Benchmark Results of dataset 2 (now marked dataset 1)

GZHoffie · Jan 26, 2023 · 3b50e7b · 3b50e7b
1 parent 49527ed
commit 3b50e7b
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Showing 16 changed files with 161 additions and 191 deletions.
diff --git a/bucket_map/benchmark/benchmark.sh b/bucket_map/benchmark/benchmark.sh
@@ -2,7 +2,7 @@
 
 GENOME_FILE="/mnt/d/genome/Egu.v3.genome_f.fasta"
 BENCHMARK_PATH="/home/zhenhao/bucket-map/bucket_map/benchmark"
-QUERY_FILE="/mnt/d/genome/test/sim_illumina_1M.fastq"
+QUERY_FILE="/mnt/d/genome/test/sim_150_1M.fastq"
 INDICATOR="egu"
 
 # initialize benchmark directory if it doesnt exist

diff --git a/bucket_map/benchmark/benchmark_map.sh b/bucket_map/benchmark/benchmark_map.sh
@@ -11,20 +11,20 @@ INDEX_INDICATOR=$3
 cd "${BENCHMARK_PATH}/index"
 
 # run bowtie2 to map the reads
-#echo "Mapping using bowtie2"
-#/usr/bin/time -o "${BENCHMARK_PATH}/log/bowtie2_map.time" -v bowtie2 -x "${INDEX_INDICATOR}_bowtie" -U ${FASTQ_PATH} -S "${BENCHMARK_PATH}/output/bowtie2_map.sam" &> "${BENCHMARK_PATH}/log/bowtie2_map.log"
+echo "Mapping using bowtie2"
+/usr/bin/time -o "${BENCHMARK_PATH}/log/bowtie2_map.time" -v bowtie2 -x "${INDEX_INDICATOR}_bowtie" -U ${FASTQ_PATH} -S "${BENCHMARK_PATH}/output/bowtie2_map.sam" &> "${BENCHMARK_PATH}/log/bowtie2_map.log"
 
 # run bwa to map the reads
-#echo "Mapping using bwa"
-#/usr/bin/time -o "${BENCHMARK_PATH}/log/bwa_map.time" -v bwa mem "${INDEX_INDICATOR}_bwa" ${FASTQ_PATH} > "${BENCHMARK_PATH}/output/bwa_map.sam" 2> "${BENCHMARK_PATH}/log/bwa_map.log"
+echo "Mapping using bwa"
+/usr/bin/time -o "${BENCHMARK_PATH}/log/bwa_map.time" -v bwa mem "${INDEX_INDICATOR}_bwa" ${FASTQ_PATH} > "${BENCHMARK_PATH}/output/bwa_map.sam" 2> "${BENCHMARK_PATH}/log/bwa_map.log"
 
 # run subread to map the reads
-#echo "Mapping using subread"
-#/usr/bin/time -o "${BENCHMARK_PATH}/log/subread_map.time" -v subread-align --SAMoutput -i "${INDEX_INDICATOR}_subread" -r ${FASTQ_PATH} -t 1 -o "${BENCHMARK_PATH}/output/subread_map.sam" &> "${BENCHMARK_PATH}/log/subread_map.log"
+echo "Mapping using subread"
+/usr/bin/time -o "${BENCHMARK_PATH}/log/subread_map.time" -v subread-align --SAMoutput -i "${INDEX_INDICATOR}_subread" -r ${FASTQ_PATH} -t 1 -o "${BENCHMARK_PATH}/output/subread_map.sam" &> "${BENCHMARK_PATH}/log/subread_map.log"
 
 # run minimap2
-#echo "Mapping using minimap2"
-#/usr/bin/time -o "${BENCHMARK_PATH}/log/minimap2_map.time" -v minimap2 -a "${INDEX_INDICATOR}_minimap.mmi" ${FASTQ_PATH} > "${BENCHMARK_PATH}/output/minimap2_map.sam" 2> "${BENCHMARK_PATH}/log/minimap2_map.log"
+echo "Mapping using minimap2"
+/usr/bin/time -o "${BENCHMARK_PATH}/log/minimap2_map.time" -v minimap2 -a "${INDEX_INDICATOR}_minimap.mmi" ${FASTQ_PATH} > "${BENCHMARK_PATH}/output/minimap2_map.sam" 2> "${BENCHMARK_PATH}/log/minimap2_map.log"
 
 # run bucketmap
 echo "Mapping using BucketMap"

diff --git a/bucket_map/benchmark/log/bowtie2_map.log b/bucket_map/benchmark/log/bowtie2_map.log
@@ -1,6 +1,6 @@
 1000000 reads; of these:
   1000000 (100.00%) were unpaired; of these:
-    1096 (0.11%) aligned 0 times
-    449108 (44.91%) aligned exactly 1 time
-    549796 (54.98%) aligned >1 times
-99.89% overall alignment rate
+    754 (0.08%) aligned 0 times
+    381230 (38.12%) aligned exactly 1 time
+    618016 (61.80%) aligned >1 times
+99.92% overall alignment rate
diff --git a/bucket_map/benchmark/log/bowtie2_map.time b/bucket_map/benchmark/log/bowtie2_map.time
@@ -1,21 +1,21 @@
-	Command being timed: "bowtie2 -x egu_bowtie -U /mnt/d/genome/test/sim_illumina_1M.fastq -S /home/zhenhao/bucket-map/bucket_map/benchmark/output/bowtie2_map.sam"
-	User time (seconds): 852.35
-	System time (seconds): 1.33
+	Command being timed: "bowtie2 -x egu_bowtie -U /mnt/d/genome/test/sim_150_1M.fastq -S /home/zhenhao/bucket-map/bucket_map/benchmark/output/bowtie2_map.sam"
+	User time (seconds): 403.08
+	System time (seconds): 3.29
 	Percent of CPU this job got: 99%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 14:21.50
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 6:48.80
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 1968900
+	Maximum resident set size (kbytes): 1965552
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 102
+	Major (requiring I/O) page faults: 114
 	Minor (reclaiming a frame) page faults: 8740
-	Voluntary context switches: 97183
-	Involuntary context switches: 636
+	Voluntary context switches: 47922
+	Involuntary context switches: 436
 	Swaps: 0
-	File system inputs: 3866056
-	File system outputs: 1382648
+	File system inputs: 3912064
+	File system outputs: 792880
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0

diff --git a/bucket_map/benchmark/log/bucketmap_align_map.log b/bucket_map/benchmark/log/bucketmap_align_map.log
@@ -3,10 +3,10 @@
 [INFO]		Set q-gram shape to be: [1,1,1,0,1,1,1,0,1,0,1,1] with number of effective characters: 9
 [ERROR]		The specified file already exists in directory: "/home/zhenhao/bucket-map/bucket_map/benchmark/index/egu_bucketmap.qgram".
 [BENCHMARK]	Number of Q-grams with distinguishability >= 0.499981: 252427 (96.2933%).
-[BENCHMARK]	Elapsed time for loading index files: 15.571 s.
+[BENCHMARK]	Elapsed time for loading index files: 15.649 s.
 [INFO]		Successfully loaded "/home/zhenhao/bucket-map/bucket_map/benchmark/index/egu_bucketmap.qgram".
-[BENCHMARK]	Elapsed time for bucket mapping: 62.939 s (62.939 μs/seq).
-[BENCHMARK]	Total time used for building k-mer index for each bucket: 202.868 s.
-[BENCHMARK]	Total time used for finding exact location of the sequences: 6.124 s (6.124 μs/seq).
-[BENCHMARK]	Total mapped locations: 1141838 (1.14184 per sequence).
-[BENCHMARK]	Total time used for alignment verification and output: 69.636 s (60.9859 μs per pairwise alignment).
+[BENCHMARK]	Elapsed time for bucket mapping: 55.334 s (55.334 μs/seq).
+[BENCHMARK]	Total time used for building k-mer index for each bucket: 216.264 s.
+[BENCHMARK]	Total time used for finding exact location of the sequences: 5.719 s (5.719 μs/seq).
+[BENCHMARK]	Total mapped locations: 1259479 (1.25948 per sequence).
+[BENCHMARK]	Total time used for alignment verification and output: 51.045 s (40.5287 μs per pairwise alignment).
diff --git a/bucket_map/benchmark/log/bucketmap_align_map.time b/bucket_map/benchmark/log/bucketmap_align_map.time
@@ -1,21 +1,21 @@
-	Command being timed: "bucketmap_align --version-check 0 -i egu_bucketmap -q /mnt/d/genome/test/sim_illumina_1M.fastq -o /home/zhenhao/bucket-map/bucket_map/benchmark/output/bucketmap_align_map.sam"
-	User time (seconds): 385.71
-	System time (seconds): 2.07
+	Command being timed: "bucketmap_align --version-check 0 -i egu_bucketmap -q /mnt/d/genome/test/sim_150_1M.fastq -o /home/zhenhao/bucket-map/bucket_map/benchmark/output/bucketmap_align_map.sam"
+	User time (seconds): 374.66
+	System time (seconds): 1.34
 	Percent of CPU this job got: 99%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 6:30.88
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 6:18.28
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 865640
+	Maximum resident set size (kbytes): 866584
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 0
-	Minor (reclaiming a frame) page faults: 137679
-	Voluntary context switches: 14549
-	Involuntary context switches: 297
+	Major (requiring I/O) page faults: 13
+	Minor (reclaiming a frame) page faults: 138580
+	Voluntary context switches: 10958
+	Involuntary context switches: 193
 	Swaps: 0
-	File system inputs: 0
-	File system outputs: 1429848
+	File system inputs: 1848
+	File system outputs: 837824
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0

diff --git a/bucket_map/benchmark/log/bucketmap_map.log b/bucket_map/benchmark/log/bucketmap_map.log
@@ -3,10 +3,10 @@
 [INFO]		Set q-gram shape to be: [1,1,1,0,1,1,1,0,1,0,1,1] with number of effective characters: 9
 [ERROR]		The specified file already exists in directory: "/home/zhenhao/bucket-map/bucket_map/benchmark/index/egu_bucketmap.qgram".
 [BENCHMARK]	Number of Q-grams with distinguishability >= 0.499981: 252427 (96.2933%).
-[BENCHMARK]	Elapsed time for loading index files: 15.735 s.
+[BENCHMARK]	Elapsed time for loading index files: 16.803 s.
 [INFO]		Successfully loaded "/home/zhenhao/bucket-map/bucket_map/benchmark/index/egu_bucketmap.qgram".
-[BENCHMARK]	Elapsed time for bucket mapping: 61.281 s (61.281 μs/seq).
-[BENCHMARK]	Total time used for building k-mer index for each bucket: 190.608 s.
-[BENCHMARK]	Total time used for finding exact location of the sequences: 5.96 s (5.96 μs/seq).
-[BENCHMARK]	Total mapped locations: 1145380 (1.14538 per sequence).
-[BENCHMARK]	Total time used for alignment verification and output: 3.187 s (2.78248 μs per pairwise alignment).
+[BENCHMARK]	Elapsed time for bucket mapping: 54.044 s (54.044 μs/seq).
+[BENCHMARK]	Total time used for building k-mer index for each bucket: 180.486 s.
+[BENCHMARK]	Total time used for finding exact location of the sequences: 5.14 s (5.14 μs/seq).
+[BENCHMARK]	Total mapped locations: 1260792 (1.26079 per sequence).
+[BENCHMARK]	Total time used for alignment verification and output: 2.004 s (1.58948 μs per pairwise alignment).
diff --git a/bucket_map/benchmark/log/bucketmap_map.time b/bucket_map/benchmark/log/bucketmap_map.time
@@ -1,21 +1,21 @@
-	Command being timed: "bucketmap --version-check 0 -i egu_bucketmap -q /mnt/d/genome/test/sim_illumina_1M.fastq -o /home/zhenhao/bucket-map/bucket_map/benchmark/output/bucketmap_map.sam"
-	User time (seconds): 305.03
-	System time (seconds): 1.19
-	Percent of CPU this job got: 97%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 5:12.65
+	Command being timed: "bucketmap --version-check 0 -i egu_bucketmap -q /mnt/d/genome/test/sim_150_1M.fastq -o /home/zhenhao/bucket-map/bucket_map/benchmark/output/bucketmap_map.sam"
+	User time (seconds): 288.54
+	System time (seconds): 1.72
+	Percent of CPU this job got: 98%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 4:53.57
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 865604
+	Maximum resident set size (kbytes): 866576
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 0
-	Minor (reclaiming a frame) page faults: 137770
-	Voluntary context switches: 15141
-	Involuntary context switches: 110
+	Major (requiring I/O) page faults: 35
+	Minor (reclaiming a frame) page faults: 138500
+	Voluntary context switches: 11005
+	Involuntary context switches: 361
 	Swaps: 0
-	File system inputs: 1219184
-	File system outputs: 1425232
+	File system inputs: 1703336
+	File system outputs: 830096
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0

diff --git a/bucket_map/benchmark/log/bwa_map.log b/bucket_map/benchmark/log/bwa_map.log
@@ -1,64 +1,34 @@
 [M::bwa_idx_load_from_disk] read 0 ALT contigs
-[M::process] read 33334 sequences (10000189 bp)...
-[M::process] read 33334 sequences (10000161 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.062 CPU sec, 19.015 real sec
-[M::process] read 33334 sequences (10000229 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.058 CPU sec, 18.974 real sec
-[M::process] read 33334 sequences (10000185 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.634 CPU sec, 18.548 real sec
-[M::process] read 33334 sequences (10000184 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.937 CPU sec, 18.848 real sec
-[M::process] read 33334 sequences (10000098 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.862 CPU sec, 18.767 real sec
-[M::process] read 33334 sequences (10000072 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.215 CPU sec, 18.132 real sec
-[M::process] read 33334 sequences (10000205 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.848 CPU sec, 18.772 real sec
-[M::process] read 33334 sequences (10000179 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.321 CPU sec, 19.243 real sec
-[M::process] read 33334 sequences (10000201 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.397 CPU sec, 19.323 real sec
-[M::process] read 33334 sequences (10000218 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.666 CPU sec, 18.575 real sec
-[M::process] read 33334 sequences (10000153 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.696 CPU sec, 18.608 real sec
-[M::process] read 33334 sequences (10000154 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.774 CPU sec, 18.685 real sec
-[M::process] read 33334 sequences (10000113 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.487 CPU sec, 18.398 real sec
-[M::process] read 33334 sequences (10000180 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.164 CPU sec, 19.070 real sec
-[M::process] read 33334 sequences (10000156 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.309 CPU sec, 18.222 real sec
-[M::process] read 33334 sequences (10000204 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.050 CPU sec, 18.955 real sec
-[M::process] read 33334 sequences (10000185 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.470 CPU sec, 19.364 real sec
-[M::process] read 33334 sequences (10000106 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.594 CPU sec, 18.507 real sec
-[M::process] read 33334 sequences (10000287 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.112 CPU sec, 18.040 real sec
-[M::process] read 33334 sequences (10000122 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.780 CPU sec, 18.700 real sec
-[M::process] read 33334 sequences (10000230 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.569 CPU sec, 18.488 real sec
-[M::process] read 33334 sequences (10000214 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.355 CPU sec, 18.274 real sec
-[M::process] read 33334 sequences (10000211 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.583 CPU sec, 18.494 real sec
-[M::process] read 33334 sequences (10000157 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.781 CPU sec, 18.692 real sec
-[M::process] read 33334 sequences (10000189 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.631 CPU sec, 18.555 real sec
-[M::process] read 33334 sequences (10000208 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 18.175 CPU sec, 18.090 real sec
-[M::process] read 33334 sequences (10000251 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.095 CPU sec, 19.032 real sec
-[M::process] read 33334 sequences (10000162 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.234 CPU sec, 19.158 real sec
-[M::process] read 33314 sequences (9994033 bp)...
-[M::mem_process_seqs] Processed 33334 reads in 19.433 CPU sec, 19.363 real sec
-[M::mem_process_seqs] Processed 33314 reads in 18.992 CPU sec, 18.944 real sec
+[M::process] read 66668 sequences (10000175 bp)...
+[M::process] read 66668 sequences (10000287 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 18.795 CPU sec, 18.643 real sec
+[M::process] read 66668 sequences (10000135 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.630 CPU sec, 17.552 real sec
+[M::process] read 66668 sequences (10000223 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.410 CPU sec, 17.312 real sec
+[M::process] read 66668 sequences (10000261 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.501 CPU sec, 17.408 real sec
+[M::process] read 66668 sequences (10000265 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.450 CPU sec, 17.368 real sec
+[M::process] read 66668 sequences (10000098 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 18.071 CPU sec, 17.977 real sec
+[M::process] read 66666 sequences (10000004 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.534 CPU sec, 17.406 real sec
+[M::process] read 66668 sequences (10000072 bp)...
+[M::mem_process_seqs] Processed 66666 reads in 17.302 CPU sec, 17.216 real sec
+[M::process] read 66668 sequences (10000216 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.559 CPU sec, 17.467 real sec
+[M::process] read 66668 sequences (10000055 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.334 CPU sec, 17.244 real sec
+[M::process] read 66668 sequences (10000213 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.413 CPU sec, 17.312 real sec
+[M::process] read 66668 sequences (10000285 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.240 CPU sec, 17.156 real sec
+[M::process] read 66666 sequences (10000069 bp)...
+[M::mem_process_seqs] Processed 66668 reads in 17.184 CPU sec, 17.093 real sec
+[M::process] read 66652 sequences (9997620 bp)...
+[M::mem_process_seqs] Processed 66666 reads in 17.334 CPU sec, 17.252 real sec
+[M::mem_process_seqs] Processed 66652 reads in 16.991 CPU sec, 16.959 real sec
 [main] Version: 0.7.17-r1198-dirty
-[main] CMD: bwa mem egu_bwa /mnt/d/genome/test/sim_illumina_1M.fastq
-[main] Real time: 565.573 sec; CPU: 565.984 sec
+[main] CMD: bwa mem egu_bwa /mnt/d/genome/test/sim_150_1M.fastq
+[main] Real time: 268.062 sec; CPU: 266.583 sec
diff --git a/bucket_map/benchmark/log/bwa_map.time b/bucket_map/benchmark/log/bwa_map.time
@@ -1,21 +1,21 @@
-	Command being timed: "bwa mem egu_bwa /mnt/d/genome/test/sim_illumina_1M.fastq"
-	User time (seconds): 563.19
-	System time (seconds): 2.79
-	Percent of CPU this job got: 100%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 9:25.61
+	Command being timed: "bwa mem egu_bwa /mnt/d/genome/test/sim_150_1M.fastq"
+	User time (seconds): 262.19
+	System time (seconds): 4.39
+	Percent of CPU this job got: 99%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 4:28.09
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 2995356
+	Maximum resident set size (kbytes): 3038680
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 25
-	Minor (reclaiming a frame) page faults: 436960
-	Voluntary context switches: 53780
-	Involuntary context switches: 246
+	Major (requiring I/O) page faults: 5
+	Minor (reclaiming a frame) page faults: 56498
+	Voluntary context switches: 30144
+	Involuntary context switches: 97
 	Swaps: 0
-	File system inputs: 5816928
-	File system outputs: 1336672
+	File system inputs: 5816552
+	File system outputs: 750368
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0

diff --git a/bucket_map/benchmark/log/minimap2_map.log b/bucket_map/benchmark/log/minimap2_map.log
@@ -1,8 +1,8 @@
-[M::main::8.939*0.77] loaded/built the index for 932 target sequence(s)
-[M::mm_mapopt_update::11.852*0.71] mid_occ = 1428
+[M::main::7.910*0.65] loaded/built the index for 932 target sequence(s)
+[M::mm_mapopt_update::9.191*0.70] mid_occ = 1428
 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 932
-[M::mm_idx_stat::12.569*0.73] distinct minimizers: 61720831 (52.90% are singletons); average occurrences: 5.186; average spacing: 5.315; total length: 1701312507
-[M::worker_pipeline::526.566*2.80] mapped 1000000 sequences
+[M::mm_idx_stat::9.840*0.72] distinct minimizers: 61720831 (52.90% are singletons); average occurrences: 5.186; average spacing: 5.315; total length: 1701312507
+[M::worker_pipeline::179.711*2.83] mapped 1000000 sequences
 [M::main] Version: 2.24-r1150-dirty
-[M::main] CMD: minimap2 -a egu_minimap.mmi /mnt/d/genome/test/sim_illumina_1M.fastq
-[M::main] Real time: 526.711 sec; CPU: 1475.605 sec; Peak RSS: 5.867 GB
+[M::main] CMD: minimap2 -a egu_minimap.mmi /mnt/d/genome/test/sim_150_1M.fastq
+[M::main] Real time: 179.799 sec; CPU: 508.878 sec; Peak RSS: 5.638 GB
diff --git a/bucket_map/benchmark/log/minimap2_map.time b/bucket_map/benchmark/log/minimap2_map.time
@@ -1,21 +1,21 @@
-	Command being timed: "minimap2 -a egu_minimap.mmi /mnt/d/genome/test/sim_illumina_1M.fastq"
-	User time (seconds): 1461.92
-	System time (seconds): 13.80
-	Percent of CPU this job got: 280%
-	Elapsed (wall clock) time (h:mm:ss or m:ss): 8:46.86
+	Command being timed: "minimap2 -a egu_minimap.mmi /mnt/d/genome/test/sim_150_1M.fastq"
+	User time (seconds): 504.34
+	System time (seconds): 4.63
+	Percent of CPU this job got: 282%
+	Elapsed (wall clock) time (h:mm:ss or m:ss): 2:59.93
 	Average shared text size (kbytes): 0
 	Average unshared data size (kbytes): 0
 	Average stack size (kbytes): 0
 	Average total size (kbytes): 0
-	Maximum resident set size (kbytes): 6151476
+	Maximum resident set size (kbytes): 5911816
 	Average resident set size (kbytes): 0
-	Major (requiring I/O) page faults: 225912
-	Minor (reclaiming a frame) page faults: 3258999
-	Voluntary context switches: 279159
-	Involuntary context switches: 1892
+	Major (requiring I/O) page faults: 12
+	Minor (reclaiming a frame) page faults: 1515937
+	Voluntary context switches: 35303
+	Involuntary context switches: 533
 	Swaps: 0
-	File system inputs: 11306232
-	File system outputs: 1504968
+	File system inputs: 8084016
+	File system outputs: 1011496
 	Socket messages sent: 0
 	Socket messages received: 0
 	Signals delivered: 0