WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.

[ChrisSteel-bio]

Not sure if this is a bug or something wrong with my bam files. Any help on solving/debugging would be welcomed. Running mutect2 returns >100,000 warnings of more than two reads with the same name found. The bams were processing following best practices. The header of the log file:

Mutect2 -R resources/hg38/genome/d
975 efault/genome.fa -L resources/hg38/a.interval_list -I recal/RBL3_diagnostic.bam -I recal/RBL3_germline.bam -I recal/RBL3_diagnostic.bam -I recal/RBL3_relapse1.bam -I recal/RBL
976 3_relapse2.bam -I recal/RBL3_PDX.bam -normal RBL3_germline_hg38 --germline-resource resources/hg38/gnomad/af-only-gnomad.hg38.vcf.gz --panel-of-normals resources/hg38/pon/1000
977 g_pon.hg38.vcf.gz --f1r2-tar-gz results/RBL3/f1r2.tar.gz --read-filter NotSupplementaryAlignmentReadFilter --read-filter NotSecondaryAlignmentReadFilter --native-pair-hmm-thre
978 ads 20 -O results/RBL3/unfiltered.vcf
979 17:07:51.270 WARN GATKReadFilterPluginDescriptor - Redundant enabled filter (NotSecondaryAlignmentReadFilter) is enabled for this tool by default
980 17:07:51.313 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/rds/project/rds-cyiwgCzJok8/WES_snakemake/.snakemake/conda/773770bb2edb9f4c58fb17b5017e1f
981 be_/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
982 17:07:51.633 INFO Mutect2 - ------------------------------------------------------------
983 17:07:51.635 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
984 17:07:51.635 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
985 17:07:51.635 INFO Mutect2 - Executing as cjs236@cpu-r-25 on Linux v4.18.0-553.16.1.el8_10.x86_64 amd64
986 17:07:51.635 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.11-internal+0-adhoc..src
987 17:07:51.635 INFO Mutect2 - Start Date/Time: August 28, 2024 at 5:07:51 PM BST
988 17:07:51.635 INFO Mutect2 - ------------------------------------------------------------
989 17:07:51.635 INFO Mutect2 - ------------------------------------------------------------
990 17:07:51.636 INFO Mutect2 - HTSJDK Version: 4.1.0
991 17:07:51.636 INFO Mutect2 - Picard Version: 3.1.1
992 17:07:51.636 INFO Mutect2 - Built for Spark Version: 3.5.0
993 17:07:51.636 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
994 17:07:51.636 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
995 17:07:51.636 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
996 17:07:51.636 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
997 17:07:51.636 INFO Mutect2 - Deflater: IntelDeflater
998 17:07:51.637 INFO Mutect2 - Inflater: IntelInflater
999 17:07:51.637 INFO Mutect2 - GCS max retries/reopens: 20
1000 17:07:51.637 INFO Mutect2 - Requester pays: disabled
1001 17:07:51.637 INFO Mutect2 - Initializing engine
1002 17:07:51.856 INFO FeatureManager - Using codec VCFCodec to read file file:///rds/project/rds-cyiwgCzJok8/WES_snakemake/resources/hg38/pon/1000g_pon.hg38.vcf.gz
1003 17:07:51.918 INFO FeatureManager - Using codec VCFCodec to read file file:///rds/project/rds-cyiwgCzJok8/WES_snakemake/resources/hg38/gnomad/af-only-gnomad.hg38.vcf.gz
1004 17:07:51.981 INFO FeatureManager - Using codec IntervalListCodec to read file file:///rds/project/rds-cyiwgCzJok8/WES_snakemake/resources/hg38/a.interval_list
1005 17:07:52.756 INFO IntervalArgumentCollection - Processing 36458262 bp from intervals
1006 17:07:52.849 INFO Mutect2 - Done initializing engine
1007 17:07:52.856 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/rds/project/rds-cyiwgCzJok8/WES_snakemake/.snakemake/conda/773770bb2edb9f4c58fb17b5017e1fbe_/sh
1008 are/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
1009 17:07:52.859 INFO NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/rds/project/rds-cyiwgCzJok8/WES_snakemake/.snakemake/conda/773770bb2edb9f4c58fb17b5017e
1010 1fbe_/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
1011 17:07:52.860 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
1012 17:07:52.860 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
1013 17:07:52.867 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/rds/project/rds-cyiwgCzJok8/WES_snakemake/.snakemake/conda/773770bb2edb9f4c58fb17b5017e1f
1014 be_/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
1015 17:07:52.881 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
1016 17:07:52.881 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 17:07:52.882 INFO IntelPairHmm - Available threads: 20
17:07:52.882 INFO IntelPairHmm - Requested threads: 20
17:07:52.882 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
17:07:52.941 INFO ProgressMeter - Starting traversal
17:07:52.941 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
17:07:54.578 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.812 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.812 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.812 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.812 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.812 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
17:07:54.813 WARN Fragment - More than two reads with the same name found. Using two reads randomly to combine as a fragment.
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