I am getting an error running mutect2 with panel of normals on some samples, but not others. Mutect2 w/o a panel of normals works well on all the samples, and when I run validatesamfiles on the bam files that fail, I get that there are no errors. Not sure what could be causing this error. 

I run the following command on all the samples:

On the samples that have an error I get the following log:

[eam255@r206u22n03.mccleary scripts]$ nano KNPH99-1.mutect.out
[eam255@r206u22n03.mccleary scripts]$ cat KNPH99-1.mutect.out 
19:11:00.737 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/vast/palmer/apps/avx2/software/GATK/4.4.0.0-GCCcore-10.2.0-Java-17/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compre
ssion.so
19:11:00.832 INFO  Mutect2 - ------------------------------------------------------------
19:11:00.838 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.4.0.0
19:11:00.838 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
19:11:00.838 INFO  Mutect2 - Executing as eam255@r209u11n01.mccleary.ycrc.yale.edu on Linux v4.18.0-372.52.1.el8_6.x86_64 amd64
19:11:00.838 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.4+8
19:11:00.838 INFO  Mutect2 - Start Date/Time: September 8, 2023 at 7:11:00 PM EDT
19:11:00.838 INFO  Mutect2 - ------------------------------------------------------------
19:11:00.838 INFO  Mutect2 - ------------------------------------------------------------
19:11:00.839 INFO  Mutect2 - HTSJDK Version: 3.0.5
19:11:00.839 INFO  Mutect2 - Picard Version: 3.0.0
19:11:00.839 INFO  Mutect2 - Built for Spark Version: 3.3.1
19:11:00.839 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:11:00.839 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:11:00.840 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:11:00.840 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:11:00.840 INFO  Mutect2 - Deflater: IntelDeflater
19:11:00.840 INFO  Mutect2 - Inflater: IntelInflater
19:11:00.840 INFO  Mutect2 - GCS max retries/reopens: 20
19:11:00.840 INFO  Mutect2 - Requester pays: disabled
19:11:00.841 INFO  Mutect2 - Initializing engine
19:11:00.913 INFO  Mutect2 - Shutting down engine
[September 8, 2023 at 7:11:00 PM EDT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=19327352832
java.lang.RuntimeException: Cannot use index file with textual SAM file
        at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:442)
        at htsjdk.samtools.SamReaderFactory.open(SamReaderFactory.java:106)
        at org.broadinstitute.hellbender.engine.ReadsPathDataSource.<init>(ReadsPathDataSource.java:245)
        at org.broadinstitute.hellbender.engine.ReadsPathDataSource.<init>(ReadsPathDataSource.java:181)
        at org.broadinstitute.hellbender.engine.GATKTool.initializeReads(GATKTool.java:453)
        at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:724)
        at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:79)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:147)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /vast/palmer/apps/avx2/software/GATK/4.4.0.0-GCCcore-10.2.0-Java-17/gatk-package-4.4.0.0-local.jar