[0.000000] Reading roadmap file ./velveth_out/Roadmaps [3.586429] 4154736 roadmaps read [3.587893] Creating insertion markers [4.668401] Ordering insertion markers [6.160696] Counting preNodes [6.542716] 1022251 preNodes counted, creating them now [7.534766] Sequence 1000000 / 4154736 [8.104283] Sequence 2000000 / 4154736 [8.654085] Sequence 3000000 / 4154736 [9.201918] Sequence 4000000 / 4154736 [9.286948] Adjusting marker info... [9.587635] Connecting preNodes [9.751427] Connecting 1000000 / 4154736 [9.960571] Connecting 2000000 / 4154736 [10.186806] Connecting 3000000 / 4154736 [10.438184] Connecting 4000000 / 4154736 [10.479421] Cleaning up memory [10.483937] Done creating preGraph [10.483938] Concatenation... [10.796197] Renumbering preNodes [10.796202] Initial preNode count 1022251 [10.845376] Destroyed 736060 preNodes [10.845380] Concatenation over! [10.845381] Clipping short tips off preGraph [10.931351] Concatenation... [10.981147] Renumbering preNodes [10.981150] Initial preNode count 286191 [10.985644] Destroyed 281186 preNodes [10.985645] Concatenation over! [10.985646] 194999 tips cut off [10.985646] 5005 nodes left [10.985741] Writing into pregraph file ./velveth_out/PreGraph... [11.015334] Reading read set file ./velveth_out/Sequences; [11.242257] 4154736 sequences found [12.962089] Done [14.403005] Reading pre-graph file ./velveth_out/PreGraph [14.403048] Graph has 5005 nodes and 4154736 sequences [14.415052] Scanning pre-graph file ./velveth_out/PreGraph for k-mers [14.428327] 674384 kmers found [14.447075] Sorting kmer occurrence table ... [14.597536] Sorting done. [14.597538] Computing acceleration table... [14.612667] Computing offsets... [14.614660] Ghost Threading through reads 0 / 4154736 [14.622363] Ghost Threading through reads 1000000 / 4154736 [14.630063] Ghost Threading through reads 2000000 / 4154736 [14.637776] Ghost Threading through reads 3000000 / 4154736 [14.645498] Ghost Threading through reads 4000000 / 4154736 [14.646702] === Ghost-Threaded in 0.032042 s [14.646703] Threading through reads 0 / 4154736 [15.464559] Threading through reads 1000000 / 4154736 [16.275706] Threading through reads 2000000 / 4154736 [17.073016] Threading through reads 3000000 / 4154736 [17.886256] Threading through reads 4000000 / 4154736 [18.011130] === Threaded in 3.364427 s [18.022783] Correcting graph with cutoff 0.200000 [18.023062] Determining eligible starting points [18.025928] Done listing starting nodes [18.025929] Initializing todo lists [18.026223] Done with initialization [18.026224] Activating arc lookup table [18.026448] Done activating arc lookup table [18.030192] Concatenation... [18.030325] Renumbering nodes [18.030325] Initial node count 5005 [18.030383] Removed 114 null nodes [18.030383] Concatenation over! [18.030383] Clipping short tips off graph, drastic [18.031270] Concatenation... [18.039233] Renumbering nodes [18.039234] Initial node count 4891 [18.039251] Removed 4522 null nodes [18.039251] Concatenation over! [18.039252] 369 nodes left [18.039324] Writing into graph file ./velveth_out/Graph... [18.086183] WARNING: NO COVERAGE CUTOFF PROVIDED [18.086184] Velvet will probably leave behind many detectable errors [18.086184] See manual for instructions on how to set the coverage cutoff parameter [18.086185] Removing contigs with coverage < -1.000000... [18.086790] Concatenation... [18.086798] Renumbering nodes [18.086798] Initial node count 369 [18.086799] Removed 0 null nodes [18.086800] Concatenation over! [18.086805] Concatenation... [18.086812] Renumbering nodes [18.086812] Initial node count 369 [18.086813] Removed 0 null nodes [18.086813] Concatenation over! [18.086814] Clipping short tips off graph, drastic [18.086822] Concatenation... [18.086829] Renumbering nodes [18.086829] Initial node count 369 [18.086829] Removed 0 null nodes [18.086830] Concatenation over! [18.086830] 369 nodes left [18.086830] WARNING: NO EXPECTED COVERAGE PROVIDED [18.086831] Velvet will be unable to resolve any repeats [18.086831] See manual for instructions on how to set the expected coverage parameter [18.086831] Concatenation... [18.086837] Renumbering nodes [18.086837] Initial node count 369 [18.086838] Removed 0 null nodes [18.086838] Concatenation over! [18.086838] Removing reference contigs with coverage < -1.000000... [18.086849] Concatenation... [18.086855] Renumbering nodes [18.086855] Initial node count 369 [18.086856] Removed 0 null nodes [18.086856] Concatenation over! [18.104312] Writing contigs into ./velveth_out/contigs.fa... [18.132796] Writing into stats file ./velveth_out/stats.txt... [18.133505] Writing into graph file ./velveth_out/LastGraph... Final graph has 369 nodes and n50 of 7028, max 36746, total 657295, using 0/4154736 reads