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jermpjermp
committedFeb 12, 2023
benchmarks updated
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‎benchmarks/README.md

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@@ -15,8 +15,13 @@ The datasets can be downloaded from [zenodo](https://zenodo.org/record/7239205#.
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For streaming queries we used FASTQ files downloaded from [ENA](https://www.ebi.ac.uk/ena/browser/home), using accession numbers:
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- elegans: SRR16288382
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- elegans: SRR16288382
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- cod: SRR12858649
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- kestrel: SRR11449743
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- human: SRR5833294
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The query times are relative to the following configuration:
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- Processor: Intel i9-9900K @ 3.60 GHz;
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- Compiler: gcc 11.2.0;
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- OS: GNU/Linux 5.13.0-52-generic x86_64.

‎benchmarks/sshash.canon.streaming_query_log

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2023-02-07 12:43:51: performing queries from file '/data2/DNA/queries/SRR5901135.fastq.gz'...
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2023-02-07 12:45:27: DONE
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2023-02-07 21:35:42: performing queries from file '/data2/DNA/queries/SRR16288382_1.fastq.gz'...
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2023-02-07 21:42:26: DONE
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==== query report:
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num_kmers = 792953816
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num_positive_kmers = 11201 (0.00141257%)
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num_searches = 10923/11201 (97.5181%)
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num_extensions = 278/11201 (2.48192%)
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elapsed = 96434.8 millisec / 96.4348 sec / 1.60725 min / 121.615 ns/kmer
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2023-02-07 12:45:27: performing queries from file '/data2/DNA/queries/SRR5901135.fastq.gz'...
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2023-02-07 12:46:29: DONE
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num_kmers = 2849620920
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num_positive_kmers = 2475259037 (86.8627%)
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num_searches = 1340695937/2475259037 (54.1639%)
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num_extensions = 1134563100/2475259037 (45.8361%)
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elapsed = 404175 millisec / 404.175 sec / 6.73625 min / 141.835 ns/kmer
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2023-02-07 21:42:26: performing queries from file '/data2/DNA/queries/SRR16288382_1.fastq.gz'...
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2023-02-07 21:47:40: DONE
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==== query report:
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num_kmers = 719118597
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num_positive_kmers = 0 (0%)
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num_searches = 0/0 (-nan%)
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num_extensions = 0/0 (-nan%)
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elapsed = 61845.9 millisec / 61.8459 sec / 1.03077 min / 86.0024 ns/kmer
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2023-02-07 12:46:29: performing queries from file '/data2/DNA/queries/SRR5901135.fastq.gz'...
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2023-02-07 12:47:21: DONE
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num_kmers = 2469671464
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num_positive_kmers = 1995797497 (80.8123%)
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num_searches = 1050159375/1995797497 (52.6185%)
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num_extensions = 945638122/1995797497 (47.3815%)
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elapsed = 314614 millisec / 314.614 sec / 5.24357 min / 127.391 ns/kmer
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2023-02-07 21:47:40: performing queries from file '/data2/DNA/queries/SRR16288382_1.fastq.gz'...
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2023-02-07 21:53:39: DONE
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==== query report:
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num_kmers = 646255023
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num_positive_kmers = 0 (0%)
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num_searches = 0/0 (-nan%)
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num_extensions = 0/0 (-nan%)
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elapsed = 52134 millisec / 52.134 sec / 0.8689 min / 80.6709 ns/kmer
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num_kmers = 2089722008
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num_positive_kmers = 1567619555 (75.0157%)
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num_searches = 814271235/1567619555 (51.9432%)
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num_extensions = 753348320/1567619555 (48.0568%)
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elapsed = 359057 millisec / 359.057 sec / 5.98428 min / 171.82 ns/kmer
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2023-02-07 12:47:21: performing queries from file '/data2/DNA/queries/SRR12858649.fastq.gz'...
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2023-02-07 12:47:48: DONE

‎benchmarks/sshash.regular.streaming_query_log

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2023-02-06 19:49:08: performing queries from file '/data2/DNA/queries/SRR5901135.fastq.gz'...
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2023-02-06 19:54:04: DONE
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2023-02-07 21:12:01: performing queries from file '/data2/DNA/queries/SRR16288382_1.fastq.gz'...
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2023-02-07 21:19:13: DONE
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==== query report:
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num_kmers = 792953816
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num_positive_kmers = 11201 (0.00141257%)
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num_searches = 10955/11201 (97.8038%)
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num_extensions = 246/11201 (2.19623%)
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elapsed = 295397 millisec / 295.397 sec / 4.92328 min / 372.527 ns/kmer
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2023-02-06 19:54:04: performing queries from file '/data2/DNA/queries/SRR5901135.fastq.gz'...
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2023-02-06 19:59:02: DONE
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num_kmers = 2849620920
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num_positive_kmers = 2475259037 (86.8627%)
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num_searches = 1399102570/2475259037 (56.5235%)
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num_extensions = 1076156467/2475259037 (43.4765%)
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elapsed = 432031 millisec / 432.031 sec / 7.20051 min / 151.61 ns/kmer
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2023-02-07 21:19:13: performing queries from file '/data2/DNA/queries/SRR16288382_1.fastq.gz'...
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2023-02-07 21:26:22: DONE
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==== query report:
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num_kmers = 719118597
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num_positive_kmers = 0 (0%)
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num_searches = 0/0 (-nan%)
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num_extensions = 0/0 (-nan%)
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elapsed = 298789 millisec / 298.789 sec / 4.97982 min / 415.493 ns/kmer
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2023-02-06 19:59:02: performing queries from file '/data2/DNA/queries/SRR5901135.fastq.gz'...
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2023-02-06 20:05:39: DONE
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num_kmers = 2469671464
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num_positive_kmers = 1995797497 (80.8123%)
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num_searches = 1079727026/1995797497 (54.1%)
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num_extensions = 916070471/1995797497 (45.9%)
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elapsed = 428959 millisec / 428.959 sec / 7.14932 min / 173.691 ns/kmer
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2023-02-07 21:26:22: performing queries from file '/data2/DNA/queries/SRR16288382_1.fastq.gz'...
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2023-02-07 21:35:42: DONE
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==== query report:
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num_kmers = 646255023
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num_positive_kmers = 0 (0%)
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num_searches = 0/0 (-nan%)
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num_extensions = 0/0 (-nan%)
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elapsed = 396728 millisec / 396.728 sec / 6.61214 min / 613.888 ns/kmer
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num_kmers = 2089722008
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num_positive_kmers = 1567619555 (75.0157%)
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num_searches = 830693880/1567619555 (52.9908%)
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num_extensions = 736925675/1567619555 (47.0092%)
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elapsed = 559344 millisec / 559.344 sec / 9.3224 min / 267.664 ns/kmer
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2023-02-06 20:05:39: performing queries from file '/data2/DNA/queries/SRR12858649.fastq.gz'...
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2023-02-06 20:06:07: DONE

‎script/streaming_query.sh

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### regular indexes
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./sshash query -i celegans.k31.sshash -q /data2/DNA/queries/SRR5901135.fastq.gz >> sshash.regular.streaming_query_log
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./sshash query -i celegans.k47.sshash -q /data2/DNA/queries/SRR5901135.fastq.gz >> sshash.regular.streaming_query_log
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./sshash query -i celegans.k63.sshash -q /data2/DNA/queries/SRR5901135.fastq.gz >> sshash.regular.streaming_query_log
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./sshash query -i celegans.k31.sshash -q /data2/DNA/queries/SRR16288382_1.fastq.gz >> sshash.regular.streaming_query_log
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./sshash query -i celegans.k47.sshash -q /data2/DNA/queries/SRR16288382_1.fastq.gz >> sshash.regular.streaming_query_log
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./sshash query -i celegans.k63.sshash -q /data2/DNA/queries/SRR16288382_1.fastq.gz >> sshash.regular.streaming_query_log
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./sshash query -i cod.k31.sshash -q /data2/DNA/queries/SRR12858649.fastq.gz >> sshash.regular.streaming_query_log
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./sshash query -i cod.k47.sshash -q /data2/DNA/queries/SRR12858649.fastq.gz >> sshash.regular.streaming_query_log
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### canonical indexes
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./sshash query -i celegans.k31.canon.sshash -q /data2/DNA/queries/SRR5901135.fastq.gz >> sshash.canon.streaming_query_log
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./sshash query -i celegans.k47.canon.sshash -q /data2/DNA/queries/SRR5901135.fastq.gz >> sshash.canon.streaming_query_log
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./sshash query -i celegans.k63.canon.sshash -q /data2/DNA/queries/SRR5901135.fastq.gz >> sshash.canon.streaming_query_log
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./sshash query -i celegans.k31.canon.sshash -q /data2/DNA/queries/SRR16288382_1.fastq.gz >> sshash.canon.streaming_query_log
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./sshash query -i celegans.k47.canon.sshash -q /data2/DNA/queries/SRR16288382_1.fastq.gz >> sshash.canon.streaming_query_log
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./sshash query -i celegans.k63.canon.sshash -q /data2/DNA/queries/SRR16288382_1.fastq.gz >> sshash.canon.streaming_query_log
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./sshash query -i cod.k31.canon.sshash -q /data2/DNA/queries/SRR12858649.fastq.gz >> sshash.canon.streaming_query_log
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./sshash query -i cod.k47.canon.sshash -q /data2/DNA/queries/SRR12858649.fastq.gz >> sshash.canon.streaming_query_log

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