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

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 https://software.broadinstitute.org/gatk
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 - [INITIALIZATION COMPLETE; STARTING PROCESSING]
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

Thanks!

Answers

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