If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

DiskReadEndsMap error

hello,I run a batch of markdup for mary samples on a servers, echo sample's script likes below:
java -jar MarkDuplicates.jar MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 INPUT=17S0001690/Bwa/17S0001690.sort.bam OUTPUT=17S0001690.sort.dup.bam METRICS_FILE=17S0001690/Bwa/17S0001690.dup.metrics VALIDATION_STRINGENCY=SILENT && \
samtools index 17S0001690.sort.dup.bam
but some samples have exception:

4s. Last read position: chr3:122,545,708
INFO 2018-03-13 20:06:59 MarkDuplicates Tracking 31974 as yet unmatched pairs. 2768 records in RAM.
INFO 2018-03-13 20:08:02 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 63s. Last read position: chr3:155,832,010
INFO 2018-03-13 20:08:02 MarkDuplicates Tracking 32064 as yet unmatched pairs. 1323 records in RAM.
[Tue Mar 13 20:08:25 CST 2018] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 4.42 minutes.
Exception in thread "main" net.sf.picard.PicardException: Error spilling ReadEndsMap to disk.
at net.sf.picard.sam.DiskReadEndsMap$Codec.encode(
at net.sf.picard.sam.DiskReadEndsMap$Codec.encode(
at net.sf.picard.sam.CoordinateSortedPairInfoMap.put(
at net.sf.picard.sam.DiskReadEndsMap.put(
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(
at net.sf.picard.sam.MarkDuplicates.doWork(
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
at net.sf.picard.sam.MarkDuplicates.main(
Caused by: Input/output error
at Method)
at net.sf.picard.sam.DiskReadEndsMap$Codec.encode(
... 7 more
is it out of memory in server?

Best Answer


Sign In or Register to comment.