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Remove superseded command column
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@bede
bede committed Nov 22, 2023
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Showing 1 changed file with 31 additions and 19 deletions.
50 changes: 31 additions & 19 deletions paper/supplementary-table-1.tsv
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dataset tool database command command_2 time_1 time_2 time_3 time_median rss_max_1 rss_max_2 rss_max_3 rss_max_median reads_total bp_total reads_retained_before_repair reads_retained reads_removed reads_retained_pc throughput_mbp
human-illumina-10x Hostile 0.0.2 human-t2t-hla hostile clean --threads 8 --fastq1 /data/bench2/real/human/err194147_10x.r1.fastq.gz --fastq2 /data/bench2/real/human/err194147_10x.r2.fastq.gz > hostile_bt2.illumina.human.human.json /usr/bin/time -v sh -c 'hostile clean --threads 8 --fastq1 /data/bench2/real/human/err194147_10x.r1.fastq.gz --fastq2 /data/bench2/real/human/err194147_10x.r2.fastq.gz > hostile_bt2.illumina.human.human-masked-bacteria-mycobacteria.json --force' 1320 1393 1383 1383 3864004 3864316 3863344 4 404580418 40862622218 262830 404317588 0.064964% 29.55
human-ont-10x Hostile 0.0.2 human-t2t-hla hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/real/human/rel7.10x.fastq.gz > hostile_mm2.ont.human.human.json /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/real/human/rel7.10x.fastq.gz > hostile_mm2.ont.human.human-masked-bacteria-mycobacteria.json --force' 2738 2738 2720 2738 13890848 13598396 13778948 14 2498111 20803445891 950 2497161 0.038029% 7.60
bacteria-illumina Hostile 0.0.2 human-t2t-hla hostile clean --threads 8 --fastq1 /data/bench2/simulated/bacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/bacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.bacteria.human.json /usr/bin/time -v sh -c 'hostile clean --threads 8 --fastq1 /data/bench2/simulated/bacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/bacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.bacteria.human-masked-bacteria-mycobacteria.json --force' 1279 1283 1297 1283 3726140 3730504 3726224 4 273511602 41026740300 273511300 302 99.999890% 31.98
bacteria-ont Hostile 0.0.2 human-t2t-hla hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/simulated/bacteria/ont.fastq.gz > hostile_mm2.ont.bacteria.human.json /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/simulated/bacteria/ont.fastq.gz > hostile_mm2.ont.bacteria.human-masked-bacteria-mycobacteria.json --force' 1862 1860 1872 1862 12537268 12529228 12511360 13 8230970 41026721665 8230079 891 99.989175% 22.03
mycobacteria-illumina Hostile 0.0.2 human-t2t-hla hostile clean --threads 8 --fastq1 /data/bench2/simulated/mycobacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/mycobacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.mycobacteria.human.json /usr/bin/time -v sh -c 'hostile clean --threads 8 --fastq1 /data/bench2/simulated/mycobacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/mycobacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.mycobacteria.human-masked-bacteria-mycobacteria.json --force' 225 226 230 226 2839536 2843196 2823176 3 51360128 7704019200 51360120 8 99.999984% 34.09
mycobacteria-ont Hostile 0.0.2 human-t2t-hla hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/simulated/mycobacteria/ont.fastq.gz > hostile_mm2.ont.mycobacteria.human.json /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/simulated/mycobacteria/ont.fastq.gz > hostile_mm2.ont.mycobacteria.human-masked-bacteria-mycobacteria.json --force' 394 394 398 394 12533760 12510344 12540200 13 1544982 7704017435 1544974 8 99.999482% 19.55
human-illumina-10x Hostile 0.0.2 human-t2t-hla-argos985-mycob140 hostile clean --threads 8 --custom-index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/real/human/err194147_10x.r1.fastq.gz --fastq2 /data/bench2/real/human/err194147_10x.r2.fastq.gz > hostile_bt2.illumina.human.human-masked-bacteria-mycobacteria.json /usr/bin/time -v sh -c 'hostile clean --threads 8 --index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/real/human/err194147_10x.r1.fastq.gz --fastq2 /data/bench2/real/human/err194147_10x.r2.fastq.gz > hostile_bt2.illumina.human.human-masked-bacteria-mycobacteria.json --force' 1377 1378 1411 1378 3860404 3860312 3861184 4 404580418 40862622218 263312 404317106 0.065083% 29.65
human-ont-10x Hostile 0.0.2 human-t2t-hla-argos985-mycob140 hostile clean --aligner minimap2 --threads 8 --custom-index /data/bench2/human/human-masked-bacteria-mycobacteria.fa --fastq1 /data/bench2/real/human/rel7.10x.fastq.gz > hostile_mm2.ont.human.human-masked-bacteria-mycobacteria.json /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --index /data/bench2/human/human-masked-bacteria-mycobacteria.fa.gz --fastq1 /data/bench2/real/human/rel7.10x.fastq.gz > hostile_mm2.ont.human.human-masked-bacteria-mycobacteria.json --force' 2740 2736 2817 2740 13810392 13788332 13705464 14 2498111 20803445891 951 2497160 0.038069% 7.59
bacteria-illumina Hostile 0.0.2 human-t2t-hla-argos985-mycob140 hostile clean --threads 8 --custom-index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/simulated/bacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/bacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.bacteria.human-masked-bacteria-mycobacteria.json /usr/bin/time -v sh -c 'hostile clean --threads 8 --index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/simulated/bacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/bacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.bacteria.human-masked-bacteria-mycobacteria.json --force' 1314 1312 1329 1314 3723500 3724348 3724800 4 273511602 41026740300 273511446 156 99.999943% 31.22
bacteria-ont Hostile 0.0.2 human-t2t-hla-argos985-mycob140 hostile clean --aligner minimap2 --threads 8 --custom-index /data/bench2/human/human-masked-bacteria-mycobacteria.fa --fastq1 /data/bench2/simulated/bacteria/ont.fastq.gz > hostile_mm2.ont.bacteria.human-masked-bacteria-mycobacteria.json /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --index /data/bench2/human/human-masked-bacteria-mycobacteria.fa.gz --fastq1 /data/bench2/simulated/bacteria/ont.fastq.gz > hostile_mm2.ont.bacteria.human-masked-bacteria-mycobacteria.json --force' 1870 1855 1854 1855 12529248 12539188 12509636 13 8230970 41026721665 8230719 251 99.996951% 22.12
mycobacteria-illumina Hostile 0.0.2 human-t2t-hla-argos985-mycob140 hostile clean --threads 8 --custom-index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/simulated/mycobacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/mycobacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.mycobacteria.human-masked-bacteria-mycobacteria.json /usr/bin/time -v sh -c 'hostile clean --threads 8 --index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/simulated/mycobacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/mycobacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.mycobacteria.human-masked-bacteria-mycobacteria.json --force' 229 230 236 230 2833772 2821884 2819500 3 51360128 7704019200 51360128 0 100.000000% 33.50
mycobacteria-ont Hostile 0.0.2 human-t2t-hla-argos985-mycob140 hostile clean --aligner minimap2 --threads 8 --custom-index /data/bench2/human/human-masked-bacteria-mycobacteria.fa --fastq1 /data/bench2/simulated/mycobacteria/ont.fastq.gz > hostile_mm2.ont.mycobacteria.human-masked-bacteria-mycobacteria.json /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --index /data/bench2/human/human-masked-bacteria-mycobacteria.fa.gz --fastq1 /data/bench2/simulated/mycobacteria/ont.fastq.gz > hostile_mm2.ont.mycobacteria.human-masked-bacteria-mycobacteria.json --force' 394 394 399 394 12544588 12513100 12513196 13 1544982 7704017435 1544982 0 100.000000% 19.55
human-illumina-10x HRRT 2.1.0 default zcat /data/bench2/real/human/err194147_10x.r12.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.human.fastq.gz /usr/bin/time -v sh -c 'zcat /data/bench2/real/human/err194147_10x.r12.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.human.fastq.gz' 901 885 910 901 17644804 17644900 17644900 18 404580418 40862622218 2930152 318232 404262186 0.078657% 45.35
human-ont-10x HRRT 2.1.0 default zcat /data/bench2/real/human/rel7.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.human.fastq.gz /usr/bin/time -v sh -c 'zcat /data/bench2/real/human/rel7.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.human.fastq.gz' 410 414 426 414 1262620 1262388 1262872 1 2498111 20803445891 933 2497178 0.037348% 50.25
bacteria-illumina HRRT 2.1.0 default zcat /data/bench2/simulated/bacteria/illumina.read12.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.bacteria.fastq.gz /usr/bin/time -v sh -c 'zcat /data/bench2/simulated/bacteria/illumina.read12.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.bacteria.fastq.gz' 4412 4634 4491 4491 1000312 1000108 1000352 1 273511602 41026740300 273508206 273504828 6774 99.997523% 9.14
bacteria-ont HRRT 2.1.0 default zcat /data/bench2/simulated/bacteria/ont.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.bacteria.fastq.gz /usr/bin/time -v sh -c 'zcat /data/bench2/simulated/bacteria/ont.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.bacteria.fastq.gz' 4538 4980 4617 4617 1041480 1041612 1041428 1 8230970 41026721665 8230065 905 99.989005% 8.89
mycobacteria-illumina HRRT 2.1.0 default zcat /data/bench2/simulated/mycobacteria/illumina.read12.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.mycobacteria.fastq.gz /usr/bin/time -v sh -c 'zcat /data/bench2/simulated/mycobacteria/illumina.read12.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.mycobacteria.fastq.gz' 779 807 785 785 999976 999976 999976 1 51360128 7704019200 51360060 51360000 128 99.999751% 9.81
mycobacteria-ont HRRT 2.1.0 default zcat /data/bench2/simulated/mycobacteria/ont.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.mycobacteria.fastq.gz /usr/bin/time -v sh -c 'zcat /data/bench2/simulated/mycobacteria/ont.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.mycobacteria.fastq.gz' 770 786 773 773 1042132 1042212 1042124 1 1544982 7704017435 1544961 21 99.998641% 9.97
dataset tool database command time_1 time_2 time_3 time_median rss_max_1 rss_max_2 rss_max_3 rss_max_median reads_total bp_total reads_retained_before_repair reads_retained reads_removed reads_retained_pc throughput_mbp
human-illumina-10x Hostile 0.0.2 human-t2t-hla /usr/bin/time -v sh -c 'hostile clean --threads 8 --fastq1 /data/bench2/real/human/err194147_10x.r1.fastq.gz --fastq2 /data/bench2/real/human/err194147_10x.r2.fastq.gz > hostile_bt2.illumina.human.human-masked-bacteria-mycobacteria.json --force' 1320 1393 1383 1383 3864004 3864316 3863344 4 404580418 40862622218 262830 404317588 0.064964% 29.55
human-ont-10x Hostile 0.0.2 human-t2t-hla /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/real/human/rel7.10x.fastq.gz > hostile_mm2.ont.human.human-masked-bacteria-mycobacteria.json --force' 2738 2738 2720 2738 13890848 13598396 13778948 14 2498111 20803445891 950 2497161 0.038029% 7.60
bacteria-illumina Hostile 0.0.2 human-t2t-hla /usr/bin/time -v sh -c 'hostile clean --threads 8 --fastq1 /data/bench2/simulated/bacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/bacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.bacteria.human-masked-bacteria-mycobacteria.json --force' 1279 1283 1297 1283 3726140 3730504 3726224 4 273511602 41026740300 273511300 302 99.999890% 31.98
bacteria-ont Hostile 0.0.2 human-t2t-hla /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/simulated/bacteria/ont.fastq.gz > hostile_mm2.ont.bacteria.human-masked-bacteria-mycobacteria.json --force' 1862 1860 1872 1862 12537268 12529228 12511360 13 8230970 41026721665 8230079 891 99.989175% 22.03
mycobacteria-illumina Hostile 0.0.2 human-t2t-hla /usr/bin/time -v sh -c 'hostile clean --threads 8 --fastq1 /data/bench2/simulated/mycobacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/mycobacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.mycobacteria.human-masked-bacteria-mycobacteria.json --force' 225 226 230 226 2839536 2843196 2823176 3 51360128 7704019200 51360120 8 99.999984% 34.09
mycobacteria-ont Hostile 0.0.2 human-t2t-hla /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --fastq1 /data/bench2/simulated/mycobacteria/ont.fastq.gz > hostile_mm2.ont.mycobacteria.human-masked-bacteria-mycobacteria.json --force' 394 394 398 394 12533760 12510344 12540200 13 1544982 7704017435 1544974 8 99.999482% 19.55
human-illumina-10x Hostile 0.0.2 human-t2t-hla-argos985-mycob140 /usr/bin/time -v sh -c 'hostile clean --threads 8 --index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/real/human/err194147_10x.r1.fastq.gz --fastq2 /data/bench2/real/human/err194147_10x.r2.fastq.gz > hostile_bt2.illumina.human.human-masked-bacteria-mycobacteria.json --force' 1377 1378 1411 1378 3860404 3860312 3861184 4 404580418 40862622218 263312 404317106 0.065083% 29.65
human-ont-10x Hostile 0.0.2 human-t2t-hla-argos985-mycob140 /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --index /data/bench2/human/human-masked-bacteria-mycobacteria.fa.gz --fastq1 /data/bench2/real/human/rel7.10x.fastq.gz > hostile_mm2.ont.human.human-masked-bacteria-mycobacteria.json --force' 2740 2736 2817 2740 13810392 13788332 13705464 14 2498111 20803445891 951 2497160 0.038069% 7.59
bacteria-illumina Hostile 0.0.2 human-t2t-hla-argos985-mycob140 /usr/bin/time -v sh -c 'hostile clean --threads 8 --index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/simulated/bacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/bacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.bacteria.human-masked-bacteria-mycobacteria.json --force' 1314 1312 1329 1314 3723500 3724348 3724800 4 273511602 41026740300 273511446 156 99.999943% 31.22
bacteria-ont Hostile 0.0.2 human-t2t-hla-argos985-mycob140 /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --index /data/bench2/human/human-masked-bacteria-mycobacteria.fa.gz --fastq1 /data/bench2/simulated/bacteria/ont.fastq.gz > hostile_mm2.ont.bacteria.human-masked-bacteria-mycobacteria.json --force' 1870 1855 1854 1855 12529248 12539188 12509636 13 8230970 41026721665 8230719 251 99.996951% 22.12
mycobacteria-illumina Hostile 0.0.2 human-t2t-hla-argos985-mycob140 /usr/bin/time -v sh -c 'hostile clean --threads 8 --index /data/bench2/human/bowtie2/human-masked-bacteria-mycobacteria --fastq1 /data/bench2/simulated/mycobacteria/illumina.read1.fastq.gz --fastq2 /data/bench2/simulated/mycobacteria/illumina.read2.fastq.gz > hostile_bt2.illumina.mycobacteria.human-masked-bacteria-mycobacteria.json --force' 229 230 236 230 2833772 2821884 2819500 3 51360128 7704019200 51360128 0 100.000000% 33.50
mycobacteria-ont Hostile 0.0.2 human-t2t-hla-argos985-mycob140 /usr/bin/time -v sh -c 'hostile clean --aligner minimap2 --threads 8 --index /data/bench2/human/human-masked-bacteria-mycobacteria.fa.gz --fastq1 /data/bench2/simulated/mycobacteria/ont.fastq.gz > hostile_mm2.ont.mycobacteria.human-masked-bacteria-mycobacteria.json --force' 394 394 399 394 12544588 12513100 12513196 13 1544982 7704017435 1544982 0 100.000000% 19.55
human-illumina-10x HRRT 2.1.0 default /usr/bin/time -v sh -c 'zcat /data/bench2/real/human/err194147_10x.r12.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.human.fastq.gz' 901 885 910 901 17644804 17644900 17644900 18 404580418 40862622218 2930152 318232 404262186 0.078657% 45.35
human-ont-10x HRRT 2.1.0 default /usr/bin/time -v sh -c 'zcat /data/bench2/real/human/rel7.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.human.fastq.gz' 410 414 426 414 1262620 1262388 1262872 1 2498111 20803445891 933 2497178 0.037348% 50.25
bacteria-illumina HRRT 2.1.0 default /usr/bin/time -v sh -c 'zcat /data/bench2/simulated/bacteria/illumina.read12.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.bacteria.fastq.gz' 4412 4634 4491 4491 1000312 1000108 1000352 1 273511602 41026740300 273508206 273504828 6774 99.997523% 9.14
bacteria-ont HRRT 2.1.0 default /usr/bin/time -v sh -c 'zcat /data/bench2/simulated/bacteria/ont.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.bacteria.fastq.gz' 4538 4980 4617 4617 1041480 1041612 1041428 1 8230970 41026721665 8230065 905 99.989005% 8.89
mycobacteria-illumina HRRT 2.1.0 default /usr/bin/time -v sh -c 'zcat /data/bench2/simulated/mycobacteria/illumina.read12.10x.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.illumina.mycobacteria.fastq.gz' 779 807 785 785 999976 999976 999976 1 51360128 7704019200 51360060 51360000 128 99.999751% 9.81
mycobacteria-ont HRRT 2.1.0 default /usr/bin/time -v sh -c 'zcat /data/bench2/simulated/mycobacteria/ont.fastq.gz | /data/bench2/sra-human-scrubber/scripts/scrub.sh -x -p 8 | pigz -p 8 > scrubber.ont.mycobacteria.fastq.gz' 770 786 773 773 1042132 1042212 1042124 1 1544982 7704017435 1544961 21 99.998641% 9.97
human-illumina-10x Kraken 2.1.3 standard_20230605 404580418 40862622218 42438 404537980 0.010489%
human-ont-10x Kraken 2.1.3 standard_20230605 2498111 20803445891 2498111 100.000000%
bacteria-illumina Kraken 2.1.3 standard_20230605 273511602 41026740300 273507734 3868 99.998586%
bacteria-ont Kraken 2.1.3 standard_20230605 8230970 41026721665 8230970 100.000000%
mycobacteria-illumina Kraken 2.1.3 standard_20230605 51360128 7704019200 51360128 100.000000%
mycobacteria-ont Kraken 2.1.3 standard_20230605 1544982 7704017435 1544982 100.000000%
human-illumina-10x Kraken 2.1.3 standard_8gb_20230605 404580418 40862622218 16561404 388019014 4.093476%
human-ont-10x Kraken 2.1.3 standard_8gb_20230605 2498111 20803445891 2498111 100.000000%
bacteria-illumina Kraken 2.1.3 standard_8gb_20230605 273511602 41026740300 273503332 8270 99.996976%
bacteria-ont Kraken 2.1.3 standard_8gb_20230605 8230970 41026721665 8230970 100.000000%
mycobacteria-illumina Kraken 2.1.3 standard_8gb_20230605 51360128 7704019200 51360128 100.000000%
mycobacteria-ont Kraken 2.1.3 standard_8gb_20230605 1544982 7704017435 1544982 100.000000%

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