BWA Recovery Mode

Running with the latest (4.2.1-1) parabricks image with fq2bam, I’m finding alignment goes very quickly up until BWA encounters some problematic parts of the fastq(?) and needs to enter recovery mode for those reads. Based on back of napkin calculation, this triples the time required to align one set of fastqs. Example log below.

Is this the smith-waterman alignment-based paired-end recovery mode of BWA? Is there any way around the significant speed penalties that it incurs without simply disabling this functionality (and thereby making the alignment worse)

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /tmp/culibl01/ERR4559646_1.fastq and /tmp/culibl01/ERR4559646_2.fastq
[Parabricks Options Mesg]: @RG\tID:ERR4559646.1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:ERR4559646.1.1
[PB Info 2024-Feb-15 15:27:57] ------------------------------------------------------------------------------
[PB Info 2024-Feb-15 15:27:57] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2024-Feb-15 15:27:57] ||                           Version 4.2.1-1.beta4                          ||
[PB Info 2024-Feb-15 15:27:57] ||                      GPU-PBBWA mem, Sorting Phase-I                      ||
[PB Info 2024-Feb-15 15:27:57] ------------------------------------------------------------------------------
[PB Info 2024-Feb-15 15:27:57] Mode = pair-ended-gpu
[PB Info 2024-Feb-15 15:27:57] Running with 1 GPU(s), using 4 stream(s) per device with 16 worker threads per GPU
[PB Info 2024-Feb-15 15:28:07] # 100  0  3  1  0   0 pool:  1 376295764 bases/GPU/minute: 2257774584.0
[PB Info 2024-Feb-15 15:28:17] # 100  0  4  0  0   0 pool:  3 1019784341 bases/GPU/minute: 3860931462.0
[PB Info 2024-Feb-15 15:28:27] # 100  0  4  1  0   0 pool:  2 1742526796 bases/GPU/minute: 4336454730.0
[PB Info 2024-Feb-15 15:28:37] # 100  3  2  3  0   0 pool:  2 2386246789 bases/GPU/minute: 3862319958.0
[PB Info 2024-Feb-15 15:28:47] # 100  0  5  0  0   0 pool:  5 3079238566 bases/GPU/minute: 4157950662.0
[PB Info 2024-Feb-15 15:28:57] # 99  0  5  0  0   0 pool:  6 3752474794 bases/GPU/minute: 4039417368.0
[PB Info 2024-Feb-15 15:29:07] # 100  0  5  1  0   0 pool:  4 4435583518 bases/GPU/minute: 4098652344.0
[PB Info 2024-Feb-15 15:29:17] # 100  1  4  1  0   0 pool:  4 5089076473 bases/GPU/minute: 3920957730.0
[PB Info 2024-Feb-15 15:29:27] # 100  3  6  2  0   0 pool:  2 5722748993 bases/GPU/minute: 3802035120.0
[PB Info 2024-Feb-15 15:29:37] # 100  2  7  0  0   0 pool:  4 6386056040 bases/GPU/minute: 3979842282.0
[PB Info 2024-Feb-15 15:29:47] # 100  0  9  0  0   0 pool:  5 7049432173 bases/GPU/minute: 3980256798.0
[PB Info 2024-Feb-15 15:29:57] # 100  0  9  0  0   0 pool:  4 7722672509 bases/GPU/minute: 4039442016.0
[PB Info 2024-Feb-15 15:30:07] # 100  0  9  2  0   0 pool:  2 8415804915 bases/GPU/minute: 4158794436.0
[PB Info 2024-Feb-15 15:30:17] # 100  2  7  1  0   0 pool:  3 9029741746 bases/GPU/minute: 3683620986.0
[PB Info 2024-Feb-15 15:30:27] # 100  0  9  0  0   0 pool:  5 9683289591 bases/GPU/minute: 3921287070.0
[PB Info 2024-Feb-15 15:30:37] # 100  1  8  1  0   0 pool:  3 10336748204 bases/GPU/minute: 3920751678.0
[PB Info 2024-Feb-15 15:30:47] # 100  0  9  0  0   0 pool:  7 10940785324 bases/GPU/minute: 3624222720.0
[PB Info 2024-Feb-15 15:30:57] # 100  4  5  2  0   0 pool:  4 11584547906 bases/GPU/minute: 3862575492.0
[PB Info 2024-Feb-15 15:31:07] # 100  0  9  0  0   0 pool:  6 12287589254 bases/GPU/minute: 4218248088.0
[PB Info 2024-Feb-15 15:31:17] # 100  1  8  1  0   0 pool:  5 12941168400 bases/GPU/minute: 3921474876.0
[PB Info 2024-Feb-15 15:31:27] # 100  0  9  0  0   0 pool:  7 13604603952 bases/GPU/minute: 3980613312.0
[PB Info 2024-Feb-15 15:31:37] # 98  0  8  0  0   0 pool:  9 14297800828 bases/GPU/minute: 4159181256.0
[PB Info 2024-Feb-15 15:31:47] # 100  0  9  0  0   0 pool:  7 14961187527 bases/GPU/minute: 3980320194.0
[PB Info 2024-Feb-15 15:31:57] # 100  7  2  8  0   0 pool:  1 15535585245 bases/GPU/minute: 3446386308.0
[PB Info 2024-Feb-15 15:32:07] # 100  0  9  0  0   0 pool: 10 16209039372 bases/GPU/minute: 4040724762.0
[PB Info 2024-Feb-15 15:32:17] # 100  0 21  0  0   0 pool: 11 16714291653 bases/GPU/minute: 3031513686.0
[PB Info 2024-Feb-15 15:32:27] # 100  0 21  0  0   0 pool: 11 17328424445 bases/GPU/minute: 3684796752.0
[PB Info 2024-Feb-15 15:32:37] # 100  0 21  0  0   0 pool: 12 17982039996 bases/GPU/minute: 3921693306.0
[PB Info 2024-Feb-15 15:32:47] # 100  1 20  1  0   0 pool: 10 18566453091 bases/GPU/minute: 3506478570.0
[PB Info 2024-Feb-15 15:32:57] # 100  1 20  2  0   0 pool:  9 19230098339 bases/GPU/minute: 3981871488.0
[PB Info 2024-Feb-15 15:33:07] # 100  0 21  0  0   0 pool: 11 19903590079 bases/GPU/minute: 4040950440.0
[PB Info 2024-Feb-15 15:33:17] # 100  1 20  0  0   0 pool: 11 20507842012 bases/GPU/minute: 3625511598.0
[PB Info 2024-Feb-15 15:33:27] # 96  0 21  0  0   0 pool: 15 20804929624 bases/GPU/minute: 1782525672.0
[PB Info 2024-Feb-15 15:33:37] # 77  0 21  1  0   0 pool: 33 20983556028 bases/GPU/minute: 1071758424.0
[PB Info 2024-Feb-15 15:33:47] Pair-ended recovery mode for batch with 140967936 (both ends) reads before itself
[PB Info 2024-Feb-15 15:33:47] # 68  1 19  1  0   0 pool: 43 21083350089 bases/GPU/minute: 598764366.0
[PB Info 2024-Feb-15 15:33:54] Pair-ended recovery mode for batch with 140902400 (both ends) reads before itself
[PB Info 2024-Feb-15 15:33:57] # 58 10  9 10  0   0 pool: 45 21103293622 bases/GPU/minute: 119661198.0
[PB Info 2024-Feb-15 15:34:01] Single-ended recovery mode for batch with 141819904 (both ends) reads before itself
[PB Info 2024-Feb-15 15:34:07] # 50 16  2 17  0   0 pool: 47 21123237945 bases/GPU/minute: 119665938.0
[PB Info 2024-Feb-15 15:34:13] Single-ended recovery mode for batch with 142737408 (both ends) reads before itself
[PB Info 2024-Feb-15 15:34:17] # 37 28  0 19  1   0 pool: 47 21123237945 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:34:23] Pair-ended recovery mode for batch with 141819904 (both ends) reads before itself
[PB Info 2024-Feb-15 15:34:24] Pair-ended recovery mode for batch with 141099008 (both ends) reads before itself
[PB Info 2024-Feb-15 15:34:27] # 20 44  0 19  1   0 pool: 48 21133289746 bases/GPU/minute: 60310806.0
[PB Info 2024-Feb-15 15:34:35] Single-ended recovery mode for batch with 144965632 (both ends) reads before itself
[PB Info 2024-Feb-15 15:34:37] #  5 58  0 19  2   0 pool: 48 21133289746 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:34:47] #  0 67  0 19  2   0 pool: 48 21133289746 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:34:57] #  0 67  0 19  2   0 pool: 48 21133289746 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:35:07] #  0 67  0 19  2   0 pool: 48 21133289746 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:35:17] #  0 67  0 19  2   0 pool: 48 21133289746 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:35:27] #  0 67  0 19  2   0 pool: 48 21133289746 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:35:37] #  0 67  0 19  2   0 pool: 48 21133289746 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:35:47] #  0 67  0 18  1   0 pool: 50 21153301338 bases/GPU/minute: 120069552.0
[PB Info 2024-Feb-15 15:35:57] #  0 67  0 18  1   0 pool: 50 21153301338 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:36:07] Pair-ended recovery mode for batch with 142737408 (both ends) reads before itself
[PB Info 2024-Feb-15 15:36:07] #  0 67  0 18  1   0 pool: 50 21153301338 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:36:17] #  0 66  0 18  0   0 pool: 52 21173507754 bases/GPU/minute: 121238496.0
[PB Info 2024-Feb-15 15:36:27] #  0 66  0 18  0   0 pool: 52 21173507754 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:36:36] Pair-ended recovery mode for batch with 141754368 (both ends) reads before itself
[PB Info 2024-Feb-15 15:36:37] #  0 56  0 19  0   0 pool: 61 21264526874 bases/GPU/minute: 546114720.0
[PB Info 2024-Feb-15 15:36:47] #  0 56  0 19  0   0 pool: 61 21264526874 bases/GPU/minute: 0.0
[PB Info 2024-Feb-15 15:36:54] Pair-ended recovery mode for batch with 141885440 (both ends) reads before itself