We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

BQSR can‘t run!

Hello!
I’m running BQSR with GATK v4.0.4.0. And I met some problems that I cannot get the right output file.
The command line is:
$GATK --java-options "-Xmx10240m -Djava.io.tmpdir=./" BaseRecalibratorSpark -R $GENOME -I $sample-md_rl.bam --known-sites /home/gaotiangang/niuguohao/201806call/50100-step5-3/combined_1.raw_snp.vcf -O $sample.4.table --spark-master local[4]
$GATK --java-options "-Xmx10240m -Djava.io.tmpdir=./" ApplyBQSRSpark -I $sample-md_rl.bam -bqsr $sample.4.table -O $sample.4.bam --spark-master local[4]
echo "BQSR 1 over "

But I got these lines back almost everytime ,
18/07/25 08:13:23 ERROR Executor: Exception in task 9.0 in stage 1.0 (TID 191)
java.io.IOException: Failed to create local dir in /home/gaotiangang/niuguohao/201806call/50-step5-7/niuguohao/blockmgr-accb99db-cd04-4a44-a018-0672408e3f03/1d.
at org.apache.spark.storage.DiskBlockManager.getFile(DiskBlockManager.scala:70)
at org.apache.spark.storage.DiskBlockManager.getFile(DiskBlockManager.scala:80)
at org.apache.spark.shuffle.IndexShuffleBlockResolver.getDataFile(IndexShuffleBlockResolver.scala:55)
at org.apache.spark.shuffle.sort.UnsafeShuffleWriter.closeAndWriteOutput(UnsafeShuffleWriter.java:212)
at org.apache.spark.shuffle.sort.UnsafeShuffleWriter.write(UnsafeShuffleWriter.java:169)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
18/07/25 08:13:23 INFO TaskSetManager: Starting task 11.0 in stage 1.0 (TID 193, localhost, executor driver, partition 11, PROCESS_LOCAL, 4906 bytes)
18/07/25 08:13:23 INFO Executor: Running task 11.0 in stage 1.0 (TID 193)
18/07/25 08:13:23 WARN TaskSetManager: Lost task 9.0 in stage 1.0 (TID 191, localhost, executor driver): java.io.IOException: Failed to create local dir in /home/gaotiangang/niuguohao/201806call/50-step5-7/niuguohao/blockmgr-accb99db-cd04-4a44-a018-0672408e3f03/1d.
at org.apache.spark.storage.DiskBlockManager.getFile(DiskBlockManager.scala:70)
at org.apache.spark.storage.DiskBlockManager.getFile(DiskBlockManager.scala:80)
at org.apache.spark.shuffle.IndexShuffleBlockResolver.getDataFile(IndexShuffleBlockResolver.scala:55)
at org.apache.spark.shuffle.sort.UnsafeShuffleWriter.closeAndWriteOutput(UnsafeShuffleWriter.java:212)
at org.apache.spark.shuffle.sort.UnsafeShuffleWriter.write(UnsafeShuffleWriter.java:169)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

Does that mean I set something wrong in my command line?

Thanks !

Tagged:

Answers

Sign In or Register to comment.