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 October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

GATK IndelRealigner error: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated

longsonglongsong Member

I am a newbie of GATK.

Could anyone help me with my problem as following?

I tried to run the following code on HPC:

module load samtools/1.6
module load gatk/3.8.0
module load java/jdk1.8.0_45
module load picard/2.18.4

java -jar -Xmx64g /usr/local/gatk/3.8.0/GenomeAnalysisTK.jar \
-T IndelRealigner \
-targetIntervals "$TmpIntervalsFile" \
-o "$SortedRealignedBamFile" \
-I "$TmpSortedBamFile" \
-R "$ReferenceFastaFile"

But I got the following error message (only some part of message)

INFO 20:15:12,323 HelpFormatter - -----------------------------------------------------------------------------------
INFO 20:15:12,325 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 20:15:12,325 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 20:15:12,325 HelpFormatter - For support and documentation go to
INFO 20:15:12,325 HelpFormatter - [Thu Apr 11 20:15:12 AEST 2019] Executing on Linux 2.6.32-696.16.1.el6.x86_64 amd64
INFO 20:15:12,325 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14
INFO 20:15:12,328 HelpFormatter - Program Args: -T IndelRealigner -targetIntervals Alignments/S111.mq30.sorted.bam.indel.intervals -o Alignments/S111.mq30.sorted.indelRealigned.bam -I Alignments/S111.mq30.sorted.bam -R Reference/myReference.fasta
INFO 20:15:12,331 HelpFormatter - Executing as [email protected] on Linux 2.6.32-696.16.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.


INFO 20:15:12,640 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 20:15:12,641 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 20:15:12,733 ReadShardBalancer$1 - Loading BAM index data
INFO 20:15:12,734 ReadShardBalancer$1 - Done loading BAM index data
/var/spool/PBS/mom_priv/jobs/3123226[2].pbsserver.SC: line 121: 158546 Aborted (core dumped) java -jar -Xmx64g /usr/local/gatk/3.8.0/GenomeAnalysisTK.jar -T IndelRealigner -targetIntervals "$TmpIntervalsFile" -o "$SortedRealignedBamFile" -I "$TmpSortedBamFile" -R "$ReferenceFastaFile"
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated



Sign In or Register to comment.