a) GATK version used : GATK3

b) Exact GATK commands used

#!/bin/sh

SPECIES=flounder
COHORTID=NS
INPUTPATH=/data/shin0727/Data/FlatFish/2016/BQSR
REFERENCEPATH=/data/shin0727/Data/FlatFish/fReference
mkdir /data/shin0727/Data/FlatFish/2016/RealignerTargetCreator
OUTPUTPATH= /data/shin0727/Data/FlatFish/2016/RealignerTargetCreator
NTHREAD=4

for SAMPLEID in `cat /data/shin0727/Data/FlatFish/2016/SAMPLELIST.${COHORTID}.lst`
do
/data/shin0727/ExomeSeq/src_packages/jdk-8u251-linux-x64/jdk1.8.0_251/bin/java \
-jar ./src_packages/GenomeAnalysisTK-3.8-1-0/GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-R ${REFERENCEPATH}/${SPECIES}Reference.fa \
-nt ${NTHREAD} \
-I ${INPUTPATH}/${SAMPLEID}.sorted.markduplicates.fixmate.BQSR.bam \
-o ${OUTPUTPATH}/${SAMPLEID}.sorted.markduplicates.fixmate.BQSR.intervals
done

c) The entire error log if applicable.

mkdir: cannot create directory ‘/data/shin0727/Data/FlatFish/2016/RealignerTargetCreator’: File exists
step10.GATK3_RealignerTargetCreator.sh: 8: step10.GATK3_RealignerTargetCreator.sh: /data/shin0727/Data/FlatFish/2016/RealignerTargetCreator: Permission denied
INFO 15:11:06,615 HelpFormatter - ------------------------------------------------------------------------------------
INFO 15:11:06,617 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50
INFO 15:11:06,618 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 15:11:06,618 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 15:11:06,618 HelpFormatter - [Fri Apr 24 15:11:06 KST 2020] Executing on Linux 5.3.0-46-generic amd64
INFO 15:11:06,618 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_251-b08
INFO 15:11:06,621 HelpFormatter - Program Args: -T RealignerTargetCreator -R /data/shin0727/Data/FlatFish/fReference/flounderReference.fa -nt 4 -I /data/shin0727/Data/FlatFish/2016/BQSR/NS-11.sorted.markduplicates.fixmate.BQSR.bam -o /NS-11.sorted.markduplicates.fixmate.BQSR.intervals
INFO 15:11:06,641 HelpFormatter - Executing as shin0727@node200 on Linux 5.3.0-46-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_251-b08.
INFO 15:11:06,642 HelpFormatter - Date/Time: 2020/04/24 15:11:06
INFO 15:11:06,642 HelpFormatter - ------------------------------------------------------------------------------------
INFO 15:11:06,642 HelpFormatter - ------------------------------------------------------------------------------------
INFO 15:11:06,648 NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/shin0727/ExomeSeq/src_packages/GenomeAnalysisTK-3.8-1-0/GenomeAnalysisTK.jar!/com/intel/gkl/native/libgkl_compression.so
INFO 15:11:06,676 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 15:11:06,676 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 15:11:06,677 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:11:06,956 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 15:11:06,991 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:11:07,033 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
INFO 15:11:07,099 MicroScheduler - Running the GATK in parallel mode with 4 total threads, 1 CPU thread(s) for each of 4 data thread(s), of 28 processors available on this machine
INFO 15:11:07,196 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 15:11:07,310 GenomeAnalysisEngine - Done preparing for traversal
INFO 15:11:07,310 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:11:07,311 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 15:11:07,311 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 15:11:07,390 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:11:07,394 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00
INFO 15:11:07,394 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:11:07,398 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00
INFO 15:11:07,398 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:11:07,403 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00
INFO 15:11:37,328 ProgressMeter - CHR3:3465525 4.3650736E7 30.0 s 0.0 s 8.6% 5.8 m 5.3 m
INFO 15:12:07,346 ProgressMeter - CHR5:14700549 1.02364752E8 60.0 s 0.0 s 20.2% 4.9 m 3.9 m
INFO 15:12:37,369 ProgressMeter - CHR8:4978453 1.60516519E8 90.0 s 0.0 s 31.7% 4.7 m 3.2 m
INFO 15:13:07,370 ProgressMeter - CHR10:16274213 2.15094163E8 120.0 s 0.0 s 42.5% 4.7 m 2.7 m
INFO 15:13:37,374 ProgressMeter - CHR13:4283025 2.75532966E8 2.5 m 0.0 s 54.5% 4.6 m 2.1 m
INFO 15:14:07,400 ProgressMeter - CHR16:15175785 3.35977521E8 3.0 m 0.0 s 66.4% 4.5 m 91.0 s
INFO 15:14:37,704 ProgressMeter - CHR19:2590873 3.9512577E8 3.5 m 0.0 s 78.1% 4.5 m 58.0 s
INFO 15:15:07,705 ProgressMeter - CHR22:8480729 4.53935139E8 4.0 m 0.0 s 89.7% 4.5 m 27.0 s
##### ERROR --
##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to retrieve result
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:190)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
Caused by: htsjdk.samtools.SAMException: Error opening file for writing: NS-11.sorted.markduplicates.fixmate.BQSR.intervals
at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:589)
at htsjdk.samtools.util.IOUtil.openFileForBufferedWriting(IOUtil.java:597)
at htsjdk.samtools.util.IOUtil.openFileForBufferedWriting(IOUtil.java:604)
at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.onTraversalDone(RealignerTargetCreator.java:271)
at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.onTraversalDone(RealignerTargetCreator.java:117)
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.notifyTraversalDone(HierarchicalMicroScheduler.java:226)
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:183)
... 5 more
Caused by: java.io.FileNotFoundException: /NS-11.sorted.markduplicates.fixmate.BQSR.intervals (Permission denied)
at java.io.FileOutputStream.open0(Native Method)
at java.io.FileOutputStream.open(FileOutputStream.java:270)
at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:585)
... 11 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to retrieve result
##### ERROR ------------------------------------------------------------------------------------------
INFO 15:15:40,756 HelpFormatter - ------------------------------------------------------------------------------------
INFO 15:15:40,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50
INFO 15:15:40,791 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 15:15:40,791 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 15:15:40,791 HelpFormatter - [Fri Apr 24 15:15:40 KST 2020] Executing on Linux 5.3.0-46-generic amd64
INFO 15:15:40,791 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_251-b08
INFO 15:15:40,793 HelpFormatter - Program Args: -T RealignerTargetCreator -R /data/shin0727/Data/FlatFish/fReference/flounderReference.fa -nt 4 -I /data/shin0727/Data/FlatFish/2016/BQSR/NS-10.sorted.markduplicates.fixmate.BQSR.bam -o /NS-10.sorted.markduplicates.fixmate.BQSR.intervals
INFO 15:15:40,801 HelpFormatter - Executing as shin0727@node200 on Linux 5.3.0-46-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_251-b08.
INFO 15:15:40,801 HelpFormatter - Date/Time: 2020/04/24 15:15:40
INFO 15:15:40,801 HelpFormatter - ------------------------------------------------------------------------------------
INFO 15:15:40,801 HelpFormatter - ------------------------------------------------------------------------------------
INFO 15:15:40,815 NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/shin0727/ExomeSeq/src_packages/GenomeAnalysisTK-3.8-1-0/GenomeAnalysisTK.jar!/com/intel/gkl/native/libgkl_compression.so
INFO 15:15:40,850 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 15:15:40,850 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 15:15:40,850 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:15:41,260 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 15:15:41,266 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:15:41,336 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
INFO 15:15:41,390 MicroScheduler - Running the GATK in parallel mode with 4 total threads, 1 CPU thread(s) for each of 4 data thread(s), of 28 processors available on this machine
INFO 15:15:41,581 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 15:15:41,687 GenomeAnalysisEngine - Done preparing for traversal
INFO 15:15:41,688 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:15:41,688 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 15:15:41,688 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 15:15:41,787 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:15:41,794 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 15:15:41,795 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:15:41,800 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00
INFO 15:15:41,800 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 15:15:41,811 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 15:16:11,730 ProgressMeter - CHR2:16664429 3.6559154E7 30.0 s 0.0 s 7.2% 6.9 m 6.4 m
INFO 15:16:41,731 ProgressMeter - CHR4:24384093 8.6976802E7 60.0 s 0.0 s 17.2% 5.8 m 4.8 m
INFO 15:17:11,733 ProgressMeter - CHR7:10049693 1.40642659E8 90.0 s 0.0 s 27.8% 5.4 m 3.9 m
INFO 15:17:41,734 ProgressMeter - CHR9:21521793 1.98283706E8 120.0 s 0.0 s 39.2% 5.1 m 3.1 m
INFO 15:18:11,734 ProgressMeter - CHR11:19666101 2.44206735E8 2.5 m 0.0 s 48.3% 5.2 m 2.7 m
INFO 15:18:41,735 ProgressMeter - CHR13:12040057 2.83282598E8 3.0 m 0.0 s 56.0% 5.4 m 2.4 m
INFO 15:19:11,736 ProgressMeter - CHR16:6191869 3.26982705E8 3.5 m 0.0 s 64.6% 5.4 m 114.0 s
INFO 15:19:41,737 ProgressMeter - CHR17:17795625 3.68414928E8 4.0 m 0.0 s 72.8% 5.5 m 89.0 s
INFO 15:20:11,738 ProgressMeter - CHR20:6988585 4.08863349E8 4.5 m 0.0 s 80.8% 5.6 m 64.0 s
INFO 15:20:41,739 ProgressMeter - CHR22:4670541 4.50134051E8 5.0 m 0.0 s 89.0% 5.6 m 37.0 s
INFO 15:21:11,741 ProgressMeter - CHR24:2793681 4.89690152E8 5.5 m 0.0 s 96.8% 5.7 m 10.0 s
##### ERROR --
##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to retrieve result
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:190)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
Caused by: htsjdk.samtools.SAMException: Error opening file for writing: NS-10.sorted.markduplicates.fixmate.BQSR.intervals
at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:589)
at htsjdk.samtools.util.IOUtil.openFileForBufferedWriting(IOUtil.java:597)
at htsjdk.samtools.util.IOUtil.openFileForBufferedWriting(IOUtil.java:604)
at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.onTraversalDone(RealignerTargetCreator.java:271)
at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.onTraversalDone(RealignerTargetCreator.java:117)
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.notifyTraversalDone(HierarchicalMicroScheduler.java:226)
at org.broadinstitute.gatk.engine.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:183)
... 5 more
Caused by: java.io.FileNotFoundException: /NS-10.sorted.markduplicates.fixmate.BQSR.intervals (Permission denied)
at java.io.FileOutputStream.open0(Native Method)
at java.io.FileOutputStream.open(FileOutputStream.java:270)
at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
at htsjdk.samtools.util.IOUtil.openFileForWriting(IOUtil.java:585)
... 11 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to retrieve result
##### ERROR ------------------------------------------------------------------------------------------