Hello. I thought this is an interesting error to report. Pipeline was running from

--step prepare_recalibration

. Some samples went through this step just fine.

'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR_SPARK:GATK4SPARK_BASERECALIBRATOR (ID29)'                                                                                                                         
                                                                                                                                                                                                                                             
Caused by:                                                                                                                                                  
  Process `NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR_SPARK:GATK4SPARK_BASERECALIBRATOR (ID29)` terminated with an error exit status (1)                                                                                                        
                                                   
  cat <<-END_VERSIONS > versions.yml                                                                                                                                
  "NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR_SPARK:GATK4SPARK_BASERECALIBRATOR":                                                                                      
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')                                                                                       
  END_VERSIONS                                                                                                                                                      
                                                                                                                                                                    
Command exit status:                                                                                                                                                
  1                                                                                                                                                                 
Command output:                                                                                                                                                     
  (empty)                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                         
Command error:                                                                                                                                                      
  11:25:37.514 WARN  Utils - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.                                                                                                                                                                                                                                        
[...]                                                                                                                                                                                                                                                                                                    
  11:25:37.524 ERROR SparkUI - Failed to bind SparkUI                                                                                                               
  java.net.BindException: Failed to bind to /0.0.0.0:4056: Service 'SparkUI' failed after 16 retries (starting from 4040)! Consider explicitly setting the appropriate port for the service 'SparkUI' (for example spark.ui.port for SparkUI) to an available port or increasing spark.port.maxRetries.                                  
        at org.sparkproject.jetty.server.ServerConnector.openAcceptChannel(ServerConnector.java:349) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                      
        at org.sparkproject.jetty.server.ServerConnector.open(ServerConnector.java:310) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                   
        at org.sparkproject.jetty.server.AbstractNetworkConnector.doStart(AbstractNetworkConnector.java:80) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                    
        at org.sparkproject.jetty.server.ServerConnector.doStart(ServerConnector.java:234) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                                     
        at org.sparkproject.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:73) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                            
        at org.apache.spark.ui.JettyUtils$.newConnector$1(JettyUtils.scala:304) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                                                
        at org.apache.spark.ui.JettyUtils$.httpConnect$1(JettyUtils.scala:335) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                                                 
        at org.apache.spark.ui.JettyUtils$.$anonfun$startJettyServer$6(JettyUtils.scala:338) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                                   
        at org.apache.spark.ui.JettyUtils$.$anonfun$startJettyServer$6$adapted(JettyUtils.scala:338) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                           
        at org.apache.spark.util.Utils$.$anonfun$startServiceOnPort$2(Utils.scala:2256) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                                        
        at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:158) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                               
        at org.apache.spark.util.Utils$.startServiceOnPort(Utils.scala:2248) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                                                                   
        at org.apache.spark.ui.JettyUtils$.startJettyServer(JettyUtils.scala:339) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                         
        at org.apache.spark.ui.WebUI.initServer(WebUI.scala:145) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                          
        at org.apache.spark.ui.SparkUI.bind(SparkUI.scala:145) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                            
        at org.apache.spark.SparkContext.$anonfun$new$14(SparkContext.scala:511) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                          
        at org.apache.spark.SparkContext.$anonfun$new$14$adapted(SparkContext.scala:511) ~[gatk-package-4.5.0.0-local.jar:4.5.0.0]                                  
        at scala.Option.foreach(Option.scala:407) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                          
        at org.apache.spark.SparkContext.<init>(SparkContext.scala:511) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                    
        at org.apache.spark.api.java.JavaSparkContext.<init>(JavaSparkContext.scala:58) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                    
        at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.createSparkContext(SparkContextFactory.java:185) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                      
        at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.getSparkContext(SparkContextFactory.java:117) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                         
        at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:28) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                           
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                   
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                                                                                                                                      
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217) [gatk-package-4.5.0.0-local.jar:4.5.0.0]              
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                         
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                     
        at org.broadinstitute.hellbender.Main.main(Main.java:306) [gatk-package-4.5.0.0-local.jar:4.5.0.0]                                                          
  11:25:37.539 INFO  DiskBlockManager - Shutdown hook called                                                                                                        
  11:25:37.549 INFO  ShutdownHookManager - Shutdown hook called                                                                                                     
  11:25:37.551 INFO  ShutdownHookManager - Deleting directory spark-a83784c4-69e5-4dd3-9e12-f91c17003b19/userFiles-1f2357b3-80e8-4797-aa86-20192df377c1             
  11:25:37.556 INFO  ShutdownHookManager - Deleting directory spark-a83784c4-69e5-4dd3-9e12-f91c17003b19

spark shakefist