Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/7a/2f6363deefdf3aa28599cf69cf6053/.command.sh
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.0123
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.fai
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.bwt.2bit.64
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/e1/9db74a20d7f737a10a7fe95e3d353e/nf_gui_test_four.1.fastp.fq.gz
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.pac
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.ann
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/7a/2f6363deefdf3aa28599cf69cf6053/.command.run
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/e1/9db74a20d7f737a10a7fe95e3d353e/nf_gui_test_four.2.fastp.fq.gz
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.amb
==> STAGING COMPLETE (11 inputs)
Looking to launch executable "/opt/conda/bin/bwa-mem2.avx512bw", simd = .avx512bw
Launching executable "/opt/conda/bin/bwa-mem2.avx512bw"
-----------------------------
Executing in AVX512 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: hg38.fa
* Entering FMI_search
* Index file found. Loading index from hg38.fa.bwt.2bit.64
* Reference seq len for bi-index = 6418572211
* sentinel-index: 2729492284
* Count:
0, 1
1, 1879238230
2, 3209286106
3, 4539333982
4, 6418572211
* Reading other elements of the index from files hg38.fa
* Index prefix: hg38.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = hg38.fa.0123
* Reference genome size: 6418572210 bp
* Done reading reference genome !!
------------------------------------------
1. Memory pre-allocation for Chaining: 696.7080 MB
2. Memory pre-allocation for BSW: 958.4681 MB
3. Memory pre-allocation for BWT: 309.2567 MB
------------------------------------------
* Threads used (compute): 4
* No. of pipeline threads: 2
[0000] read_chunk: 50000000, work_chunk_size: 50000139, nseq: 380326
[0000][ M::kt_pipeline] read 380326 sequences (50000139 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 50000148, nseq: 381042
[0000][ M::kt_pipeline] read 381042 sequences (50000148 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 380326
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189165, 0, 0)
[0000][PE] skip orientation FF as there are not enough pairs
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (136, 169, 202)
[0000][PE] low and high boundaries for computing mean and std.dev: (4, 334)
[0000][PE] mean and std.dev: (169.10, 48.71)
[0000][PE] low and high boundaries for proper pairs: (1, 400)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 380326 reads in 44.665 CPU sec, 11.023 real sec
[0000] Reallocating initial memory allocations!!
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 50000071, nseq: 382130
[0000][ M::kt_pipeline] read 382130 sequences (50000071 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 381042
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189142, 0, 0)
[0000][PE] skip orientation FF as there are not enough pairs
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (136, 170, 202)
[0000][PE] low and high boundaries for computing mean and std.dev: (4, 334)
[0000][PE] mean and std.dev: (169.51, 49.26)
[0000][PE] low and high boundaries for proper pairs: (1, 400)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 381042 reads in 44.967 CPU sec, 11.115 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 50000104, nseq: 382024
[0000][ M::kt_pipeline] read 382024 sequences (50000104 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 382130
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 190068, 0, 0)
[0000][PE] skip orientation FF as there are not enough pairs
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (134, 168, 202)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 338)
[0000][PE] mean and std.dev: (168.42, 49.72)
[0000][PE] low and high boundaries for proper pairs: (1, 406)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 382130 reads in 44.121 CPU sec, 10.880 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 29717809, nseq: 226420
[0000][ M::kt_pipeline] read 226420 sequences (29717809 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 382024
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189753, 0, 0)
[0000][PE] skip orientation FF as there are not enough pairs
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (135, 168, 201)
[0000][PE] low and high boundaries for computing mean and std.dev: (3, 333)
[0000][PE] mean and std.dev: (168.22, 49.27)
[0000][PE] low and high boundaries for proper pairs: (1, 399)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 382024 reads in 44.370 CPU sec, 11.004 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 226420
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 112442, 0, 0)
[0000][PE] skip orientation FF as there are not enough pairs
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (135, 168, 202)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 336)
[0000][PE] mean and std.dev: (168.92, 48.89)
[0000][PE] low and high boundaries for proper pairs: (1, 403)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 226420 reads in 25.795 CPU sec, 6.432 real sec
[0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 4
Processor is running @3000.484954 MHz
Runtime profile:
Time taken for main_mem function: 62.15 sec
IO times (sec) :
Reading IO time (reads) avg: 3.08, (3.08, 3.08)
Writing IO time (SAM) avg: 1.06, (1.06, 1.06)
Reading IO time (Reference Genome) avg: 3.89, (3.89, 3.89)
Index read time avg: 6.09, (6.09, 6.09)
Overall time (sec) (Excluding Index reading time):
PROCESS() (Total compute time + (read + SAM) IO time) : 51.42
MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 50.45, (50.45, 50.45)
SAM Processing time (sec):
--WORKER_SAM avg: 16.20, (16.20, 16.20)
Kernels' compute time (sec):
Total kernel (smem+sal+bsw) time avg: 34.05, (34.05, 34.05)
SMEM compute avg: 21.92, (21.95, 21.89)
SAL compute avg: 2.76, (2.76, 2.75)
MEM_SA avg: 1.67, (1.68, 1.66)
BSW time, avg: 8.78, (8.79, 8.77)
Important parameter settings:
BATCH_SIZE: 512
MAX_SEQ_LEN_REF: 256
MAX_SEQ_LEN_QER: 128
MAX_SEQ_LEN8: 128
SEEDS_PER_READ: 500
SIMD_WIDTH8 X: 64
SIMD_WIDTH16 X: 32
AVG_SEEDS_PER_READ: 64
[bam_sort_core] merging from 0 files and 4 in-memory blocks...