Additional info:

a) The reference genome and the SRA are different strains of the same subspecies

b) Reference genome used

https://www.ncbi.nlm.nih.gov/assembly/GCA_900231445.1/ 

c) SRA File used (Illumina paired end reads)

https://www.ncbi.nlm.nih.gov/sra/SRX688079[accn] 

REQUIRED for all errors and issues:
a) GATK version used:

Not sure, I think the most recent?

b) Exact command used:

java -jar /clusterfs/vector/home/groups/software/sl-7.x86_64/modules/picard/2.9.0/lib/picard.jar SortSam I=SRR1559585.extrapreprocessed O=SRR1559585.sorted SORT_ORDER=coordinate

c) Entire program log:

[Tue May 03 16:00:00 PDT 2022] picard.sam.SortSam INPUT=SRR1559585.extrapreprocessed OUTPUT=SRR1559585.sorted SORT_ORDER=coordinate    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue May 03 16:00:00 PDT 2022] Executing as marcusvarni@ln001.brc on Linux 3.10.0-1160.31.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Picard version: 2.9.0-SNAPSHOT
[Tue May 03 16:00:00 PDT 2022] picard.sam.SortSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1011351552
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 25875, Read name SRR1559585.12924, Insert size out of range
        at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:448)
        at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:796)
        at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:781)
        at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:751)
        at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:569)
        at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:543)
        at picard.sam.SortSam.doWork(SortSam.java:99)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

d) What I tried:

1. I first tried cleaning the file up after checking it's validity using ValidateSamFile

2. java -jar /clusterfs/vector/home/groups/software/sl-7.x86_64/modules/picard/2.9.0/lib/picard.jar CleanSam\
         I=SRR1559585.preprocessed \
         O=SRR1559585.extrapreprocessed 

3.  I then tried to do ValidateSamFile (I got the same issue prior to cleaning so I did not include the first ValidateSamFile)

4. java -jar /clusterfs/vector/home/groups/software/sl-7.x86_64/modules/picard/2.9.0/lib/picard.jar ValidateSamFile \
         I=SRR1559585.extrapreprocessed \
         MODE=SUMMARY 

5. Here is the result

6. (base) [marcusvarni@ln001 SvevoSVCBackup]$ java -jar /clusterfs/vector/home/groups/software/sl-7.x86_64/modules/picard/2.9.0/lib/picard.jar ValidateSamFile \
   >       I=SRR1559585.extrapreprocessed \
   >       MODE=SUMMARY
   [Tue May 03 16:02:27 PDT 2022] picard.sam.ValidateSamFile INPUT=SRR1559585.extrapreprocessed MODE=SUMMARY    MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
   [Tue May 03 16:02:27 PDT 2022] Executing as marcusvarni@ln001.brc on Linux 3.10.0-1160.31.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Picard version: 2.9.0-SNAPSHOT
   INFO    2022-05-03 16:03:22     SamFileValidator        Validated Read    10,000,000 records.  Elapsed time: 00:00:54s.  Time for last 10,000,000:   54s.  Last read position: LT934114.1:752,073,531
   INFO    2022-05-03 16:04:15     SamFileValidator        Validated Read    20,000,000 records.  Elapsed time: 00:01:47s.  Time for last 10,000,000:   53s.  Last read position: LT934117.1:577,404,702
   INFO    2022-05-03 16:05:08     SamFileValidator        Validated Read    30,000,000 records.  Elapsed time: 00:02:40s.  Time for last 10,000,000:   53s.  Last read position: LT934116.1:302,764,743
   INFO    2022-05-03 16:06:01     SamFileValidator        Validated Read    40,000,000 records.  Elapsed time: 00:03:33s.  Time for last 10,000,000:   52s.  Last read position: LT934114.1:26,117,261
   INFO    2022-05-03 16:06:57     SamFileValidator        Validated Read    50,000,000 records.  Elapsed time: 00:04:29s.  Time for last 10,000,000:   56s.  Last read position: LT934112.1:95,106,473
   INFO    2022-05-03 16:07:51     SamFileValidator        Validated Read    60,000,000 records.  Elapsed time: 00:05:23s.  Time for last 10,000,000:   54s.  Last read position: LT934119.1:576,450,723
   INFO    2022-05-03 16:08:44     SamFileValidator        Validated Read    70,000,000 records.  Elapsed time: 00:06:16s.  Time for last 10,000,000:   52s.  Last read position: LT934123.1:415,133,202
   
   
   ## HISTOGRAM    java.lang.String
   Error Type      Count
   ERROR:INVALID_INSERT_SIZE       7166
   ERROR:MISSING_PLATFORM_VALUE    1
   
   [Tue May 03 16:09:12 PDT 2022] picard.sam.ValidateSamFile done. Elapsed time: 6.74 minutes.
   Runtime.totalMemory()=824180736
   To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp