[0.000001] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1229.dat' using 'Raw read' as FastA [3.164147] 858062 sequences found [3.164152] Done [3.164218] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1228.dat' using 'Raw read' as FastA [4.034333] 314389 sequences found [4.034337] Done [4.034427] Reading read set file hsv.beforedigipe.35/Sequences; [4.552407] 1172451 sequences found [6.813522] Done [6.813531] 1172451 sequences in total. [6.813602] Writing into roadmap file hsv.beforedigipe.35/Roadmaps... [7.905229] Inputting sequences... [7.905239] Inputting sequence 0 / 1172451 [21.186145] Inputting sequence 1000000 / 1172451 [21.985580] === Sequences loaded in 14.162731 s [21.985637] Done inputting sequences [21.985639] Destroying splay table [22.415403] Splay table destroyed [0.000001] Reading roadmap file hsv.beforedigipe.35/Roadmaps [2.301692] 1172451 roadmaps read [2.306153] Creating insertion markers [2.578647] Ordering insertion markers [3.569258] Counting preNodes [3.695161] 586123 preNodes counted, creating them now [7.412925] Sequence 1000000 / 1172451 [7.661503] Adjusting marker info... [7.777244] Connecting preNodes [9.345128] Connecting 1000000 / 1172451 [9.393139] Cleaning up memory [9.402733] Done creating preGraph [9.402742] Concatenation... [9.749712] Renumbering preNodes [9.749722] Initial preNode count 586123 [9.789138] Destroyed 307152 preNodes [9.789149] Concatenation over! [9.789151] Clipping short tips off preGraph [10.183763] Concatenation... [10.377505] Renumbering preNodes [10.377515] Initial preNode count 278971 [10.404437] Destroyed 124021 preNodes [10.404446] Concatenation over! [10.404447] 93482 tips cut off [10.404449] 154950 nodes left [10.404522] Writing into pregraph file hsv.beforedigipe.35/PreGraph... [11.233994] Reading read set file hsv.beforedigipe.35/Sequences; [11.755023] 1172451 sequences found [14.095261] Done [15.195159] Reading pre-graph file hsv.beforedigipe.35/PreGraph [15.195620] Graph has 154950 nodes and 1172451 sequences [15.540559] Scanning pre-graph file hsv.beforedigipe.35/PreGraph for k-mers [15.673963] 1870035 kmers found [16.302343] Sorting kmer occurence table ... [18.698068] Sorting done. [18.698082] Computing acceleration table... [18.775645] Computing offsets... [18.804925] Ghost Threading through reads 0 / 1172451 [35.069724] Ghost Threading through reads 1000000 / 1172451 [35.854896] === Ghost-Threaded in 17.049971 s [35.854913] Threading through reads 0 / 1172451 [53.968000] Threading through reads 1000000 / 1172451 [54.982319] === Threaded in 19.127406 s [55.193958] Correcting graph with cutoff 0.200000 [55.231981] Determining eligible starting points [55.533036] Done listing starting nodes [55.533045] Initializing todo lists [55.611415] Done with initilization [55.611426] Activating arc lookup table [55.728200] Done activating arc lookup table [55.808786] 10000 / 154950 nodes visited [56.308402] 20000 / 154950 nodes visited [56.820109] 30000 / 154950 nodes visited [57.154264] 40000 / 154950 nodes visited [57.362028] 50000 / 154950 nodes visited [57.597307] 60000 / 154950 nodes visited [58.382944] 70000 / 154950 nodes visited [58.831956] 80000 / 154950 nodes visited [59.054818] 90000 / 154950 nodes visited [59.183634] 100000 / 154950 nodes visited [59.332727] 110000 / 154950 nodes visited [59.673775] 120000 / 154950 nodes visited [60.246228] 130000 / 154950 nodes visited [60.610402] 140000 / 154950 nodes visited [60.758534] 150000 / 154950 nodes visited [61.088665] 160000 / 154950 nodes visited [61.463292] 170000 / 154950 nodes visited [61.863582] 180000 / 154950 nodes visited [62.080114] 190000 / 154950 nodes visited [62.203256] 200000 / 154950 nodes visited [62.226755] 210000 / 154950 nodes visited [62.247081] 220000 / 154950 nodes visited [62.248515] Concatenation... [62.270122] Renumbering nodes [62.270134] Initial node count 154950 [62.278224] Removed 46705 null nodes [62.278237] Concatenation over! [62.278239] Clipping short tips off graph, drastic [62.458765] Concatenation... [62.541155] Renumbering nodes [62.541164] Initial node count 108245 [62.571441] Removed 39972 null nodes [62.571451] Concatenation over! [62.571453] 68273 nodes left [62.571549] Writing into graph file hsv.beforedigipe.35/Graph2... [65.409269] Measuring median coverage depth... [65.481869] Median coverage depth = 2.400000 [65.482006] Removing contigs with coverage < 1.200000... [65.512735] Concatenation... [65.647922] Renumbering nodes [65.647930] Initial node count 68273 [65.651765] Removed 39680 null nodes [65.651774] Concatenation over! [65.655322] Concatenation... [65.660802] Renumbering nodes [65.660810] Initial node count 28593 [65.660883] Removed 0 null nodes [65.660885] Concatenation over! [65.660918] Clipping short tips off graph, drastic [65.709718] Concatenation... [65.730125] Renumbering nodes [65.730133] Initial node count 28593 [65.732921] Removed 6522 null nodes [65.732929] Concatenation over! [65.732930] 22071 nodes left [65.732934] Read coherency... [65.735248] Identifying unique nodes [65.737480] Done, 1717 unique nodes counted [65.737487] Trimming read tips [65.738915] Renumbering nodes [65.738923] Initial node count 22071 [65.738989] Removed 0 null nodes [65.738993] Confronted to 0 multiple hits and 0 null over 0 [65.738995] Read coherency over! [65.750044] Starting pebble resolution... [65.760802] Computing read to node mapping array sizes [65.848488] Computing read to node mappings [66.657049] Estimating library insert lengths... [66.667253] Done [66.667367] Computing direct node to node mappings [66.668639] Scaffolding node -20000 [66.700485] Scaffolding node -10000 [66.703390] Scaffolding node 0 [66.706565] Scaffolding node 10000 [66.714821] Scaffolding node 20000 [66.718354] === Nodes Scaffolded in 0.050980 s [66.765574] Preparing to correct graph with cutoff 0.200000 [67.051939] Cleaning memory [67.051971] Deactivating local correction settings [67.052893] Pebble done. [67.052898] Starting pebble resolution... [67.065395] Computing read to node mapping array sizes [67.160704] Computing read to node mappings [67.798667] Estimating library insert lengths... [67.816719] Done [67.816792] Computing direct node to node mappings [67.822085] Scaffolding node -20000 [67.835549] Scaffolding node -10000 [67.845032] Scaffolding node 0 [67.848515] Scaffolding node 10000 [67.868269] Scaffolding node 20000 [67.902624] === Nodes Scaffolded in 0.085828 s [67.909389] Preparing to correct graph with cutoff 0.200000 [68.189384] Cleaning memory [68.189395] Deactivating local correction settings [68.190260] Pebble done. [68.190267] Concatenation... [68.194634] Renumbering nodes [68.194642] Initial node count 22071 [68.196316] Removed 13 null nodes [68.197094] Concatenation over! [68.197098] Removing reference contigs with coverage < 1.200000... [68.199211] Concatenation... [68.203341] Renumbering nodes [68.203352] Initial node count 22058 [68.203413] Removed 0 null nodes [68.203981] Concatenation over! [68.210870] Writing contigs into hsv.beforedigipe.35/contigs.fa... [68.443736] Writing into stats file hsv.beforedigipe.35/stats.txt... [68.567555] Writing into graph file hsv.beforedigipe.35/LastGraph... [70.249746] Estimated Coverage = 2.400000 [70.249757] Estimated Coverage cutoff = 1.200000 Final graph has 22058 nodes and n50 of 92, max 2502, total 612029, using 355698/1172451 reads [0.000001] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1229.dat' using 'Raw read' as FastA [3.082330] 858062 sequences found [3.082334] Done [3.082393] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1228.dat' using 'Raw read' as FastA [4.084754] 314389 sequences found [4.084758] Done [4.084857] Reading read set file hsv.beforedigipe.45/Sequences; [4.444342] 1172451 sequences found [6.853665] Done [6.853673] 1172451 sequences in total. [6.853739] Writing into roadmap file hsv.beforedigipe.45/Roadmaps... [7.952515] Inputting sequences... [7.952525] Inputting sequence 0 / 1172451 [18.032869] Inputting sequence 1000000 / 1172451 [18.688255] === Sequences loaded in 10.842742 s [18.688310] Done inputting sequences [18.688312] Destroying splay table [18.985011] Splay table destroyed [0.000001] Reading roadmap file hsv.beforedigipe.45/Roadmaps [1.963731] 1172451 roadmaps read [1.968338] Creating insertion markers [2.152208] Ordering insertion markers [2.632832] Counting preNodes [2.856384] 407540 preNodes counted, creating them now [6.272212] Sequence 1000000 / 1172451 [6.741182] Adjusting marker info... [6.891219] Connecting preNodes [7.705454] Connecting 1000000 / 1172451 [7.715251] Cleaning up memory [7.722282] Done creating preGraph [7.722288] Concatenation... [7.991781] Renumbering preNodes [7.991790] Initial preNode count 407540 [8.118242] Destroyed 249447 preNodes [8.118248] Concatenation over! [8.118250] Clipping short tips off preGraph [8.302004] Concatenation... [8.410877] Renumbering preNodes [8.410901] Initial preNode count 158093 [8.455587] Destroyed 104195 preNodes [8.455601] Concatenation over! [8.455603] 83671 tips cut off [8.455604] 53898 nodes left [8.455680] Writing into pregraph file hsv.beforedigipe.45/PreGraph... [8.854662] Reading read set file hsv.beforedigipe.45/Sequences; [9.200057] 1172451 sequences found [11.557617] Done [12.557497] Reading pre-graph file hsv.beforedigipe.45/PreGraph [12.557663] Graph has 53898 nodes and 1172451 sequences [12.707930] Scanning pre-graph file hsv.beforedigipe.45/PreGraph for k-mers [12.768208] 1049506 kmers found [13.062358] Sorting kmer occurence table ... [14.216990] Sorting done. [14.217000] Computing acceleration table... [14.252991] Computing offsets... [14.293405] Ghost Threading through reads 0 / 1172451 [25.670773] Ghost Threading through reads 1000000 / 1172451 [26.068111] === Ghost-Threaded in 11.774706 s [26.068128] Threading through reads 0 / 1172451 [38.532652] Threading through reads 1000000 / 1172451 [38.926235] === Threaded in 12.858107 s [38.994542] Correcting graph with cutoff 0.200000 [38.998205] Determining eligible starting points [39.101382] Done listing starting nodes [39.101391] Initializing todo lists [39.117273] Done with initilization [39.117282] Activating arc lookup table [39.142526] Done activating arc lookup table [39.669076] 10000 / 53898 nodes visited [40.230312] 20000 / 53898 nodes visited [40.528225] 30000 / 53898 nodes visited [40.743311] 40000 / 53898 nodes visited [40.964024] 50000 / 53898 nodes visited [41.087428] 60000 / 53898 nodes visited [41.112532] 70000 / 53898 nodes visited [41.170645] Concatenation... [41.186716] Renumbering nodes [41.186725] Initial node count 53898 [41.202874] Removed 15662 null nodes [41.202883] Concatenation over! [41.202885] Clipping short tips off graph, drastic [41.319300] Concatenation... [41.420015] Renumbering nodes [41.420023] Initial node count 38236 [41.421907] Removed 21105 null nodes [41.421917] Concatenation over! [41.421919] 17131 nodes left [41.422008] Writing into graph file hsv.beforedigipe.45/Graph2... [42.118518] Measuring median coverage depth... [42.127573] Median coverage depth = 3.140000 [42.127678] Removing contigs with coverage < 1.570000... [42.134519] Concatenation... [42.163381] Renumbering nodes [42.163390] Initial node count 17131 [42.164116] Removed 9646 null nodes [42.164119] Concatenation over! [42.164413] Concatenation... [42.165257] Renumbering nodes [42.165262] Initial node count 7485 [42.165277] Removed 0 null nodes [42.165279] Concatenation over! [42.165308] Clipping short tips off graph, drastic [42.167457] Concatenation... [42.170381] Renumbering nodes [42.170386] Initial node count 7485 [42.170719] Removed 1084 null nodes [42.170721] Concatenation over! [42.170722] 6401 nodes left [42.170725] Read coherency... [42.170927] Identifying unique nodes [42.171160] Done, 1191 unique nodes counted [42.171162] Trimming read tips [42.171423] Renumbering nodes [42.171424] Initial node count 6401 [42.171437] Removed 0 null nodes [42.171439] Confronted to 0 multiple hits and 0 null over 0 [42.171440] Read coherency over! [42.182030] Starting pebble resolution... [42.191076] Computing read to node mapping array sizes [42.241716] Computing read to node mappings [42.366665] Estimating library insert lengths... [42.376779] Done [42.376820] Computing direct node to node mappings [42.389325] Scaffolding node 0 [42.406123] === Nodes Scaffolded in 0.029300 s [42.409080] Preparing to correct graph with cutoff 0.200000 [42.489722] Cleaning memory [42.489735] Deactivating local correction settings [42.489866] Pebble done. [42.489869] Starting pebble resolution... [42.498412] Computing read to node mapping array sizes [42.525040] Computing read to node mappings [42.649817] Estimating library insert lengths... [42.659942] Done [42.659958] Computing direct node to node mappings [42.672095] Scaffolding node 0 [42.694480] === Nodes Scaffolded in 0.034519 s [42.697209] Preparing to correct graph with cutoff 0.200000 [42.846000] Cleaning memory [42.846017] Deactivating local correction settings [42.850388] Pebble done. [42.850400] Concatenation... [42.851543] Renumbering nodes [42.851546] Initial node count 6401 [42.851919] Removed 52 null nodes [42.852006] Concatenation over! [42.852009] Removing reference contigs with coverage < 1.570000... [42.852379] Concatenation... [42.853084] Renumbering nodes [42.853091] Initial node count 6349 [42.853105] Removed 0 null nodes [42.853186] Concatenation over! [42.869052] Writing contigs into hsv.beforedigipe.45/contigs.fa... [43.246001] Writing into stats file hsv.beforedigipe.45/stats.txt... [43.312482] Writing into graph file hsv.beforedigipe.45/LastGraph... [43.790502] Estimated Coverage = 3.140000 [43.790513] Estimated Coverage cutoff = 1.570000 Final graph has 6349 nodes and n50 of 169, max 5753, total 413948, using 282051/1172451 reads [0.000001] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1229.dat' using 'Raw read' as FastA [3.174073] 858062 sequences found [3.174077] Done [3.174138] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1228.dat' using 'Raw read' as FastA [3.982251] 314389 sequences found [3.982254] Done [3.982352] Reading read set file hsv.beforedigipe.55/Sequences; [4.544606] 1172451 sequences found [6.882530] Done [6.882539] 1172451 sequences in total. [6.882610] Writing into roadmap file hsv.beforedigipe.55/Roadmaps... [7.989184] Inputting sequences... [7.989195] Inputting sequence 0 / 1172451 [16.064143] Inputting sequence 1000000 / 1172451 [16.642310] === Sequences loaded in 8.759880 s [16.642372] Done inputting sequences [16.642374] Destroying splay table [16.794429] Splay table destroyed [0.000001] Reading roadmap file hsv.beforedigipe.55/Roadmaps [1.774704] 1172451 roadmaps read [1.779143] Creating insertion markers [1.927932] Ordering insertion markers [2.616552] Counting preNodes [2.675882] 286922 preNodes counted, creating them now [5.858204] Sequence 1000000 / 1172451 [6.097057] Adjusting marker info... [6.168862] Connecting preNodes [6.695144] Connecting 1000000 / 1172451 [6.701157] Cleaning up memory [6.706303] Done creating preGraph [6.706308] Concatenation... [6.993492] Renumbering preNodes [6.993502] Initial preNode count 286922 [7.012440] Destroyed 193396 preNodes [7.012452] Concatenation over! [7.012454] Clipping short tips off preGraph [7.177935] Concatenation... [7.239919] Renumbering preNodes [7.239928] Initial preNode count 93526 [7.249496] Destroyed 77969 preNodes [7.249508] Concatenation over! [7.249509] 66480 tips cut off [7.249511] 15557 nodes left [7.249588] Writing into pregraph file hsv.beforedigipe.55/PreGraph... [7.469631] Reading read set file hsv.beforedigipe.55/Sequences; [7.824494] 1172451 sequences found [10.038542] Done [11.149657] Reading pre-graph file hsv.beforedigipe.55/PreGraph [11.149757] Graph has 15557 nodes and 1172451 sequences [11.220846] Scanning pre-graph file hsv.beforedigipe.55/PreGraph for k-mers [11.257017] 511790 kmers found [11.349698] Sorting kmer occurence table ... [11.734030] Sorting done. [11.734039] Computing acceleration table... [11.787052] Computing offsets... [11.793907] Ghost Threading through reads 0 / 1172451 [19.696002] Ghost Threading through reads 1000000 / 1172451 [19.941608] === Ghost-Threaded in 8.147701 s [19.941624] Threading through reads 0 / 1172451 [27.946549] Threading through reads 1000000 / 1172451 [28.208521] === Threaded in 8.266897 s [28.277650] Correcting graph with cutoff 0.200000 [28.278731] Determining eligible starting points [28.321438] Done listing starting nodes [28.321448] Initializing todo lists [28.324546] Done with initilization [28.324555] Activating arc lookup table [28.328005] Done activating arc lookup table [28.864893] 10000 / 15557 nodes visited [28.950648] Concatenation... [28.951848] Renumbering nodes [28.951853] Initial node count 15557 [28.952273] Removed 4280 null nodes [28.952276] Concatenation over! [28.952278] Clipping short tips off graph, drastic [28.965091] Concatenation... [28.982845] Renumbering nodes [28.982854] Initial node count 11277 [28.983103] Removed 7675 null nodes [28.983105] Concatenation over! [28.983107] 3602 nodes left [28.983189] Writing into graph file hsv.beforedigipe.55/Graph2... [29.233347] Measuring median coverage depth... [29.234995] Median coverage depth = 5.718919 [29.235047] Removing contigs with coverage < 2.859459... [29.237085] Concatenation... [29.247442] Renumbering nodes [29.247450] Initial node count 3602 [29.247541] Removed 2485 null nodes [29.247543] Concatenation over! [29.247586] Concatenation... [29.247641] Renumbering nodes [29.247642] Initial node count 1117 [29.247646] Removed 0 null nodes [29.247647] Concatenation over! [29.247674] Clipping short tips off graph, drastic [29.247839] Concatenation... [29.248311] Renumbering nodes [29.248313] Initial node count 1117 [29.248348] Removed 177 null nodes [29.248349] Concatenation over! [29.248351] 940 nodes left [29.248353] Read coherency... [29.248371] Identifying unique nodes [29.248399] Done, 368 unique nodes counted [29.248400] Trimming read tips [29.248445] Renumbering nodes [29.248446] Initial node count 940 [29.248449] Removed 0 null nodes [29.248451] Confronted to 0 multiple hits and 0 null over 0 [29.248453] Read coherency over! [29.258934] Starting pebble resolution... [29.291360] Computing read to node mapping array sizes [29.307313] Computing read to node mappings [29.356617] Estimating library insert lengths... [29.366846] Done [29.366886] Computing direct node to node mappings [29.370074] Scaffolding node 0 [29.373154] === Nodes Scaffolded in 0.006265 s [29.392565] Preparing to correct graph with cutoff 0.200000 [29.400927] Cleaning memory [29.400931] Deactivating local correction settings [29.400955] Pebble done. [29.400957] Starting pebble resolution... [29.409431] Computing read to node mapping array sizes [29.425018] Computing read to node mappings [29.471195] Estimating library insert lengths... [29.481292] Done [29.481308] Computing direct node to node mappings [29.483905] Scaffolding node 0 [29.486481] === Nodes Scaffolded in 0.005168 s [29.487140] Preparing to correct graph with cutoff 0.200000 [29.492008] Cleaning memory [29.492016] Deactivating local correction settings [29.516196] Pebble done. [29.516202] Concatenation... [29.516943] Renumbering nodes [29.516945] Initial node count 940 [29.516979] Removed 199 null nodes [29.516989] Concatenation over! [29.516991] Removing reference contigs with coverage < 2.859459... [29.517024] Concatenation... [29.517055] Renumbering nodes [29.517057] Initial node count 741 [29.517060] Removed 0 null nodes [29.517068] Concatenation over! [29.523755] Writing contigs into hsv.beforedigipe.55/contigs.fa... [29.647057] Writing into stats file hsv.beforedigipe.55/stats.txt... [29.652322] Writing into graph file hsv.beforedigipe.55/LastGraph... [29.920011] Estimated Coverage = 5.718919 [29.920021] Estimated Coverage cutoff = 2.859459 Final graph has 741 nodes and n50 of 2053, max 11085, total 235553, using 232749/1172451 reads [0.000000] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1229.dat' using 'Raw read' as FastA [2.969484] 858062 sequences found [2.969487] Done [2.969546] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1228.dat' using 'Raw read' as FastA [3.895805] 314389 sequences found [3.895809] Done [3.895908] Reading read set file hsv.beforedigipe.65/Sequences; [4.255316] 1172451 sequences found [6.966354] Done [6.966363] 1172451 sequences in total. [6.966433] Writing into roadmap file hsv.beforedigipe.65/Roadmaps... [7.748510] Inputting sequences... [7.748520] Inputting sequence 0 / 1172451 [14.144352] Inputting sequence 1000000 / 1172451 [14.514040] === Sequences loaded in 6.848535 s [14.514133] Done inputting sequences [14.514135] Destroying splay table [14.854455] Splay table destroyed [0.000001] Reading roadmap file hsv.beforedigipe.65/Roadmaps [1.617659] 1172451 roadmaps read [1.621875] Creating insertion markers [1.818248] Ordering insertion markers [2.120737] Counting preNodes [2.168910] 224798 preNodes counted, creating them now [5.285643] Sequence 1000000 / 1172451 [5.500090] Adjusting marker info... [5.561462] Connecting preNodes [5.952251] Connecting 1000000 / 1172451 [5.968083] Cleaning up memory [5.972227] Done creating preGraph [5.972231] Concatenation... [6.139838] Renumbering preNodes [6.139847] Initial preNode count 224798 [6.165935] Destroyed 160812 preNodes [6.165942] Concatenation over! [6.165944] Clipping short tips off preGraph [6.254169] Concatenation... [6.286813] Renumbering preNodes [6.286823] Initial preNode count 63986 [6.288266] Destroyed 59269 preNodes [6.288269] Concatenation over! [6.288270] 53316 tips cut off [6.288271] 4717 nodes left [6.290032] Writing into pregraph file hsv.beforedigipe.65/PreGraph... [6.404721] Reading read set file hsv.beforedigipe.65/Sequences; [7.031575] 1172451 sequences found [9.217169] Done [10.311726] Reading pre-graph file hsv.beforedigipe.65/PreGraph [10.311810] Graph has 4717 nodes and 1172451 sequences [10.332054] Scanning pre-graph file hsv.beforedigipe.65/PreGraph for k-mers [10.359173] 291763 kmers found [10.416325] Sorting kmer occurence table ... [10.596311] Sorting done. [10.596321] Computing acceleration table... [10.618565] Computing offsets... [10.646094] Ghost Threading through reads 0 / 1172451 [15.884371] Ghost Threading through reads 1000000 / 1172451 [16.163913] === Ghost-Threaded in 5.517820 s [16.163927] Threading through reads 0 / 1172451 [21.520825] Threading through reads 1000000 / 1172451 [21.674375] === Threaded in 5.510448 s [21.723600] Correcting graph with cutoff 0.200000 [21.724000] Determining eligible starting points [21.728174] Done listing starting nodes [21.728177] Initializing todo lists [21.728578] Done with initilization [21.728580] Activating arc lookup table [21.728967] Done activating arc lookup table [21.831582] Concatenation... [21.831824] Renumbering nodes [21.831826] Initial node count 4717 [21.831932] Removed 745 null nodes [21.831934] Concatenation over! [21.831935] Clipping short tips off graph, drastic [21.835025] Concatenation... [21.840013] Renumbering nodes [21.840020] Initial node count 3972 [21.840068] Removed 2973 null nodes [21.840070] Concatenation over! [21.840072] 999 nodes left [21.840164] Writing into graph file hsv.beforedigipe.65/Graph2... [22.152002] Measuring median coverage depth... [22.152372] Median coverage depth = 27.928011 [22.152427] Removing contigs with coverage < 13.964006... [22.154278] Concatenation... [22.162376] Renumbering nodes [22.162383] Initial node count 999 [22.162394] Removed 913 null nodes [22.162396] Concatenation over! [22.162400] Concatenation... [22.162403] Renumbering nodes [22.162404] Initial node count 86 [22.162405] Removed 0 null nodes [22.162406] Concatenation over! [22.162431] Clipping short tips off graph, drastic [22.162445] Concatenation... [22.162574] Renumbering nodes [22.162576] Initial node count 86 [22.162579] Removed 14 null nodes [22.162580] Concatenation over! [22.162581] 72 nodes left [22.162583] Read coherency... [22.162585] Identifying unique nodes [22.162588] Done, 50 unique nodes counted [22.162590] Trimming read tips [22.162593] Renumbering nodes [22.162594] Initial node count 72 [22.162595] Removed 0 null nodes [22.162596] Confronted to 0 multiple hits and 0 null over 0 [22.162598] Read coherency over! [22.208286] Starting pebble resolution... [22.216384] Computing read to node mapping array sizes [22.228345] Computing read to node mappings [22.328403] Estimating library insert lengths... [22.338608] Done [22.338642] Computing direct node to node mappings [22.347573] Scaffolding node 0 [22.365268] === Nodes Scaffolded in 0.026622 s [22.367799] Preparing to correct graph with cutoff 0.200000 [22.377544] Cleaning memory [22.377553] Deactivating local correction settings [22.377575] Pebble done. [22.377577] Starting pebble resolution... [22.392144] Computing read to node mapping array sizes [22.415582] Computing read to node mappings [22.484257] Estimating library insert lengths... [22.500282] Done [22.500291] Computing direct node to node mappings [22.509242] Scaffolding node 0 [22.518779] === Nodes Scaffolded in 0.018483 s [22.520817] Preparing to correct graph with cutoff 0.200000 [22.520918] Cleaning memory [22.520921] Deactivating local correction settings [22.520928] Pebble done. [22.520931] Concatenation... [22.520935] Renumbering nodes [22.520936] Initial node count 72 [22.520940] Removed 11 null nodes [22.520942] Concatenation over! [22.520944] Removing reference contigs with coverage < 13.964006... [22.520951] Concatenation... [22.520953] Renumbering nodes [22.520954] Initial node count 61 [22.520955] Removed 0 null nodes [22.520957] Concatenation over! [22.527786] Writing contigs into hsv.beforedigipe.65/contigs.fa... [22.623650] Writing into stats file hsv.beforedigipe.65/stats.txt... [22.625427] Writing into graph file hsv.beforedigipe.65/LastGraph... [22.735787] Estimated Coverage = 27.928011 [22.735798] Estimated Coverage cutoff = 13.964006 Final graph has 61 nodes and n50 of 4242, max 12319, total 123231, using 185388/1172451 reads