Hi GATK community,

I had run the GATK pipeline on Ubuntu 18 version and I had also checked the VAlidateSamFile, then there was no error.

/home//Software/gatk-4.1.9.0/gatk ValidateSamFile --java-options -Xmx30g -I 994_FCH7L2KCCX2_L8_BISvveXAAEEAAA-95.bam -O marked_duplicates_fixed_ValidatedBamFile.txt -R /media/TargetSequencing/TargetSequencing_Example/Bos_taurus_UMD_3.1.1_genome/Bos_taurus_NCBI_UMD_3.1.1/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/version0.6.0/genome.fa

But When I have updated my system Ubuntu 20 version, And I have used the exact same version of all softwares including GATK. Then on the same checked files, When I ran the same command, Now I am getting error.

/home/Software/gatk-4.1.9.0/gatk ValidateSamFile --java-options -Xmx30g -I 994_FCH7L2KCCX2_L8_BISvveXAAEEAAA-95.bam -O marked_duplicates_fixed_ValidatedBamFile.txt -R /media/TargetSequencing/TargetSequencing_Example/Bos_taurus_UMD_3.1.1_genome/Bos_taurus_NCBI_UMD_3.1.1/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/version0.6.0/genome.fa
Using GATK jar /home/Software/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar
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 -Xmx30g -jar /home/Software/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar ValidateSamFile -I 994_FCH7L2KCCX2_L8_BISvveXAAEEAAA-95.sam -O marked_duplicates_fixed_ValidatedBamFile.txt -R /media/TargetSequencing/TargetSequencing_Example/Bos_taurus_UMD_3.1.1_genome/Bos_taurus_NCBI_UMD_3.1.1/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/version0.6.0/genome.fa
13:23:52.972 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/Software/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Jan 04 13:23:52 IST 2022] ValidateSamFile --INPUT 994_FCH7L2KCCX2_L8_BISvveXAAEEAAA-95.sam --OUTPUT marked_duplicates_fixed_ValidatedBamFile.txt --REFERENCE_SEQUENCE /media/TargetSequencing/TargetSequencing_Example/Bos_taurus_UMD_3.1.1_genome/Bos_taurus_NCBI_UMD_3.1.1/Bos_taurus/NCBI/UMD_3.1.1/Sequence/BWAIndex/version0.6.0/genome.fa --MODE VERBOSE --MAX_OUTPUT 100 --IGNORE_WARNINGS false --VALIDATE_INDEX true --INDEX_VALIDATION_STRINGENCY EXHAUSTIVE --IS_BISULFITE_SEQUENCED false --MAX_OPEN_TEMP_FILES 8000 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Jan 04, 2022 1:23:53 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Tue Jan 04 13:23:53 IST 2022] Executing as shazia@shazia-PT on Linux 5.13.0-22-generic amd64; OpenJDK 64-Bit Server VM 11.0.13+8-Ubuntu-0ubuntu1.21.10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.9.0
ERROR 2022-01-04 13:23:54 ValidateSamFile Requesting earlier reference sequence: 15 < 16
[Tue Jan 04 13:23:54 IST 2022] picard.sam.ValidateSamFile done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1061158912
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Tool returned:
-1

Error in file:

ERROR::INVALID_TAG_NM:Record 327, Read name E00591:309:H7L2KCCX2:8:1110:21460:54910, NM tag (nucleotide differences) in file [2] does not match reality [3]
ERROR::INVALID_TAG_NM:Record 2476, Read name E00591:309:H7L2KCCX2:8:1107:28341:25165, NM tag (nucleotide differences) in file [3] does not match reality [4]
ERROR::INVALID_TAG_NM:Record 8644, Read name E00591:309:H7L2KCCX2:8:2204:9962:21526, NM tag (nucleotide differences) in file [1] does not match reality [7]
ERROR::INVALID_TAG_NM:Record 8645, Read name E00591:309:H7L2KCCX2:8:2103:24698:25042, NM tag (nucleotide differences) in file [1] does not match reality [5]
ERROR::INVALID_TAG_NM:Record 8646, Read name E00591:309:H7L2KCCX2:8:1116:15534:37858, NM tag (nucleotide differences) in file [3] does not match reality [6]
ERROR::INVALID_TAG_NM:Record 8647, Read name E00591:309:H7L2KCCX2:8:1116:4574:71084, NM tag (nucleotide differences) in file [2] does not match reality [4]
ERROR::INVALID_TAG_NM:Record 8648, Read name E00591:309:H7L2KCCX2:8:1202:20679:63683, NM tag (nucleotide differences) in file [1] does not match reality [3]
ERROR::INVALID_TAG_NM:Record 8649, Read name E00591:309:H7L2KCCX2:8:1207:11718:22141, NM tag (nucleotide differences) in file [1] does not match reality [3]
ERROR::INVALID_TAG_NM:Record 8650, Read name E00591:309:H7L2KCCX2:8:1214:24282:13105, NM tag (nucleotide differences) in file [1] does not match reality [3]
ERROR::INVALID_TAG_NM:Record 8651, Read name E00591:309:H7L2KCCX2:8:2223:8207:53188, NM tag (nucleotide differences) in file [0] does not match reality [2]
ERROR::INVALID_TAG_NM:Record 8652, Read name E00591:309:H7L2KCCX2:8:2105:9110:53768, NM tag (nucleotide differences) in file [1] does not match reality [3]