:201)
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:604)
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3543)
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3508)
at org.apache.lucene.index.IndexWriter.prepareCommit(IndexWriter.java:3371)
at org.apache.lucene.index.IndexWriter.commitInternal(IndexWriter.java:3444)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3426)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3410)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:143)
... 18 more
2018-06-13 19:50:17,788 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 47% complete. Current index: Issue
2018-06-13 19:50:18,028 IssueIndexer:thread-6 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16975'
2018-06-13 19:50:18,028 IssueIndexer:thread-6 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lh.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
com.atlassian.jira.util.RuntimeIOException: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lh.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:147)
at com.atlassian.jira.index.DefaultIndexEngine$WriterReference.commit(DefaultIndexEngine.java:285)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy$2.commit(DefaultIndexEngine.java:78)
at com.atlassian.jira.index.DefaultIndexEngine$FlushPolicy.perform(DefaultIndexEngine.java:148)
at com.atlassian.jira.index.DefaultIndexEngine.write(DefaultIndexEngine.java:217)
at com.atlassian.jira.index.DefaultIndex.perform(DefaultIndex.java:36)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:431)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:412)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:334)
at com.atlassian.jira.issue.index.DefaultIssueIndexer$3$1.get(DefaultIssueIndexer.java:330)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:9)
at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:38)
at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:35)
at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:85)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues\_1lh.fdt (Operation did not complete successfully because the file contains a virus or potentially unwanted software)
at java.io.RandomAccessFile.open0(Native Method)
at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput$Descriptor.<init>(SimpleFSDirectory.java:69)
at org.apache.lucene.store.SimpleFSDirectory$SimpleFSIndexInput.<init>(SimpleFSDirectory.java:90)
at org.apache.lucene.store.FSDirectory.openInput(FSDirectory.java:345)
at org.apache.lucene.index.CompoundFileWriter.copyFile(CompoundFileWriter.java:231)
at org.apache.lucene.index.CompoundFileWriter.close(CompoundFileWriter.java:201)
at org.apache.lucene.index.DocumentsWriter.flush(DocumentsWriter.java:604)
at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3543)
at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3508)
at org.apache.lucene.index.IndexWriter.prepareCommit(IndexWriter.java:3371)
at org.apache.lucene.index.IndexWriter.commitInternal(IndexWriter.java:3444)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3426)
at org.apache.lucene.index.IndexWriter.commit(IndexWriter.java:3410)
at com.atlassian.jira.index.WriterWrapper.commit(WriterWrapper.java:143)
... 18 more

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Comment

See below (part 6):

2018-06-13 19:50:24,248 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 48% complete. Current index: Issue
2018-06-13 19:50:29,799 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 49% complete. Current index: Issue
2018-06-13 19:50:35,999 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 50% complete. Current index: Issue
2018-06-13 19:50:42,424 IssueIndexer:thread-7 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 51% complete. Current index: Issue
2018-06-13 19:50:48,380 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 52% complete. Current index: Issue
2018-06-13 19:50:54,570 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 53% complete. Current index: Issue
2018-06-13 19:51:00,800 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 54% complete. Current index: Issue
2018-06-13 19:51:07,551 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 55% complete. Current index: Issue
2018-06-13 19:51:13,966 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 56% complete. Current index: Issue
2018-06-13 19:51:20,176 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 57% complete. Current index: Issue
2018-06-13 19:51:26,252 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 58% complete. Current index: Issue
2018-06-13 19:51:27,042 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16979'
2018-06-13 19:51:27,047 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing completed with 1 errors
com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors
at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:192)
at com.atlassian.jira.index.FutureResult.await(FutureResult.java:32)
at com.atlassian.jira.index.AccumulatingResultBuilder.collectResult(AccumulatingResultBuilder.java:120)
at com.atlassian.jira.index.AccumulatingResultBuilder.addInternal(AccumulatingResultBuilder.java:73)
at com.atlassian.jira.index.AccumulatingResultBuilder.add(AccumulatingResultBuilder.java:42)
at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:1167)
at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:1136)
at com.atlassian.jira.issue.index.DefaultIndexManager.access$100(DefaultIndexManager.java:97)
at com.atlassian.jira.issue.index.DefaultIndexManager$2.run(DefaultIndexManager.java:342)
at com.atlassian.jira.issue.index.DefaultIndexManager.withReindexLock(DefaultIndexManager.java:382)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:337)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:287) <+3> (NativeMethodAccessorImpl.java:62) (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
at com.sun.proxy.$Proxy15.reIndexAll(Unknown Source)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:75)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:55)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:59)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:528)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:491)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:254)
at java.lang.Thread.run(Thread.java:745)
2018-06-13 19:51:27,047 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16978'
2018-06-13 19:51:27,047 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing completed with 1 errors
com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors
at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:192)
at com.atlassian.jira.index.FutureResult.await(FutureResult.java:32)
at com.atlassian.jira.index.AccumulatingResultBuilder.collectResult(AccumulatingResultBuilder.java:120)
at com.atlassian.jira.index.AccumulatingResultBuilder.addInternal(AccumulatingResultBuilder.java:73)
at com.atlassian.jira.index.AccumulatingResultBuilder.add(AccumulatingResultBuilder.java:42)
at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:1167)
at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:1136)
at com.atlassian.jira.issue.index.DefaultIndexManager.access$100(DefaultIndexManager.java:97)
at com.atlassian.jira.issue.index.DefaultIndexManager$2.run(DefaultIndexManager.java:342)
at com.atlassian.jira.issue.index.DefaultIndexManager.withReindexLock(DefaultIndexManager.java:382)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:337)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:287) <+3> (NativeMethodAccessorImpl.java:62) (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
at com.sun.proxy.$Proxy15.reIndexAll(Unknown Source)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:75)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:55)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:59)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:528)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:491)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:254)
at java.lang.Thread.run(Thread.java:745)
2018-06-13 19:51:27,052 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16977'
2018-06-13 19:51:27,052 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing completed with 1 errors
com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors
at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:192)
at com.atlassian.jira.index.FutureResult.await(FutureResult.java:32)
at com.atlassian.jira.index.AccumulatingResultBuilder.collectResult(AccumulatingResultBuilder.java:120)
at com.atlassian.jira.index.AccumulatingResultBuilder.addInternal(AccumulatingResultBuilder.java:73)
at com.atlassian.jira.index.AccumulatingResultBuilder.add(AccumulatingResultBuilder.java:42)
at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:1167)
at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:1136)
at com.atlassian.jira.issue.index.DefaultIndexManager.access$100(DefaultIndexManager.java:97)
at com.atlassian.jira.issue.index.DefaultIndexManager$2.run(DefaultIndexManager.java:342)
at com.atlassian.jira.issue.index.DefaultIndexManager.withReindexLock(DefaultIndexManager.java:382)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:337)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:287) <+3> (NativeMethodAccessorImpl.java:62) (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
at com.sun.proxy.$Proxy15.reIndexAll(Unknown Source)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:75)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:55)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:59)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:528)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:491)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:254)
at java.lang.Thread.run(Thread.java:745)
2018-06-13 19:51:27,052 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16975'
2018-06-13 19:51:27,052 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing completed with 1 errors
com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors
at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:192)
at com.atlassian.jira.index.FutureResult.await(FutureResult.java:32)
at com.atlassian.jira.index.AccumulatingResultBuilder.collectResult(AccumulatingResultBuilder.java:120)
at com.atlassian.jira.index.AccumulatingResultBuilder.addInternal(AccumulatingResultBuilder.java:73)
at com.atlassian.jira.index.AccumulatingResultBuilder.add(AccumulatingResultBuilder.java:42)
at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:1167)
at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:1136)
at com.atlassian.jira.issue.index.DefaultIndexManager.access$100(DefaultIndexManager.java:97)
at com.atlassian.jira.issue.index.DefaultIndexManager$2.run(DefaultIndexManager.java:342)
at com.atlassian.jira.issue.index.DefaultIndexManager.withReindexLock(DefaultIndexManager.java:382)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:337)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:287) <+3> (NativeMethodAccessorImpl.java:62) (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
at com.sun.proxy.$Proxy15.reIndexAll(Unknown Source)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:75)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:55)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:59)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:528)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:491)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:254)
at java.lang.Thread.run(Thread.java:745)

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Comment

See below (part 7):

2018-06-13 19:51:27,057 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing failed for Issue - '16974'
2018-06-13 19:51:27,057 JiraTaskExectionThread-1 WARN jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] Indexing completed with 1 errors
com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors
at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:192)
at com.atlassian.jira.index.FutureResult.await(FutureResult.java:32)
at com.atlassian.jira.index.AccumulatingResultBuilder.collectResult(AccumulatingResultBuilder.java:120)
at com.atlassian.jira.index.AccumulatingResultBuilder.addInternal(AccumulatingResultBuilder.java:73)
at com.atlassian.jira.index.AccumulatingResultBuilder.add(AccumulatingResultBuilder.java:42)
at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:1167)
at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:1136)
at com.atlassian.jira.issue.index.DefaultIndexManager.access$100(DefaultIndexManager.java:97)
at com.atlassian.jira.issue.index.DefaultIndexManager$2.run(DefaultIndexManager.java:342)
at com.atlassian.jira.issue.index.DefaultIndexManager.withReindexLock(DefaultIndexManager.java:382)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:337)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:287) <+3> (NativeMethodAccessorImpl.java:62) (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
at com.sun.proxy.$Proxy15.reIndexAll(Unknown Source)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:75)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:55)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:59)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:528)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:491)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:254)
at java.lang.Thread.run(Thread.java:745)
2018-06-13 19:51:32,702 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 59% complete. Current index: Issue
2018-06-13 19:51:38,653 IssueIndexer:thread-7 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 60% complete. Current index: Issue
2018-06-13 19:51:44,923 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 61% complete. Current index: Issue
2018-06-13 19:51:50,638 IssueIndexer:thread-10 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 62% complete. Current index: Issue
2018-06-13 19:51:56,404 IssueIndexer:thread-10 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 63% complete. Current index: Issue
2018-06-13 19:52:02,045 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 64% complete. Current index: Issue
2018-06-13 19:52:08,233 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 65% complete. Current index: Issue
2018-06-13 19:52:14,740 IssueIndexer:thread-10 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 66% complete. Current index: Issue
2018-06-13 19:52:21,083 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 67% complete. Current index: Issue
2018-06-13 19:52:26,156 IssueIndexer:thread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 68% complete. Current index: Issue
2018-06-13 19:52:32,039 IssueIndexer:thread-9 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 69% complete. Current index: Issue
2018-06-13 19:52:38,118 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 70% complete. Current index: Issue
2018-06-13 19:52:44,234 IssueIndexer:thread-7 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 71% complete. Current index: Issue
2018-06-13 19:52:50,702 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 72% complete. Current index: Issue
2018-06-13 19:52:57,562 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 73% complete. Current index: Issue
2018-06-13 19:53:04,547 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 74% complete. Current index: Issue
2018-06-13 19:53:12,508 IssueIndexer:thread-10 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 75% complete. Current index: Issue
2018-06-13 19:53:19,153 IssueIndexer:thread-9 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 76% complete. Current index: Issue
2018-06-13 19:53:25,019 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 77% complete. Current index: Issue
2018-06-13 19:53:31,174 IssueIndexer:thread-9 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 78% complete. Current index: Issue
2018-06-13 19:53:37,174 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 79% complete. Current index: Issue
2018-06-13 19:53:42,810 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 80% complete. Current index: Issue
2018-06-13 19:53:49,140 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 81% complete. Current index: Issue
2018-06-13 19:53:53,395 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 82% complete. Current index: Issue
2018-06-13 19:53:59,341 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 83% complete. Current index: Issue
2018-06-13 19:54:04,485 IssueIndexer:thread-6 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 84% complete. Current index: Issue
2018-06-13 19:54:10,748 IssueIndexer:thread-9 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 85% complete. Current index: Issue
2018-06-13 19:54:18,989 IssueIndexer:thread-9 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 86% complete. Current index: Issue
2018-06-13 19:54:26,553 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 87% complete. Current index: Issue
2018-06-13 19:54:35,532 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 88% complete. Current index: Issue
2018-06-13 19:54:42,700 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 89% complete. Current index: Issue
2018-06-13 19:54:49,899 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 90% complete. Current index: Issue
2018-06-13 19:54:56,499 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 91% complete. Current index: Issue
2018-06-13 19:55:03,984 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 92% complete. Current index: Issue
2018-06-13 19:55:12,160 IssueIndexer:thread-3 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 93% complete. Current index: Issue
2018-06-13 19:55:18,785 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 94% complete. Current index: Issue
2018-06-13 19:55:25,915 IssueIndexer:thread-4 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 95% complete. Current index: Issue
2018-06-13 19:55:32,421 IssueIndexer:thread-8 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 96% complete. Current index: Issue
2018-06-13 19:55:37,871 IssueIndexer:thread-2 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 97% complete. Current index: Issue
2018-06-13 19:55:44,226 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 98% complete. Current index: Issue
2018-06-13 19:55:50,307 IssueIndexer:thread-5 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing is 99% complete. Current index: Issue
2018-06-13 19:55:54,897 JiraTaskExectionThread-1 ERROR jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [jira.util.index.CompositeIndexLifecycleManager] Reindex All FAILED. Indexer: DefaultIndexManager: paths: [E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\comments, E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\issues, E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\changes, E:\Program Files\Atlassian\Application Data\JIRA\caches\indexes\worklogs]
com.atlassian.jira.index.IndexingFailureException: Indexing completed with 5 errors
at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:192)
at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:1169)
at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:1136)
at com.atlassian.jira.issue.index.DefaultIndexManager.access$100(DefaultIndexManager.java:97)
at com.atlassian.jira.issue.index.DefaultIndexManager$2.run(DefaultIndexManager.java:342)
at com.atlassian.jira.issue.index.DefaultIndexManager.withReindexLock(DefaultIndexManager.java:382)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:337)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:287) <+3> (NativeMethodAccessorImpl.java:62) (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
at com.sun.proxy.$Proxy15.reIndexAll(Unknown Source)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:75)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:55)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:59)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16)
at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:24)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:528)
at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:491)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:254)
at java.lang.Thread.run(Thread.java:745)
2018-06-13 19:55:54,902 JiraTaskExectionThread-1 INFO jschock 1185x192x1 cwe81y 10.10.10.5 /secure/admin/IndexReIndex.jspa [action.admin.index.IndexAdminImpl] Re-indexing finished
2018-06-13 20:05:37,527 atlassian-scheduler-quartz1.clustered_Worker-2 ERROR [com.atlassian.scheduler.JobRunnerResponse] Unable to synchronise directory
com.atlassian.crowd.exception.DirectoryNotFoundException: Directory <10000> does not exist
at com.atlassian.jira.crowd.embedded.JiraDirectorySynchroniser.runJob(JiraDirectorySynchroniser.java:71)
at com.atlassian.scheduler.core.JobLauncher.runJob(JobLauncher.java:136)
at com.atlassian.scheduler.core.JobLauncher.launchAndBuildResponse(JobLauncher.java:101)
at com.atlassian.scheduler.core.JobLauncher.launch(JobLauncher.java:80)
at com.atlassian.scheduler.quartz1.Quartz1Job.execute(Quartz1Job.java:32)
at org.quartz.core.JobRunShell.run(JobRunShell.java:223)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
2018-06-13 21:05:37,521 atlassian-scheduler-quartz1.clustered_Worker-3 ERROR [com.atlassian.scheduler.JobRunnerResponse] Unable to synchronise directory
com.atlassian.crowd.exception.DirectoryNotFoundException: Directory <10000> does not exist
at com.atlassian.jira.crowd.embedded.JiraDirectorySynchroniser.runJob(JiraDirectorySynchroniser.java:71)
at com.atlassian.scheduler.core.JobLauncher.runJob(JobLauncher.java:136)
at com.atlassian.scheduler.core.JobLauncher.launchAndBuildResponse(JobLauncher.java:101)
at com.atlassian.scheduler.core.JobLauncher.launch(JobLauncher.java:80)
at com.atlassian.scheduler.quartz1.Quartz1Job.execute(Quartz1Job.java:32)
at org.quartz.core.JobRunShell.run(JobRunShell.java:223)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)
2018-06-13 21:32:58,217 atlassian-scheduler-quartz1.clustered_Worker-4 INFO [atlassian.servicedesk.lifecycle]

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How do I resolve 500 errors received while re-indexing?

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