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

Question

[longsogn]

I am a newbie of NGS.

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

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 lson5430@hpc001 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  20:15:12,332 HelpFormatter - Date/Time: 2019/04/11 20:15:12 
INFO  20:15:12,332 HelpFormatter - ----------------------------------------------------------------------------------- 
INFO  20:15:12,332 HelpFormatter - ----------------------------------------------------------------------------------- 
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/usr/local/gatk/3.8.0/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO  20:15:12,478 GenomeAnalysisEngine - Deflater: IntelDeflater 
INFO  20:15:12,478 GenomeAnalysisEngine - Inflater: IntelInflater 
INFO  20:15:12,479 GenomeAnalysisEngine - Strictness is SILENT 
INFO  20:15:12,537 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  20:15:12,542 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  20:15:12,566 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 
INFO  20:15:12,637 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  20:15:12,640 GenomeAnalysisEngine - Done preparing for traversal 
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!

[ATpoint]

EOF marker is absent. The input is probably truncated

Your BAM is corrupted, probably during an upstream step. Please post commands how the BAM was made.

[WouterDeCoster]

It says your input is corrupted. What's the output of samtools quickcheck on your bam file?