Help? GATK -T IndelRealigner error: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
Entering edit mode
2.0 years ago
longsogn • 0

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 
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/
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 -                 | 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


alignment software error • 997 views
Entering edit mode

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.

Entering edit mode

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


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