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errors.txt
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Andreia:~/environment $ nextflow run hackahton2.nf -resume
N E X T F L O W ~ version 20.10.0
Launching `hackahton2.nf` [sick_descartes] - revision: a1ed0d7ef7
reads: /home/ec2-user/environment/data/ggal/*_{1,2}.*fq
ref: /home/ec2-user/environment/data/ggal/transcriptome.fa
output: /home/ec2-user/environment/result_alignment/out
executor > local (3)
[e3/e000ba] process > index [100%] 1 of 1, cached: 1 ✔
[fb/3a2d1a] process > align (3) [100%] 3 of 3, cached: 3 ✔
[fd/5376a0] process > sam_to_sorted_index_bam (3) [100%] 3 of 3, cached: 3 ✔
[d4/9bcea8] process > markDuplicatesSpark (3) [ 0%] 0 of 3
Error executing process > 'markDuplicatesSpark (2)'
Caused by:
Process `markDuplicatesSpark (2)` terminated with an error exit status (3)
Command executed:
mkdir tmp
gatk --java-options "-Djava.io.tmpdir=tmp" MarkDuplicatesSpark -I lung_aligned_reads_sorted.bam -M lung_dedup_metrics.txt -O lung_sorted_dedup.bam --remove-sequencing-duplicates
Command exit status:
3
Command output:
(empty)
Command error:
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: javax.security.auth.login.LoginException: java.lang.NullPointerException: invalid null input: name
at com.sun.security.auth.UnixPrincipal.<init>(UnixPrincipal.java:71)
at com.sun.security.auth.module.UnixLoginModule.login(UnixLoginModule.java:133)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at javax.security.auth.login.LoginContext.invoke(LoginContext.java:755)
at javax.security.auth.login.LoginContext.access$000(LoginContext.java:195)
at javax.security.auth.login.LoginContext$4.run(LoginContext.java:682)
at javax.security.auth.login.LoginContext$4.run(LoginContext.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.login.LoginContext.invokePriv(LoginContext.java:680)
at javax.security.auth.login.LoginContext.login(LoginContext.java:587)
at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:841)
at org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:803)
at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:676)
at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2422)
at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2422)
at scala.Option.getOrElse(Option.scala:121)
at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2422)
at org.apache.spark.SparkContext.<init>(SparkContext.scala:293)
at org.apache.spark.api.java.JavaSparkContext.<init>(JavaSparkContext.scala:58)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.createSparkContext(SparkContextFactory.java:185)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.getSparkContext(SparkContextFactory.java:117)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:28)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
at javax.security.auth.login.LoginContext.invoke(LoginContext.java:856)
at javax.security.auth.login.LoginContext.access$000(LoginContext.java:195)
at javax.security.auth.login.LoginContext$4.run(LoginContext.java:682)
at javax.security.auth.login.LoginContext$4.run(LoginContext.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.login.LoginContext.invokePriv(LoginContext.java:680)
at javax.security.auth.login.LoginContext.login(LoginContext.java:587)
at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:841)
... 17 more
Using GATK jar /gatk/gatk-package-4.1.3.0-local.jar
executor > local (3)
[e3/e000ba] process > index [100%] 1 of 1, cached: 1 ✔[fb/3a2d1a] process > align (3) [100%] 3 of 3, cached: 3 ✔[fd/5376a0] process > sam_to_sorted_index_bam (3) [100%] 3 of 3, cached: 3 ✔
[d4/9bcea8] process > markDuplicatesSpark (3) [100%] 1 of 1, failed: 1
Error executing process > 'markDuplicatesSpark (2)'
Caused by:
Process `markDuplicatesSpark (2)` terminated with an error exit status (3)
Command executed:
mkdir tmp
gatk --java-options "-Djava.io.tmpdir=tmp" MarkDuplicatesSpark -I lung_aligned_reads_sorted.bam -M lung_dedup_metrics.txt -O lung_sorted_dedup.bam --remove-sequencing-duplicates
Command exit status:
3
Command output:
(empty)
Command error:
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: javax.security.auth.login.LoginException: java.lang.NullPointerException: invalid null input: name
at com.sun.security.auth.UnixPrincipal.<init>(UnixPrincipal.java:71)
at com.sun.security.auth.module.UnixLoginModule.login(UnixLoginModule.java:133)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at javax.security.auth.login.LoginContext.invoke(LoginContext.java:755)
at javax.security.auth.login.LoginContext.access$000(LoginContext.java:195)
at javax.security.auth.login.LoginContext$4.run(LoginContext.java:682)
at javax.security.auth.login.LoginContext$4.run(LoginContext.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.login.LoginContext.invokePriv(LoginContext.java:680)
at javax.security.auth.login.LoginContext.login(LoginContext.java:587)
at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:841)
at org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:803)
at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:676)
at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2422)
at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2422)
at scala.Option.getOrElse(Option.scala:121)
at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2422)
at org.apache.spark.SparkContext.<init>(SparkContext.scala:293)
at org.apache.spark.api.java.JavaSparkContext.<init>(JavaSparkContext.scala:58)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.createSparkContext(SparkContextFactory.java:185)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.getSparkContext(SparkContextFactory.java:117)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:28)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
at javax.security.auth.login.LoginContext.invoke(LoginContext.java:856)
at javax.security.auth.login.LoginContext.access$000(LoginContext.java:195)
at javax.security.auth.login.LoginContext$4.run(LoginContext.java:682)
at javax.security.auth.login.LoginContext$4.run(LoginContext.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.login.LoginContext.invokePriv(LoginContext.java:680)
at javax.security.auth.login.LoginContext.login(LoginContext.java:587)
at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:841)
... 17 more
Using GATK jar /gatk/gatk-package-4.1.3.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Djava.io.tmpdir=tmp -jar /gatk/gatk-package-4.1.3.0-local.jar MarkDuplicatesSpark -I lung_aligned_reads_sorted.bam -M lung_dedup_metrics.txt -O lung_sorted_dedup.bam --remove-sequencing-duplicates
Work dir:
/home/ec2-user/environment/work/6c/ba0de5f50742d52505282b3cec118a
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line