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2023-11-03 18:10:19,470 INFO /home/jimshawster/mambaforge/bin/opal.py -g gs_marine_short.noplasmids.profile marmgCAMI2_short_read_sample_0-9.bracken_2.2.profile marmgCAMI2_short_read_sample_0-9.ccmetagen_1.1.3.profile marmgCAMI2_short_read_sample_0-9.centrifuge_1.0.4_beta.profile marmgCAMI2_short_read_sample_0-9.dudes_0.08.profile marmgCAMI2_short_read_sample_0-9.focus_1.5.profile marmgCAMI2_short_read_sample_0-9.LSHvec_1dfe822.profile marmgCAMI2_short_read_sample_0-9.metalign_0.6.2_default.profile marmgCAMI2_short_read_sample_0-9.metalign_0.6.2_precise.profile marmgCAMI2_short_read_sample_0-9.metapalette_1.0.0.profile marmgCAMI2_short_read_sample_0-9.metaphlan2_2.9.22.profile marmgCAMI2_short_read_sample_0-9.metaphyler_1.25.profile marmgCAMI2_short_read_sample_0-9.motus_2.5.1.profile marmgCAMI2_short_read_sample_0-9.tipp_4.3.10.profile -o rerun_opal | ||
2023-11-03 18:10:19,470 INFO Loading profiles... | ||
2023-11-03 18:10:20,209 INFO done | ||
2023-11-03 18:10:20,209 INFO Computing metrics... | ||
2023-11-03 18:11:54,812 INFO done | ||
2023-11-03 18:11:54,813 INFO Saving computed metrics... | ||
2023-11-03 18:11:55,136 INFO done | ||
2023-11-03 18:11:55,136 INFO Creating beta diversity plots... | ||
2023-11-03 18:12:18,943 INFO done | ||
2023-11-03 18:12:18,944 INFO Creating rarefaction curves... | ||
2023-11-03 18:12:19,575 INFO done | ||
2023-11-03 18:12:19,575 INFO Creating more plots... | ||
2023-11-03 18:12:28,764 INFO done | ||
2023-11-03 18:12:28,764 INFO Computing rankings... | ||
2023-11-03 18:12:29,262 INFO done | ||
2023-11-03 18:12:29,262 INFO Creating HTML page... | ||
2023-11-03 18:12:37,668 INFO done | ||
2023-11-03 18:12:37,668 INFO OPAL finished successfully. All results have been saved to /mnt/disks/1tb/cami/kmcp-manuscript-data-r2/3.figures/fig2-cami2-marine/rerun_opal |
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tool sample Sum of abundances Weighted UniFrac error Unweighted UniFrac error L1 norm error Completeness Purity F1 score True positives False positives False negatives Taxon counts Jaccard index Shannon diversity Shannon equitability Bray-Curtis distance | ||
sylph.profile marmgCAMI2_short_read_sample_0 0.964527 0.010903953047618946 0.36183516115397124 0.056838999999999924 0.92 0.9583333333333334 0.9387755102040817 23.0 1.0 2.0 24.0 0.8846153846153846 1.699649493117513 0.5348082769672371 0.029548596183048517 | ||
sylph.profile marmgCAMI2_short_read_sample_1 0.9568490000000002 0.010003745333333368 0.2995216209806135 0.04710299999999989 0.9032258064516129 0.9333333333333333 0.9180327868852459 28.0 2.0 3.0 30.0 0.8484848484848485 1.8381406385101637 0.5404392724811136 0.02467263695977039 | ||
sylph.profile marmgCAMI2_short_read_sample_2 0.9688589999999998 0.009245576190476225 0.3353639863396895 0.03463299999999978 0.9285714285714286 0.9285714285714286 0.9285714285714286 26.0 2.0 2.0 28.0 0.8666666666666667 1.840279803039785 0.5522709657886589 0.01791477279487101 | ||
sylph.profile marmgCAMI2_short_read_sample_3 0.9658090000000003 0.010895430095238037 0.36421382744569464 0.05239099999999998 0.9354838709677419 0.9354838709677419 0.9354838709677419 29.0 2.0 2.0 31.0 0.8787878787878788 1.9404704467236091 0.565077949093448 0.02721131187806406 | ||
sylph.profile marmgCAMI2_short_read_sample_4 0.9764860000000002 0.011672512761904716 0.3584009754524677 0.06349600000000014 0.9629629629629629 0.9629629629629629 0.9629629629629629 26.0 1.0 1.0 27.0 0.9285714285714286 1.8991519627930435 0.5762275379531934 0.03263961640123254 | ||
sylph.profile marmgCAMI2_short_read_sample_5 0.968562 0.0122195338095238 0.341361243777129 0.05775799999999981 0.9310344827586207 0.9310344827586207 0.9310344827586207 27.0 2.0 2.0 29.0 0.8709677419354839 1.8895566050163097 0.5611495693931648 0.030091820743235263 | ||
sylph.profile marmgCAMI2_short_read_sample_6 0.9722749999999998 0.013912765714285694 0.38900349314162064 0.05937699999999993 0.9333333333333333 0.9333333333333333 0.9333333333333333 28.0 2.0 2.0 30.0 0.875 1.8228652572213382 0.5359480949413495 0.030998091886995826 | ||
sylph.profile marmgCAMI2_short_read_sample_7 0.9787009999999999 0.014075738095238101 0.3829796341646111 0.06870899999999992 0.9285714285714286 0.9629629629629629 0.9454545454545454 26.0 1.0 2.0 27.0 0.896551724137931 1.738398519134503 0.5274528412087431 0.03560215989234733 | ||
sylph.profile marmgCAMI2_short_read_sample_8 0.9711089999999999 0.010765023523809515 0.3801890812188627 0.04759100000000004 0.9333333333333333 0.9333333333333333 0.9333333333333333 28.0 2.0 2.0 30.0 0.875 1.6990523132061477 0.49954534316847726 0.024618254370178574 | ||
sylph.profile marmgCAMI2_short_read_sample_9 0.9751080000000001 0.014167886095238107 0.36343428458822324 0.0963460000000001 0.9310344827586207 0.9642857142857143 0.9473684210526316 27.0 1.0 2.0 28.0 0.9 1.7894050123053484 0.5370033582396369 0.049743964131228356 |
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tool sample Sum of abundances Weighted UniFrac error Unweighted UniFrac error L1 norm error Completeness Purity F1 score True positives False positives False negatives Taxon counts Jaccard index Shannon diversity Shannon equitability Bray-Curtis distance | ||
sylph.profile marmgCAMI2_short_read_sample_0 0.9556239999999999 0.010903953047618946 0.36183516115397124 0.12028000000000004 0.9357798165137615 0.9714285714285714 0.9532710280373832 102.0 3.0 7.0 105.0 0.9107142857142857 3.22497356746813 0.6929525231900555 0.06320001849551589 | ||
sylph.profile marmgCAMI2_short_read_sample_1 0.9549090000000007 0.010003745333333368 0.2995216209806135 0.07665299999999994 0.9401709401709402 0.9649122807017544 0.9523809523809523 110.0 4.0 7.0 114.0 0.9090909090909091 3.5771290944076264 0.7552743267377706 0.04027862363372004 | ||
sylph.profile marmgCAMI2_short_read_sample_2 0.9492160000000007 0.009245576190476225 0.3353639863396895 0.076676 0.9433962264150944 0.9615384615384616 0.9523809523809524 100.0 4.0 6.0 104.0 0.9090909090909091 3.354536317279872 0.7222769121135 0.04052180089376691 | ||
sylph.profile marmgCAMI2_short_read_sample_3 0.9405480000000003 0.010895430095238037 0.36421382744569464 0.10368199999999997 0.9583333333333334 0.9663865546218487 0.9623430962343097 115.0 4.0 5.0 119.0 0.9274193548387096 3.446420080673652 0.7211406203755161 0.05530213971628329 | ||
sylph.profile marmgCAMI2_short_read_sample_4 0.9390279999999998 0.011672512761904716 0.3584009754524677 0.11434600000000003 0.9405940594059405 0.95 0.9452736318407959 95.0 5.0 6.0 100.0 0.8962264150943396 3.2622336886476093 0.7083850448292738 0.06099240541979286 | ||
sylph.profile marmgCAMI2_short_read_sample_5 0.9591670000000004 0.0122195338095238 0.341361243777129 0.09982700000000007 0.9532710280373832 0.9532710280373832 0.9532710280373832 102.0 5.0 5.0 107.0 0.9107142857142857 3.34834618236741 0.7165565658372729 0.0521478529828288 | ||
sylph.profile marmgCAMI2_short_read_sample_6 0.9674250000000003 0.013912765714285694 0.38900349314162064 0.11942299999999996 0.9727272727272728 0.963963963963964 0.9683257918552037 107.0 4.0 3.0 111.0 0.9385964912280702 3.4274733816852447 0.7277739466943353 0.061824827154198396 | ||
sylph.profile marmgCAMI2_short_read_sample_7 0.9617490000000004 0.014075738095238101 0.3829796341646111 0.11989099999999998 0.9519230769230769 0.9705882352941176 0.9611650485436893 99.0 3.0 5.0 102.0 0.9252336448598131 3.3186794961759194 0.7175565414446771 0.06241562975538422 | ||
sylph.profile marmgCAMI2_short_read_sample_8 0.9687920000000001 0.010765023523809515 0.3801890812188627 0.103256 0.9568965517241379 0.9652173913043478 0.961038961038961 111.0 4.0 5.0 115.0 0.925 3.336628521565405 0.7031983664466798 0.053450612433365324 | ||
sylph.profile marmgCAMI2_short_read_sample_9 0.9675549999999999 0.014167886095238107 0.36343428458822324 0.13350099999999998 0.9489795918367347 0.9489795918367347 0.9489795918367347 93.0 5.0 5.0 98.0 0.9029126213592233 3.353915382211019 0.7315025456153287 0.06922045902931347 |
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tool sample Sum of abundances Weighted UniFrac error Unweighted UniFrac error L1 norm error Completeness Purity F1 score True positives False positives False negatives Taxon counts Jaccard index Shannon diversity Shannon equitability Bray-Curtis distance | ||
sylph.profile marmgCAMI2_short_read_sample_0 0.9955159999999985 0.010903953047618946 0.36183516115397124 0.11941000000000006 0.9226519337016574 0.9488636363636364 0.9355742296918768 167.0 9.0 14.0 176.0 0.8789473684210526 3.7282620104209454 0.7210663477536663 0.06043915440860127 | ||
sylph.profile marmgCAMI2_short_read_sample_1 0.9967020000000006 0.010003745333333368 0.2995216209806135 0.106304 0.9261083743842364 0.9591836734693877 0.9423558897243107 188.0 8.0 15.0 196.0 0.8909952606635071 4.154312926817719 0.7870827359827317 0.053618156250441355 | ||
sylph.profile marmgCAMI2_short_read_sample_2 0.9961570000000005 0.009245576190476225 0.3353639863396895 0.08807700000000002 0.9438775510204082 0.9487179487179487 0.9462915601023018 185.0 10.0 11.0 195.0 0.8980582524271845 3.9773586050909087 0.7542876802694549 0.04455428265313401 | ||
sylph.profile marmgCAMI2_short_read_sample_3 0.9913029999999999 0.010895430095238037 0.36421382744569464 0.11504299999999992 0.9353448275862069 0.9475982532751092 0.9414316702819957 217.0 12.0 15.0 229.0 0.889344262295082 4.158050475851228 0.7652306233427869 0.05848584383609139 | ||
sylph.profile marmgCAMI2_short_read_sample_4 0.9913179999999993 0.011672512761904716 0.3584009754524677 0.11475200000000005 0.9243243243243243 0.9447513812154696 0.9344262295081968 171.0 10.0 14.0 181.0 0.8769230769230769 3.9028095315015 0.7507572877369081 0.05815327669632306 | ||
sylph.profile marmgCAMI2_short_read_sample_5 0.9955710000000008 0.0122195338095238 0.341361243777129 0.11273300000000008 0.9439252336448598 0.9619047619047619 0.9528301886792454 202.0 8.0 12.0 210.0 0.9099099099099099 4.0079343198240895 0.7495518458904659 0.056789839861245674 | ||
sylph.profile marmgCAMI2_short_read_sample_6 0.996096 0.013912765714285694 0.38900349314162064 0.13968599999999998 0.9476190476190476 0.9754901960784313 0.961352657004831 199.0 5.0 11.0 204.0 0.9255813953488372 4.050581283426682 0.7616566170216685 0.07034646968352497 | ||
sylph.profile marmgCAMI2_short_read_sample_7 0.9923819999999995 0.014075738095238101 0.3829796341646111 0.1446619999999999 0.9421052631578948 0.9623655913978495 0.9521276595744681 179.0 7.0 11.0 186.0 0.9086294416243654 3.8746737515546226 0.7414583969493183 0.07323130567193073 | ||
sylph.profile marmgCAMI2_short_read_sample_8 0.9928499999999998 0.010765023523809515 0.3801890812188627 0.10682400000000007 0.9444444444444444 0.9488372093023256 0.9466357308584686 204.0 11.0 12.0 215.0 0.8986784140969163 3.8963904242821323 0.7254986100116135 0.054219876154705096 | ||
sylph.profile marmgCAMI2_short_read_sample_9 0.9902860000000004 0.014167886095238107 0.36343428458822324 0.14709600000000003 0.9388888888888889 0.9388888888888889 0.9388888888888889 169.0 11.0 11.0 180.0 0.8848167539267016 3.9301781645096674 0.7568285809723088 0.07479422131555986 |
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tool sample Sum of abundances Weighted UniFrac error Unweighted UniFrac error L1 norm error Completeness Purity F1 score True positives False positives False negatives Taxon counts Jaccard index Shannon diversity Shannon equitability Bray-Curtis distance | ||
sylph.profile marmgCAMI2_short_read_sample_0 0.9612600000000002 0.010903953047618946 0.36183516115397124 0.09064600000000002 0.9402985074626866 0.984375 0.9618320610687023 63.0 1.0 4.0 64.0 0.9264705882352942 2.8274373248511178 0.6798549678311775 0.04731125551293094 | ||
sylph.profile marmgCAMI2_short_read_sample_1 0.9613740000000002 0.010003745333333368 0.2995216209806135 0.07012800000000001 0.9166666666666666 0.9565217391304348 0.9361702127659574 66.0 3.0 6.0 69.0 0.88 3.068760307096111 0.7247716380691293 0.036605761461223824 | ||
sylph.profile marmgCAMI2_short_read_sample_2 0.9570910000000009 0.009245576190476225 0.3353639863396895 0.06164500000000003 0.9558823529411765 0.9848484848484849 0.9701492537313432 65.0 1.0 3.0 66.0 0.9420289855072463 2.933049627398927 0.7000695303069981 0.03227552813905625 | ||
sylph.profile marmgCAMI2_short_read_sample_3 0.9525040000000007 0.010895430095238037 0.36421382744569464 0.08760800000000002 0.9324324324324325 0.9583333333333334 0.9452054794520548 69.0 3.0 5.0 72.0 0.8961038961038961 3.057817415400941 0.7150002666339691 0.04608924293231286 | ||
sylph.profile marmgCAMI2_short_read_sample_4 0.9612369999999999 0.011672512761904716 0.3584009754524677 0.0906210000000001 0.90625 0.9830508474576272 0.943089430894309 58.0 1.0 6.0 59.0 0.8923076923076924 2.9600483953541468 0.7259402117271124 0.047180327134844637 | ||
sylph.profile marmgCAMI2_short_read_sample_5 0.968798 0.0122195338095238 0.341361243777129 0.10098399999999998 0.9242424242424242 0.953125 0.9384615384615383 61.0 3.0 5.0 64.0 0.8840579710144928 2.9651406213151668 0.7129656116516352 0.05221218256684734 | ||
sylph.profile marmgCAMI2_short_read_sample_6 0.9756820000000002 0.013912765714285694 0.38900349314162064 0.10543600000000004 0.9571428571428572 0.9571428571428572 0.9571428571428572 67.0 3.0 3.0 70.0 0.9178082191780822 3.0047136770116847 0.7072418599584666 0.054108812927488176 | ||
sylph.profile marmgCAMI2_short_read_sample_7 0.9730539999999998 0.014075738095238101 0.3829796341646111 0.11113 0.9545454545454546 0.9692307692307692 0.9618320610687022 63.0 2.0 3.0 65.0 0.9264705882352942 2.925434624619603 0.7008057555457093 0.05713289812319485 | ||
sylph.profile marmgCAMI2_short_read_sample_8 0.975194 0.010765023523809515 0.3801890812188627 0.090276 0.9305555555555556 0.9571428571428572 0.943661971830986 67.0 3.0 5.0 70.0 0.8933333333333333 2.8876637170136807 0.6796909382016277 0.0463761504651177 | ||
sylph.profile marmgCAMI2_short_read_sample_9 0.9795439999999997 0.014167886095238107 0.36343428458822324 0.11792599999999992 0.9193548387096774 0.9661016949152542 0.9421487603305785 57.0 2.0 5.0 59.0 0.890625 2.963824602719845 0.7268663117121271 0.0603543488029545 |
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tool sample Sum of abundances Weighted UniFrac error Unweighted UniFrac error L1 norm error Completeness Purity F1 score True positives False positives False negatives Taxon counts Jaccard index Shannon diversity Shannon equitability Bray-Curtis distance | ||
sylph.profile marmgCAMI2_short_read_sample_0 1.0000109999999987 0.010903953047618946 0.36183516115397124 0.05586299999999894 0.8823529411764706 1.0 0.9375 15.0 0.0 2.0 15.0 0.8823529411764706 1.2043493063624582 0.4447293133163754 0.027943361957150296 | ||
sylph.profile marmgCAMI2_short_read_sample_1 0.9999970000000006 0.010003745333333368 0.2995216209806135 0.04737900000000025 0.9047619047619048 1.0 0.9500000000000001 19.0 0.0 2.0 19.0 0.9047619047619048 1.2905426507693833 0.4382983175744845 0.023693563446131133 | ||
sylph.profile marmgCAMI2_short_read_sample_2 0.999997 0.009245576190476225 0.3353639863396895 0.03574900000000016 0.8636363636363636 1.0 0.9268292682926829 19.0 0.0 3.0 19.0 0.8636363636363636 1.267147349719388 0.430352728884914 0.01787443743946904 | ||
sylph.profile marmgCAMI2_short_read_sample_3 1.0000010000000001 0.010895430095238037 0.36421382744569464 0.05834700000000012 0.9090909090909091 1.0 0.9523809523809523 20.0 0.0 2.0 20.0 0.9090909090909091 1.280778435921671 0.4275343451843972 0.029173193681466394 | ||
sylph.profile marmgCAMI2_short_read_sample_4 0.9999999999999996 0.011672512761904716 0.3584009754524677 0.06787599999999987 0.9444444444444444 1.0 0.9714285714285714 17.0 0.0 1.0 17.0 0.9444444444444444 1.1956607818808018 0.42201579502975745 0.03393799999999994 | ||
sylph.profile marmgCAMI2_short_read_sample_5 1.0000029999999998 0.0122195338095238 0.341361243777129 0.0715410000000001 0.9 1.0 0.9473684210526316 18.0 0.0 2.0 18.0 0.9 1.2048577075742029 0.41685215899396666 0.03577062519718824 | ||
sylph.profile marmgCAMI2_short_read_sample_6 0.9999959999999994 0.013912765714285694 0.38900349314162064 0.08586199999999967 0.8636363636363636 1.0 0.9268292682926829 19.0 0.0 3.0 19.0 0.8636363636363636 1.1911641331918286 0.4045470602787098 0.04293087120738623 | ||
sylph.profile marmgCAMI2_short_read_sample_7 1.0000010000000004 0.014075738095238101 0.3829796341646111 0.0944570000000006 0.9 1.0 0.9473684210526316 18.0 0.0 2.0 18.0 0.9 1.1217010014669206 0.38808191313195683 0.047228712529206664 | ||
sylph.profile marmgCAMI2_short_read_sample_8 1.0000059999999995 0.010765023523809515 0.3801890812188627 0.05327399999999974 0.8695652173913043 1.0 0.9302325581395349 20.0 0.0 3.0 20.0 0.8695652173913043 1.1531030253867542 0.38491524612069855 0.026637053274106426 | ||
sylph.profile marmgCAMI2_short_read_sample_9 0.9999990000000006 0.014167886095238107 0.36343428458822324 0.10525300000000071 0.9047619047619048 1.0 0.9500000000000001 19.0 0.0 2.0 19.0 0.9047619047619048 1.161804319902714 0.3945757844272312 0.05262652631326349 |
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tool sample Sum of abundances Weighted UniFrac error Unweighted UniFrac error L1 norm error Completeness Purity F1 score True positives False positives False negatives Taxon counts Jaccard index Shannon diversity Shannon equitability Bray-Curtis distance | ||
sylph.profile marmgCAMI2_short_read_sample_0 1.0000109999999984 0.010903953047618946 0.36183516115397124 0.24874499999999997 0.9140625 0.8666666666666667 0.8897338403041826 234.0 36.0 22.0 270.0 0.8013698630136986 4.272292629098523 0.7631244412064444 0.13138650275639896 | ||
sylph.profile marmgCAMI2_short_read_sample_1 0.9999970000000016 0.010003745333333368 0.2995216209806135 0.19277900000000003 0.92 0.8903225806451613 0.9049180327868852 276.0 34.0 24.0 310.0 0.8263473053892215 4.71230496035125 0.821449589752746 0.10112323008513006 | ||
sylph.profile marmgCAMI2_short_read_sample_2 0.9999970000000001 0.009245576190476225 0.3353639863396895 0.19543700000000008 0.9306569343065694 0.8614864864864865 0.8947368421052633 255.0 41.0 19.0 296.0 0.8095238095238095 4.5025557088832375 0.7912603316231245 0.10304070708183753 | ||
sylph.profile marmgCAMI2_short_read_sample_3 1.0000009999999986 0.010895430095238037 0.36421382744569464 0.22324299999999983 0.9133858267716536 0.8765743073047859 0.8946015424164525 348.0 49.0 33.0 397.0 0.8093023255813954 4.737638645682766 0.79172611863753 0.11894234165787117 | ||
sylph.profile marmgCAMI2_short_read_sample_4 0.9999999999999999 0.011672512761904716 0.3584009754524677 0.254078 0.9133574007220217 0.8605442176870748 0.8861646234676007 253.0 41.0 24.0 294.0 0.7955974842767296 4.404113727351743 0.7748837717841964 0.13792695372722732 | ||
sylph.profile marmgCAMI2_short_read_sample_5 1.0000030000000006 0.0122195338095238 0.341361243777129 0.2579989999999997 0.9365558912386707 0.8985507246376812 0.9171597633136095 310.0 35.0 21.0 345.0 0.8469945355191257 4.472792004698084 0.7654244899143512 0.13883655591448713 | ||
sylph.profile marmgCAMI2_short_read_sample_6 0.9999959999999996 0.013912765714285694 0.38900349314162064 0.28937999999999986 0.9202453987730062 0.8797653958944281 0.8995502248875561 300.0 41.0 26.0 341.0 0.8174386920980926 4.598102549772598 0.7884422513113447 0.15427461927147915 | ||
sylph.profile marmgCAMI2_short_read_sample_7 1.0000009999999997 0.014075738095238101 0.3829796341646111 0.25606899999999977 0.9219858156028369 0.8783783783783784 0.8996539792387545 260.0 36.0 22.0 296.0 0.8176100628930818 4.427458052756383 0.7780629832429992 0.13708330009780614 | ||
sylph.profile marmgCAMI2_short_read_sample_8 1.0000059999999993 0.010765023523809515 0.3801890812188627 0.2235680000000001 0.9130434782608695 0.8848314606741573 0.8987161198288159 315.0 41.0 30.0 356.0 0.8160621761658031 4.44804006691153 0.7571221297219345 0.11937658986883783 | ||
sylph.profile marmgCAMI2_short_read_sample_9 0.999999 0.014167886095238107 0.36343428458822324 0.29776099999999966 0.922509225092251 0.8741258741258742 0.8976660682226213 250.0 36.0 21.0 286.0 0.8143322475570033 4.51593826542751 0.7984343712783616 0.16375709519119136 |