REQUIRED for all errors and issues:
a) GATK version used:4.1.3.0
b) Exact command used: gatk --java-options "-Xmx150g" PathSeqPipelineSpark     --input endometriosis.bam     --filter-bwa-image pathseq_host.fa.img     --kmer-file pathseq_host.bfi     --min-clipped-read-length 60     --microbe-fasta pathseq_microbe.fa     --microbe-bwa-image pathseq_microbe.fa.img     --taxonomy-file pathseq_taxonomy.db     --output endometriosis.pathseq.complete.bam     --scores-output endometriosis.pathseq.complete.csv     --is-host-aligned false     --filter-duplicates false     --min-score-identity .7 
c) Entire program log:23/11/12 13:43:32 INFO TaskSchedulerImpl: Removed TaskSet 16.0, whose tasks have all completed, from pool 
23/11/12 13:43:32 INFO DAGScheduler: ShuffleMapStage 16 (repartition at PathSeqPipelineSpark.java:198) finished in 7.562 s
23/11/12 13:43:32 INFO DAGScheduler: looking for newly runnable stages
23/11/12 13:43:32 INFO DAGScheduler: running: Set()
23/11/12 13:43:32 INFO DAGScheduler: waiting: Set(ShuffleMapStage 17, ResultStage 18)
23/11/12 13:43:32 INFO DAGScheduler: failed: Set()
23/11/12 13:43:32 INFO BlockManagerInfo: Removed broadcast_8_piece0 on 172.16.13.191:43771 in memory (size: 3.1 KB, free: 79.7 GB)
23/11/12 13:43:32 INFO DAGScheduler: Submitting ShuffleMapStage 17 (MapPartitionsRDD[63] at mapPartitionsToPair at PSScorer.java:68), which has no missing parents
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 160
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 150
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 157
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 202
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 165
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 173
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 210
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 158
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 168
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 154
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 172
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 211
23/11/12 13:43:32 INFO ContextCleaner: Cleaned accumulator 152
23/11/12 13:43:32 INFO MemoryStore: Block broadcast_15 stored as values in memory (estimated size 12.0 KB, free 77.2 GB)
23/11/12 13:43:32 INFO MemoryStore: Block broadcast_15_piece0 stored as bytes in memory (estimated size 6.2 KB, free 77.2 GB)
23/11/12 13:43:32 INFO BlockManagerInfo: Added broadcast_15_piece0 in memory on 172.16.13.191:43771 (size: 6.2 KB, free: 79.7 GB)
23/11/12 13:43:32 INFO SparkContext: Created broadcast 15 from broadcast at DAGScheduler.scala:1161
23/11/12 13:43:32 INFO DAGScheduler: Submitting 4 missing tasks from ShuffleMapStage 17 (MapPartitionsRDD[63] at mapPartitionsToPair at PSScorer.java:68) (first 15 tasks are for partitions Vector(0, 1, 2, 3))
23/11/12 13:43:32 INFO TaskSchedulerImpl: Adding task set 17.0 with 4 tasks
23/11/12 13:43:32 INFO TaskSetManager: Starting task 0.0 in stage 17.0 (TID 1401, localhost, executor driver, partition 0, PROCESS_LOCAL, 8036 bytes)
23/11/12 13:43:32 INFO TaskSetManager: Starting task 1.0 in stage 17.0 (TID 1402, localhost, executor driver, partition 1, ANY, 8036 bytes)
23/11/12 13:43:32 INFO TaskSetManager: Starting task 2.0 in stage 17.0 (TID 1403, localhost, executor driver, partition 2, ANY, 8036 bytes)
23/11/12 13:43:32 INFO TaskSetManager: Starting task 3.0 in stage 17.0 (TID 1404, localhost, executor driver, partition 3, ANY, 8036 bytes)
23/11/12 13:43:32 INFO Executor: Running task 0.0 in stage 17.0 (TID 1401)
23/11/12 13:43:32 INFO Executor: Running task 1.0 in stage 17.0 (TID 1402)
23/11/12 13:43:32 INFO Executor: Running task 3.0 in stage 17.0 (TID 1404)
23/11/12 13:43:32 INFO Executor: Running task 2.0 in stage 17.0 (TID 1403)
java: bwa.c:329: bwa_mem2idx: Assertion `k == l_mem' failed.
 Due to the log is too long, I can't psate all.

I want to explore the reads of bacteria in each spot of spatial transcriptome data. But after converting the spatial transcriptome raw data fasta into a bam file, I encountered a bug using the above code.