Depthofcoverage program completed successfully, but the interval_summary file is empty. The result file just shows the column names only. Can you please tell me how to get the interval summary for all bamfiles at each bed file position? 

a) GATK version used :

gatk-4.1.6.0

b) Exact GATK commands used :

/N/../gatk-4.1.6.0/gatk DepthOfCoverage \
-R /N/../Database/GATK/gatk-boundle/hg19/ucsc.hg19.fasta \
-O /N/../depthofcoverage2/mutation_depthcoverage.txt \
-I /N/../bam/bam1.bam \
-I //N/../bam/bam2.bam \
-I /N/../bam/bam3.bam \
-I /N/../bam/bam4.bam \
-I /N/../bam/bam5.bam \
-I /N/../bam/bam6.bam \
-I /N/../bam/bam7.bam \
-I /N/../bam/bam8.bam \
-L /N..bedfiles/Mutation_v2.bed \
--output-format CSV

c) The entire error log if applicable.

Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /geode2/home/u070/../gatk-4.1.6.0/gatk-package-4.1.6.0-local.jar DepthOfCoverage -R /N/../Database/GATK/gatk-boundle/hg19/ucsc.hg19.fasta -O /N/../depthofcoverage2/mutation_depthcoverage.txt -I /N/../bam/bam1.bam \ -I //N/../bam/bam2.bam \ -I /N/../bam/bam3.bam \ -I /N/../bam/bam4.bam \ -I /N/../bam/bam5.bam \ -I /N/../bam/bam6.bam \ -I /N/../bam/bam7.bam \ -I /N/../bam/bam8.bam \ -L /N..bedfiles/Mutation_v2.bed \ --output-format CSV
08:28:03.177 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/geode2/home/u070/../gatk-4.1.6.0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 13, 2020 8:28:03 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
08:28:03.454 INFO DepthOfCoverage - ------------------------------------------------------------
08:28:03.455 INFO DepthOfCoverage - The Genome Analysis Toolkit (GATK) v4.1.6.0
08:28:03.455 INFO DepthOfCoverage - For support and documentation go to https://software.broadinstitute.org/gatk/
08:28:03.456 INFO DepthOfCoverage - Executing as parkanha@c44 on Linux v3.10.0-1062.12.1.el7.x86_64 amd64
08:28:03.456 INFO DepthOfCoverage - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-b08
08:28:03.457 INFO DepthOfCoverage - Start Date/Time: May 13, 2020 8:28:03 AM EDT
08:28:03.457 INFO DepthOfCoverage - ------------------------------------------------------------
08:28:03.457 INFO DepthOfCoverage - ------------------------------------------------------------
08:28:03.458 INFO DepthOfCoverage - HTSJDK Version: 2.21.2
08:28:03.458 INFO DepthOfCoverage - Picard Version: 2.21.9
08:28:03.459 INFO DepthOfCoverage - HTSJDK Defaults.COMPRESSION_LEVEL : 2
08:28:03.459 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
08:28:03.460 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
08:28:03.460 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
08:28:03.460 INFO DepthOfCoverage - Deflater: IntelDeflater
08:28:03.461 INFO DepthOfCoverage - Inflater: IntelInflater
08:28:03.461 INFO DepthOfCoverage - GCS max retries/reopens: 20
08:28:03.461 INFO DepthOfCoverage - Requester pays: disabled
08:28:03.462 WARN DepthOfCoverage -

08:28:03.462 INFO DepthOfCoverage - Initializing engine
08:28:05.464 INFO FeatureManager - Using codec BEDCodec to read file file:///N/u/parkanha/Carbonate/bedfiles/Mutation_v2.bed
08:28:05.537 INFO IntervalArgumentCollection - Processing 999140 bp from intervals
08:28:05.547 INFO DepthOfCoverage - Done initializing engine
08:28:05.751 INFO ProgressMeter - Starting traversal
08:28:05.752 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
08:28:07.903 INFO FeatureManager - Using codec BEDCodec to read file file:///N/u/parkanha/Carbonate/bedfiles/Mutation_v2.bed
08:28:30.501 INFO ProgressMeter - chr1:8177615 0.4 1000 2424.5
08:28:53.894 INFO ProgressMeter - chr1:16199584 0.8 2000 2492.7
08:29:18.340 INFO ProgressMeter - chr1:16242620 1.2 3000 2479.8

....

15:41:24.857 INFO DepthOfCoverage - 0 read(s) filtered by: WellformedReadFilter
256168058 read(s) filtered by: NotDuplicateReadFilter
550552 read(s) filtered by: NotSecondaryAlignmentReadFilter
1004221 read(s) filtered by: MappedReadFilter
257722831 total reads filtered
15:41:24.858 INFO ProgressMeter - chrX:129189983 433.3 999140 2305.8
15:41:24.858 INFO ProgressMeter - Traversal complete. Processed 999140 total loci in 433.3 minutes.
log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
15:41:24.969 INFO DepthOfCoverage - Shutting down engine
[May 13, 2020 3:41:24 PM EDT] org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage done. Elapsed time: 433.36 minutes.
Runtime.totalMemory()=13800833024
Tool returned:
success