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Merged
jermp merged 9 commits into from
Mar 23, 2026
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Logs #91

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d45a532
more logs
jermp Mar 16, 2026
b341771
more scripts
jermp Mar 16, 2026
5f72925
minor
jermp Mar 17, 2026
6c7eb75
minor
jermp Mar 20, 2026
ab3253d
modified query script
jermp Mar 20, 2026
56325ae
added script to mix fastq files
jermp Mar 20, 2026
a59ae39
added script to mix fastq files
jermp Mar 20, 2026
7ad398a
ready for mixed workloads
jermp Mar 20, 2026
66b1ae8
added results for mixed workloads
jermp Mar 20, 2026
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6 changes: 3 additions & 3 deletions benchmarks/README.md
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Expand Up @@ -10,7 +10,7 @@ To run the benchmarks, from within the `build` directory, run

python3 ../script/build.py <log_label> <input_datasets_dir> <output_index_dir>
python3 ../script/bench.py <log_label> <input_index_dir>
python3 ../script/streaming-query-high-hit.py <log_label> <input_index_dir> <input_queries_dir>
python3 ../script/streaming-query.py <log_label> <input_index_dir> <input_queries_dir>

where `<log_label>` should be replaced by a suitable basename, e.g., the current date.

Expand All @@ -25,5 +25,5 @@ Queries were run using one thread, instead.

The results can be exported to CSV format with

python3 ../script/print_csv.py ../benchmarks/results-10-11-25/k31
python3 ../script/print_csv.py ../benchmarks/results-10-11-25/k63
python3 ../script/print_csv.py ../benchmarks/results-21-01-26/k31
python3 ../script/print_csv.py ../benchmarks/results-21-01-26/k63
6 changes: 6 additions & 0 deletions benchmarks/results-20-03-26-streaming-low-hit/k31/canon-streaming-queries.json
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{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/cod.k31.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz", "num_kmers": "695737535", "num_positive_kmers": "4754204", "num_negative_kmers": "690972341", "num_invalid_kmers": "10990", "num_searches": "3225641", "num_extensions": "1528563", "elapsed_millisec": "60246"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/kestrel.k31.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz", "num_kmers": "163287360", "num_positive_kmers": "790414", "num_negative_kmers": "162496946", "num_invalid_kmers": "0", "num_searches": "540136", "num_extensions": "250278", "elapsed_millisec": "5077"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/human.k31.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz", "num_kmers": "395433242", "num_positive_kmers": "1134", "num_negative_kmers": "395408021", "num_invalid_kmers": "24087", "num_searches": "694", "num_extensions": "440", "elapsed_millisec": "36039"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/ncbi-virus.k31.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz", "num_kmers": "1569974986", "num_positive_kmers": "1452096", "num_negative_kmers": "1567493879", "num_invalid_kmers": "1029011", "num_searches": "643932", "num_extensions": "808164", "elapsed_millisec": "132169"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/se.k31.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz", "num_kmers": "1569974986", "num_positive_kmers": "63384101", "num_negative_kmers": "1505561874", "num_invalid_kmers": "1029011", "num_searches": "9728422", "num_extensions": "53655679", "elapsed_millisec": "167203"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/hprc.k31.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz", "num_kmers": "395433242", "num_positive_kmers": "2384", "num_negative_kmers": "395406771", "num_invalid_kmers": "24087", "num_searches": "1360", "num_extensions": "1024", "elapsed_millisec": "39411"}
66 changes: 66 additions & 0 deletions benchmarks/results-20-03-26-streaming-low-hit/k31/canon-streaming-queries.log
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./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/cod.k31.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz
2026-03-20 12:14:20: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz'...
2026-03-20 12:15:20: DONE
==== query report:
num_kmers = 695737535
num_positive_kmers = 4754204 (0.683333%)
num_negative_kmers = 690972341 (99.3151%)
num_invalid_kmers = 10990 (0.00157962%)
num_searches = 3225641/4754204 (67.8482%)
num_extensions = 1528563/4754204 (32.1518%)
elapsed = 60.246 sec / 1.0041 min / 86.593 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/kestrel.k31.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz
2026-03-20 12:15:26: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz'...
2026-03-20 12:15:31: DONE
==== query report:
num_kmers = 163287360
num_positive_kmers = 790414 (0.484063%)
num_negative_kmers = 162496946 (99.5159%)
num_invalid_kmers = 0 (0%)
num_searches = 540136/790414 (68.3358%)
num_extensions = 250278/790414 (31.6642%)
elapsed = 5.077 sec / 0.0846167 min / 31.0924 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/human.k31.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz
2026-03-20 12:15:44: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz'...
2026-03-20 12:16:20: DONE
==== query report:
num_kmers = 395433242
num_positive_kmers = 1134 (0.000286774%)
num_negative_kmers = 395408021 (99.9936%)
num_invalid_kmers = 24087 (0.00609129%)
num_searches = 694/1134 (61.1993%)
num_extensions = 440/1134 (38.8007%)
elapsed = 36.039 sec / 0.60065 min / 91.138 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/ncbi-virus.k31.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz
2026-03-20 12:16:21: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz'...
2026-03-20 12:18:34: DONE
==== query report:
num_kmers = 1569974986
num_positive_kmers = 1452096 (0.0924917%)
num_negative_kmers = 1567493879 (99.842%)
num_invalid_kmers = 1029011 (0.0655431%)
num_searches = 643932/1452096 (44.345%)
num_extensions = 808164/1452096 (55.655%)
elapsed = 132.169 sec / 2.20282 min / 84.1854 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/se.k31.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz
2026-03-20 12:18:40: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz'...
2026-03-20 12:21:27: DONE
==== query report:
num_kmers = 1569974986
num_positive_kmers = 63384101 (4.03727%)
num_negative_kmers = 1505561874 (95.8972%)
num_invalid_kmers = 1029011 (0.0655431%)
num_searches = 9728422/63384101 (15.3484%)
num_extensions = 53655679/63384101 (84.6516%)
elapsed = 167.203 sec / 2.78672 min / 106.5 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/hprc.k31.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz
2026-03-20 12:21:50: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz'...
2026-03-20 12:22:29: DONE
==== query report:
num_kmers = 395433242
num_positive_kmers = 2384 (0.000602883%)
num_negative_kmers = 395406771 (99.9933%)
num_invalid_kmers = 24087 (0.00609129%)
num_searches = 1360/2384 (57.047%)
num_extensions = 1024/2384 (42.953%)
elapsed = 39.411 sec / 0.65685 min / 99.6654 ns/kmer
6 changes: 6 additions & 0 deletions benchmarks/results-20-03-26-streaming-low-hit/k31/regular-streaming-queries.json
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{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/cod.k31.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz", "num_kmers": "695737535", "num_positive_kmers": "4754204", "num_negative_kmers": "690972341", "num_invalid_kmers": "10990", "num_searches": "3225641", "num_extensions": "1528563", "elapsed_millisec": "87893"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/kestrel.k31.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz", "num_kmers": "163287360", "num_positive_kmers": "790414", "num_negative_kmers": "162496946", "num_invalid_kmers": "0", "num_searches": "540136", "num_extensions": "250278", "elapsed_millisec": "7115"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/human.k31.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz", "num_kmers": "395433242", "num_positive_kmers": "1134", "num_negative_kmers": "395408021", "num_invalid_kmers": "24087", "num_searches": "694", "num_extensions": "440", "elapsed_millisec": "54044"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/ncbi-virus.k31.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz", "num_kmers": "1569974986", "num_positive_kmers": "1452096", "num_negative_kmers": "1567493879", "num_invalid_kmers": "1029011", "num_searches": "643932", "num_extensions": "808164", "elapsed_millisec": "188208"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/se.k31.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz", "num_kmers": "1569974986", "num_positive_kmers": "63384101", "num_negative_kmers": "1505561874", "num_invalid_kmers": "1029011", "num_searches": "9728422", "num_extensions": "53655679", "elapsed_millisec": "243017"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/hprc.k31.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz", "num_kmers": "395433242", "num_positive_kmers": "2384", "num_negative_kmers": "395406771", "num_invalid_kmers": "24087", "num_searches": "1360", "num_extensions": "1024", "elapsed_millisec": "57925"}
66 changes: 66 additions & 0 deletions benchmarks/results-20-03-26-streaming-low-hit/k31/regular-streaming-queries.log
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./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/cod.k31.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz
2026-03-20 12:03:34: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz'...
2026-03-20 12:05:02: DONE
==== query report:
num_kmers = 695737535
num_positive_kmers = 4754204 (0.683333%)
num_negative_kmers = 690972341 (99.3151%)
num_invalid_kmers = 10990 (0.00157962%)
num_searches = 3225641/4754204 (67.8482%)
num_extensions = 1528563/4754204 (32.1518%)
elapsed = 87.893 sec / 1.46488 min / 126.331 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/kestrel.k31.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz
2026-03-20 12:05:03: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz'...
2026-03-20 12:05:10: DONE
==== query report:
num_kmers = 163287360
num_positive_kmers = 790414 (0.484063%)
num_negative_kmers = 162496946 (99.5159%)
num_invalid_kmers = 0 (0%)
num_searches = 540136/790414 (68.3358%)
num_extensions = 250278/790414 (31.6642%)
elapsed = 7.115 sec / 0.118583 min / 43.5735 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/human.k31.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz
2026-03-20 12:05:11: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz'...
2026-03-20 12:06:05: DONE
==== query report:
num_kmers = 395433242
num_positive_kmers = 1134 (0.000286774%)
num_negative_kmers = 395408021 (99.9936%)
num_invalid_kmers = 24087 (0.00609129%)
num_searches = 694/1134 (61.1993%)
num_extensions = 440/1134 (38.8007%)
elapsed = 54.044 sec / 0.900733 min / 136.67 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/ncbi-virus.k31.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz
2026-03-20 12:06:05: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz'...
2026-03-20 12:09:13: DONE
==== query report:
num_kmers = 1569974986
num_positive_kmers = 1452096 (0.0924917%)
num_negative_kmers = 1567493879 (99.842%)
num_invalid_kmers = 1029011 (0.0655431%)
num_searches = 643932/1452096 (44.345%)
num_extensions = 808164/1452096 (55.655%)
elapsed = 188.208 sec / 3.1368 min / 119.88 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/se.k31.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz
2026-03-20 12:09:14: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz'...
2026-03-20 12:13:17: DONE
==== query report:
num_kmers = 1569974986
num_positive_kmers = 63384101 (4.03727%)
num_negative_kmers = 1505561874 (95.8972%)
num_invalid_kmers = 1029011 (0.0655431%)
num_searches = 9728422/63384101 (15.3484%)
num_extensions = 53655679/63384101 (84.6516%)
elapsed = 243.017 sec / 4.05028 min / 154.79 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/hprc.k31.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz
2026-03-20 12:13:19: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz'...
2026-03-20 12:14:17: DONE
==== query report:
num_kmers = 395433242
num_positive_kmers = 2384 (0.000602883%)
num_negative_kmers = 395406771 (99.9933%)
num_invalid_kmers = 24087 (0.00609129%)
num_searches = 1360/2384 (57.047%)
num_extensions = 1024/2384 (42.953%)
elapsed = 57.925 sec / 0.965417 min / 146.485 ns/kmer
6 changes: 6 additions & 0 deletions benchmarks/results-20-03-26-streaming-low-hit/k63/canon-streaming-queries.json
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{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/cod.k63.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz", "num_kmers": "461383839", "num_positive_kmers": "756097", "num_negative_kmers": "460616752", "num_invalid_kmers": "10990", "num_searches": "613034", "num_extensions": "143063", "elapsed_millisec": "22347"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/kestrel.k63.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz", "num_kmers": "97972416", "num_positive_kmers": "41066", "num_negative_kmers": "97931350", "num_invalid_kmers": "0", "num_searches": "21367", "num_extensions": "19699", "elapsed_millisec": "2727"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/human.k63.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz", "num_kmers": "322085785", "num_positive_kmers": "8", "num_negative_kmers": "322073557", "num_invalid_kmers": "12220", "num_searches": "8", "num_extensions": "0", "elapsed_millisec": "13201"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/ncbi-virus.k63.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz", "num_kmers": "477818474", "num_positive_kmers": "21769", "num_negative_kmers": "477122927", "num_invalid_kmers": "673778", "num_searches": "15569", "num_extensions": "6200", "elapsed_millisec": "43117"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/se.k63.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz", "num_kmers": "477818474", "num_positive_kmers": "9842483", "num_negative_kmers": "467302213", "num_invalid_kmers": "673778", "num_searches": "5417015", "num_extensions": "4425468", "elapsed_millisec": "52375"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/hprc.k63.canon.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz", "num_kmers": "322085785", "num_positive_kmers": "21", "num_negative_kmers": "322073544", "num_invalid_kmers": "12220", "num_searches": "15", "num_extensions": "6", "elapsed_millisec": "16596"}
66 changes: 66 additions & 0 deletions benchmarks/results-20-03-26-streaming-low-hit/k63/canon-streaming-queries.log
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./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/cod.k63.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz
2026-03-20 12:26:35: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz'...
2026-03-20 12:26:57: DONE
==== query report:
num_kmers = 461383839
num_positive_kmers = 756097 (0.163876%)
num_negative_kmers = 460616752 (99.8337%)
num_invalid_kmers = 10990 (0.00238196%)
num_searches = 613034/756097 (81.0788%)
num_extensions = 143063/756097 (18.9212%)
elapsed = 22.347 sec / 0.37245 min / 48.4347 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/kestrel.k63.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz
2026-03-20 12:27:00: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz'...
2026-03-20 12:27:03: DONE
==== query report:
num_kmers = 97972416
num_positive_kmers = 41066 (0.0419159%)
num_negative_kmers = 97931350 (99.9581%)
num_invalid_kmers = 0 (0%)
num_searches = 21367/41066 (52.0309%)
num_extensions = 19699/41066 (47.9691%)
elapsed = 2.727 sec / 0.04545 min / 27.8344 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/human.k63.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz
2026-03-20 12:27:11: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz'...
2026-03-20 12:27:24: DONE
==== query report:
num_kmers = 322085785
num_positive_kmers = 8 (2.48381e-06%)
num_negative_kmers = 322073557 (99.9962%)
num_invalid_kmers = 12220 (0.00379402%)
num_searches = 8/8 (100%)
num_extensions = 0/8 (0%)
elapsed = 13.201 sec / 0.220017 min / 40.986 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/ncbi-virus.k63.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz
2026-03-20 12:27:25: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz'...
2026-03-20 12:28:08: DONE
==== query report:
num_kmers = 477818474
num_positive_kmers = 21769 (0.00455591%)
num_negative_kmers = 477122927 (99.8544%)
num_invalid_kmers = 673778 (0.141011%)
num_searches = 15569/21769 (71.5191%)
num_extensions = 6200/21769 (28.4809%)
elapsed = 43.117 sec / 0.718617 min / 90.2372 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/se.k63.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz
2026-03-20 12:28:14: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz'...
2026-03-20 12:29:07: DONE
==== query report:
num_kmers = 477818474
num_positive_kmers = 9842483 (2.05988%)
num_negative_kmers = 467302213 (97.7991%)
num_invalid_kmers = 673778 (0.141011%)
num_searches = 5417015/9842483 (55.0371%)
num_extensions = 4425468/9842483 (44.9629%)
elapsed = 52.375 sec / 0.872917 min / 109.613 ns/kmer
./sshash query -i /mnt/hd2/pibiri/DNA/sshash-indexes/hprc.k63.canon.sshash -q /mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz
2026-03-20 12:29:31: performing queries from file '/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz'...
2026-03-20 12:29:48: DONE
==== query report:
num_kmers = 322085785
num_positive_kmers = 21 (6.52e-06%)
num_negative_kmers = 322073544 (99.9962%)
num_invalid_kmers = 12220 (0.00379402%)
num_searches = 15/21 (71.4286%)
num_extensions = 6/21 (28.5714%)
elapsed = 16.596 sec / 0.2766 min / 51.5266 ns/kmer
6 changes: 6 additions & 0 deletions benchmarks/results-20-03-26-streaming-low-hit/k63/regular-streaming-queries.json
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{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/cod.k63.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR11449743_1.fastq.gz", "num_kmers": "461383839", "num_positive_kmers": "756097", "num_negative_kmers": "460616752", "num_invalid_kmers": "10990", "num_searches": "613034", "num_extensions": "143063", "elapsed_millisec": "28164"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/kestrel.k63.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR12858649.fastq.gz", "num_kmers": "97972416", "num_positive_kmers": "41066", "num_negative_kmers": "97931350", "num_invalid_kmers": "0", "num_searches": "21367", "num_extensions": "19699", "elapsed_millisec": "3165"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/human.k63.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz", "num_kmers": "322085785", "num_positive_kmers": "8", "num_negative_kmers": "322073557", "num_invalid_kmers": "12220", "num_searches": "8", "num_extensions": "0", "elapsed_millisec": "17717"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/ncbi-virus.k63.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz", "num_kmers": "477818474", "num_positive_kmers": "21769", "num_negative_kmers": "477122927", "num_invalid_kmers": "673778", "num_searches": "15569", "num_extensions": "6200", "elapsed_millisec": "52468"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/se.k63.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5833294.fastq.gz", "num_kmers": "477818474", "num_positive_kmers": "9842483", "num_negative_kmers": "467302213", "num_invalid_kmers": "673778", "num_searches": "5417015", "num_extensions": "4425468", "elapsed_millisec": "66099"}
{"index_filename": "/mnt/hd2/pibiri/DNA/sshash-indexes/hprc.k63.sshash", "query_filename": "/mnt/hd2/pibiri/DNA/queries/SRR5901135_1.fastq.gz", "num_kmers": "322085785", "num_positive_kmers": "21", "num_negative_kmers": "322073544", "num_invalid_kmers": "12220", "num_searches": "15", "num_extensions": "6", "elapsed_millisec": "22897"}
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