PARAMETERS:
 - kmer size =    20 		(-k)
 - n hashes =     4 		(-N)
 - min hashsize = 1e+08 	(-x)
 - paired =	      True 		(-p)

Estimated memory usage is 4e+08 bytes (n_hashes x min_hashsize)
--------
making hashtable
... kept 122640 of 200000 , or 61 %
... in file after_merge.fq
... kept 153866 of 400000 , or 38 %
... in file after_merge.fq
... kept 183178 of 600000 , or 30 %
... in file after_merge.fq
... kept 206362 of 800000 , or 25 %
... in file after_merge.fq
... kept 224348 of 1000000 , or 22 %
... in file after_merge.fq
... kept 243296 of 1200000 , or 20 %
... in file after_merge.fq
... kept 261944 of 1400000 , or 18 %
... in file after_merge.fq
... kept 279514 of 1600000 , or 17 %
... in file after_merge.fq
... kept 296676 of 1800000 , or 16 %
... in file after_merge.fq
... kept 312938 of 2000000 , or 15 %
... in file after_merge.fq
... kept 329636 of 2200000 , or 14 %
... in file after_merge.fq
... kept 346262 of 2400000 , or 14 %
... in file after_merge.fq
... kept 362450 of 2600000 , or 13 %
... in file after_merge.fq
... kept 378398 of 2800000 , or 13 %
... in file after_merge.fq
... kept 394822 of 3000000 , or 13 %
... in file after_merge.fq
... kept 411192 of 3200000 , or 12 %
... in file after_merge.fq
... kept 430380 of 3400000 , or 12 %
... in file after_merge.fq
... kept 449126 of 3600000 , or 12 %
... in file after_merge.fq
... kept 465978 of 3800000 , or 12 %
... in file after_merge.fq
... kept 482104 of 4000000 , or 12 %
... in file after_merge.fq
... kept 499494 of 4200000 , or 11 %
... in file after_merge.fq
... kept 517768 of 4400000 , or 11 %
... in file after_merge.fq
... kept 535452 of 4600000 , or 11 %
... in file after_merge.fq
... kept 552182 of 4800000 , or 11 %
... in file after_merge.fq
... kept 568702 of 5000000 , or 11 %
... in file after_merge.fq
... kept 586324 of 5200000 , or 11 %
... in file after_merge.fq
... kept 604940 of 5400000 , or 11 %
... in file after_merge.fq
... kept 622590 of 5600000 , or 11 %
... in file after_merge.fq
... kept 639166 of 5800000 , or 11 %
... in file after_merge.fq
... kept 655608 of 6000000 , or 10 %
... in file after_merge.fq
... kept 672550 of 6200000 , or 10 %
... in file after_merge.fq
... kept 690116 of 6400000 , or 10 %
... in file after_merge.fq
... kept 708924 of 6600000 , or 10 %
... in file after_merge.fq
... kept 726922 of 6800000 , or 10 %
... in file after_merge.fq
... kept 744220 of 7000000 , or 10 %
... in file after_merge.fq
... kept 761086 of 7200000 , or 10 %
... in file after_merge.fq
... kept 778078 of 7400000 , or 10 %
... in file after_merge.fq
... kept 795282 of 7600000 , or 10 %
... in file after_merge.fq
... kept 812338 of 7800000 , or 10 %
... in file after_merge.fq
... kept 829394 of 8000000 , or 10 %
... in file after_merge.fq
... kept 844658 of 8200000 , or 10 %
... in file after_merge.fq
... kept 860352 of 8400000 , or 10 %
... in file after_merge.fq
... kept 882658 of 8600000 , or 10 %
... in file after_merge.fq
... kept 903778 of 8800000 , or 10 %
... in file after_merge.fq
... kept 918768 of 9000000 , or 10 %
... in file after_merge.fq
... kept 934356 of 9200000 , or 10 %
... in file after_merge.fq
... kept 950550 of 9400000 , or 10 %
... in file after_merge.fq
... kept 966826 of 9600000 , or 10 %
... in file after_merge.fq
... kept 981804 of 9800000 , or 10 %
... in file after_merge.fq
... kept 996900 of 10000000 , or 9 %
... in file after_merge.fq
... kept 1012070 of 10200000 , or 9 %
... in file after_merge.fq
... kept 1027590 of 10400000 , or 9 %
... in file after_merge.fq
... kept 1042580 of 10600000 , or 9 %
... in file after_merge.fq
... kept 1057444 of 10800000 , or 9 %
... in file after_merge.fq
... kept 1072642 of 11000000 , or 9 %
... in file after_merge.fq
... kept 1087892 of 11200000 , or 9 %
... in file after_merge.fq
... kept 1105498 of 11400000 , or 9 %
... in file after_merge.fq
... kept 1123498 of 11600000 , or 9 %
... in file after_merge.fq
... kept 1139684 of 11800000 , or 9 %
... in file after_merge.fq
... kept 1155024 of 12000000 , or 9 %
... in file after_merge.fq
... kept 1171670 of 12200000 , or 9 %
... in file after_merge.fq
... kept 1189418 of 12400000 , or 9 %
... in file after_merge.fq
... kept 1207082 of 12600000 , or 9 %
... in file after_merge.fq
... kept 1223880 of 12800000 , or 9 %
... in file after_merge.fq
... kept 1240028 of 13000000 , or 9 %
... in file after_merge.fq
... kept 1255958 of 13200000 , or 9 %
... in file after_merge.fq
... kept 1272906 of 13400000 , or 9 %
... in file after_merge.fq
... kept 1290114 of 13600000 , or 9 %
... in file after_merge.fq
... kept 1306818 of 13800000 , or 9 %
... in file after_merge.fq
... kept 1323154 of 14000000 , or 9 %
... in file after_merge.fq
... kept 1339778 of 14200000 , or 9 %
... in file after_merge.fq
... kept 1356578 of 14400000 , or 9 %
... in file after_merge.fq
... kept 1374984 of 14600000 , or 9 %
... in file after_merge.fq
... kept 1393644 of 14800000 , or 9 %
... in file after_merge.fq
... kept 1410934 of 15000000 , or 9 %
... in file after_merge.fq
... kept 1428214 of 15200000 , or 9 %
... in file after_merge.fq
... kept 1445010 of 15400000 , or 9 %
... in file after_merge.fq
... kept 1462386 of 15600000 , or 9 %
... in file after_merge.fq
... kept 1480014 of 15800000 , or 9 %
... in file after_merge.fq
... kept 1497302 of 16000000 , or 9 %
... in file after_merge.fq
... kept 1514774 of 16200000 , or 9 %
... in file after_merge.fq
... kept 1529070 of 16400000 , or 9 %
... in file after_merge.fq
... kept 1544904 of 16600000 , or 9 %
... in file after_merge.fq
... kept 1568072 of 16800000 , or 9 %
... in file after_merge.fq
... kept 1587784 of 17000000 , or 9 %
... in file after_merge.fq
... kept 1601968 of 17200000 , or 9 %
... in file after_merge.fq
... kept 1616606 of 17400000 , or 9 %
... in file after_merge.fq
... kept 1631508 of 17600000 , or 9 %
... in file after_merge.fq
... kept 1646502 of 17800000 , or 9 %
... in file after_merge.fq
... kept 1660834 of 18000000 , or 9 %
... in file after_merge.fq
... kept 1675818 of 18200000 , or 9 %
... in file after_merge.fq
... kept 1690478 of 18400000 , or 9 %
... in file after_merge.fq
... kept 1705488 of 18600000 , or 9 %
... in file after_merge.fq
... kept 1719800 of 18800000 , or 9 %
... in file after_merge.fq
... kept 1734596 of 19000000 , or 9 %
... in file after_merge.fq
... kept 1749306 of 19200000 , or 9 %
... in file after_merge.fq
... kept 1764134 of 19400000 , or 9 %
... in file after_merge.fq
... kept 1781676 of 19600000 , or 9 %
... in file after_merge.fq
... kept 1799046 of 19800000 , or 9 %
... in file after_merge.fq
... kept 1814564 of 20000000 , or 9 %
... in file after_merge.fq
... kept 1829572 of 20200000 , or 9 %
... in file after_merge.fq
... kept 1845242 of 20400000 , or 9 %
... in file after_merge.fq
... kept 1861964 of 20600000 , or 9 %
... in file after_merge.fq
... kept 1879108 of 20800000 , or 9 %
... in file after_merge.fq
... kept 1894840 of 21000000 , or 9 %
... in file after_merge.fq
... kept 1910492 of 21200000 , or 9 %
... in file after_merge.fq
... kept 1926514 of 21400000 , or 9 %
... in file after_merge.fq
... kept 1943918 of 21600000 , or 8 %
... in file after_merge.fq
... kept 1960874 of 21800000 , or 8 %
... in file after_merge.fq
... kept 1976990 of 22000000 , or 8 %
... in file after_merge.fq
... kept 1992802 of 22200000 , or 8 %
... in file after_merge.fq
... kept 2008718 of 22400000 , or 8 %
... in file after_merge.fq
... kept 2025594 of 22600000 , or 8 %
... in file after_merge.fq
... kept 2043976 of 22800000 , or 8 %
... in file after_merge.fq
... kept 2062570 of 23000000 , or 8 %
... in file after_merge.fq
... kept 2079804 of 23200000 , or 8 %
... in file after_merge.fq
... kept 2096774 of 23400000 , or 8 %
... in file after_merge.fq
... kept 2113524 of 23600000 , or 8 %
... in file after_merge.fq
... kept 2130950 of 23800000 , or 8 %
... in file after_merge.fq
... kept 2148688 of 24000000 , or 8 %
... in file after_merge.fq
... kept 2166750 of 24200000 , or 8 %
... in file after_merge.fq
... kept 2184896 of 24400000 , or 8 %
... in file after_merge.fq
... kept 2198926 of 24600000 , or 8 %
... in file after_merge.fq
... kept 2217684 of 24800000 , or 8 %
... in file after_merge.fq
... kept 2241260 of 25000000 , or 8 %
... in file after_merge.fq
... kept 2258660 of 25200000 , or 8 %
... in file after_merge.fq
... kept 2272862 of 25400000 , or 8 %
... in file after_merge.fq
... kept 2288390 of 25600000 , or 8 %
... in file after_merge.fq
... kept 2304260 of 25800000 , or 8 %
... in file after_merge.fq
... kept 2318938 of 26000000 , or 8 %
... in file after_merge.fq
... kept 2333398 of 26200000 , or 8 %
... in file after_merge.fq
... kept 2347712 of 26400000 , or 8 %
... in file after_merge.fq
... kept 2362252 of 26600000 , or 8 %
... in file after_merge.fq
... kept 2377276 of 26800000 , or 8 %
... in file after_merge.fq
... kept 2391824 of 27000000 , or 8 %
... in file after_merge.fq
... kept 2406590 of 27200000 , or 8 %
... in file after_merge.fq
... kept 2421638 of 27400000 , or 8 %
... in file after_merge.fq
... kept 2436558 of 27600000 , or 8 %
... in file after_merge.fq
... kept 2454536 of 27800000 , or 8 %
... in file after_merge.fq
... kept 2474546 of 28000000 , or 8 %
... in file after_merge.fq
... kept 2489918 of 28200000 , or 8 %
... in file after_merge.fq
... kept 2505064 of 28400000 , or 8 %
... in file after_merge.fq
... kept 2520536 of 28600000 , or 8 %
... in file after_merge.fq
... kept 2537212 of 28800000 , or 8 %
... in file after_merge.fq
... kept 2554420 of 29000000 , or 8 %
... in file after_merge.fq
... kept 2569998 of 29200000 , or 8 %
... in file after_merge.fq
... kept 2585840 of 29400000 , or 8 %
... in file after_merge.fq
... kept 2602310 of 29600000 , or 8 %
... in file after_merge.fq
... kept 2619564 of 29800000 , or 8 %
... in file after_merge.fq
... kept 2636272 of 30000000 , or 8 %
... in file after_merge.fq
... kept 2652274 of 30200000 , or 8 %
... in file after_merge.fq
... kept 2668396 of 30400000 , or 8 %
... in file after_merge.fq
... kept 2685010 of 30600000 , or 8 %
... in file after_merge.fq
... kept 2702544 of 30800000 , or 8 %
... in file after_merge.fq
... kept 2721166 of 31000000 , or 8 %
... in file after_merge.fq
... kept 2739018 of 31200000 , or 8 %
... in file after_merge.fq
... kept 2756064 of 31400000 , or 8 %
... in file after_merge.fq
... kept 2773022 of 31600000 , or 8 %
... in file after_merge.fq
... kept 2790108 of 31800000 , or 8 %
... in file after_merge.fq
... kept 2807308 of 32000000 , or 8 %
... in file after_merge.fq
... kept 2824840 of 32200000 , or 8 %
... in file after_merge.fq
... kept 2843362 of 32400000 , or 8 %
... in file after_merge.fq
DONE with after_merge.fq ; kept 2857640 of 32549000 or 8 %
output in after_merge.fq.keep
Saving hashfile through after_merge.fq
...saving to afterdiginorm.kh
fp rate estimated to be 0.188
starting threads
starting writer
loading...
... filtering 0
... filtering 100000
... filtering 200000
... filtering 300000
... filtering 400000
... filtering 500000
processed 500000 / wrote 359298 / removed 140702
processed 42082111 bp / wrote 24055052 bp / removed 18027059 bp
discarded 42.8%
... filtering 600000
... filtering 700000
... filtering 800000
... filtering 900000
... filtering 1000000
processed 1000000 / wrote 658876 / removed 341124
processed 83463300 bp / wrote 40178626 bp / removed 43284674 bp
discarded 51.9%
... filtering 1100000
... filtering 1200000
... filtering 1300000
... filtering 1400000
... filtering 1500000
processed 1500000 / wrote 952494 / removed 547506
processed 125051028 bp / wrote 55579943 bp / removed 69471085 bp
discarded 55.6%
... filtering 1600000
... filtering 1700000
... filtering 1800000
... filtering 1900000
... filtering 2000000
processed 2000000 / wrote 1244224 / removed 755776
processed 166561321 bp / wrote 70854190 bp / removed 95707131 bp
discarded 57.5%
... filtering 2100000
... filtering 2200000
... filtering 2300000
... filtering 2400000
... filtering 2500000
processed 2500000 / wrote 1533673 / removed 966327
processed 208058755 bp / wrote 85953806 bp / removed 122104949 bp
discarded 58.7%
... filtering 2600000
... filtering 2700000
... filtering 2800000
done loading in sequences
DONE writing.
processed 2856040 / wrote 1737878 / removed 1118162
processed 237652164 bp / wrote 96401505 bp / removed 141250659 bp
discarded 59.4%
file with ht: afterdiginorm.kh
loading hashtable
K: 20
filtering after_merge.fq.keep
output in after_merge.fq.keep.abundfilt
splitting pe/se sequences from after_merge.fq.keep.abundfilt to after_merge.fq.keep.abundfilt.{pe,se}
... 100000
... 200000
... 300000
... 400000
... 500000
... 600000
... 700000
... 800000
... 900000
... 1000000
... 1100000
... 1200000
... 1300000
... 1400000
... 1500000
... 1600000
... 1700000
DONE; read 1737996 sequences, 633418 pairs and 471160 singletons

PARAMETERS:
 - kmer size =    20 		(-k)
 - n hashes =     4 		(-N)
 - min hashsize = 1e+08 	(-x)
 - paired =	      True 		(-p)

Estimated memory usage is 4e+08 bytes (n_hashes x min_hashsize)
--------
making hashtable
... kept 87744 of 200000 , or 43 %
... in file after_merge.fq.keep.abundfilt.pe
... kept 234310 of 400000 , or 58 %
... in file after_merge.fq.keep.abundfilt.pe
... kept 381588 of 600000 , or 63 %
... in file after_merge.fq.keep.abundfilt.pe
... kept 526828 of 800000 , or 65 %
... in file after_merge.fq.keep.abundfilt.pe
... kept 670212 of 1000000 , or 67 %
... in file after_merge.fq.keep.abundfilt.pe
... kept 811076 of 1200000 , or 67 %
... in file after_merge.fq.keep.abundfilt.pe
DONE with after_merge.fq.keep.abundfilt.pe ; kept 858038 of 1266836 or 67 %
output in after_merge.fq.keep.abundfilt.pe.keep
Saving hashfile through after_merge.fq.keep.abundfilt.pe
...saving to afterdiginorm.kh
fp rate estimated to be 0.000

PARAMETERS:
 - kmer size =    20 		(-k)
 - n hashes =     4 		(-N)
 - min hashsize = 1e+08 	(-x)
 - paired =	      False 		(-p)

Estimated memory usage is 4e+08 bytes (n_hashes x min_hashsize)
--------
making hashtable
... kept 86008 of 100000 , or 86 %
... in file after_merge.fq.keep.abundfilt.se
... kept 151422 of 200000 , or 75 %
... in file after_merge.fq.keep.abundfilt.se
... kept 212459 of 300000 , or 70 %
... in file after_merge.fq.keep.abundfilt.se
... kept 271942 of 400000 , or 67 %
... in file after_merge.fq.keep.abundfilt.se
DONE with after_merge.fq.keep.abundfilt.se ; kept 314389 of 471160 or 66 %
output in after_merge.fq.keep.abundfilt.se.keep
Saving hashfile through after_merge.fq.keep.abundfilt.se
...saving to afterdiginorm.kh
fp rate estimated to be 0.000
[0.000001] Reading file 'afterdiginorm.pe.fasta' using 'Raw read' as FastA
[2.490318] 858038 sequences found
[2.490322] Done
[2.490384] Reading file 'afterdiginorm.se.fasta' using 'Raw read' as FastA
[3.202595] 314389 sequences found
[3.202599] Done
[3.202699] Reading read set file hsv.beforedigipe.35/Sequences;
[3.571056] 1172427 sequences found
[5.478142] Done
[5.478152] 1172427 sequences in total.
[5.478218] Writing into roadmap file hsv.beforedigipe.35/Roadmaps...
[6.291556] Inputting sequences...
[6.291566] Inputting sequence 0 / 1172427
[16.568029] Inputting sequence 1000000 / 1172427
[17.332941]  === Sequences loaded in 11.148785 s
[17.333003] Done inputting sequences
[17.333006] Destroying splay table
[17.553785] Splay table destroyed
[0.000001] Reading roadmap file hsv.beforedigipe.35/Roadmaps
[1.954827] 1172427 roadmaps read
[1.959397] Creating insertion markers
[2.232117] Ordering insertion markers
[2.926785] Counting preNodes
[3.052625] 586132 preNodes counted, creating them now
[5.931301] Sequence 1000000 / 1172427
[6.179634] Adjusting marker info...
[6.297681] Connecting preNodes
[7.528020] Connecting 1000000 / 1172427
[7.576356] Cleaning up memory
[7.586593] Done creating preGraph
[7.586602] Concatenation...
[7.937275] Renumbering preNodes
[7.937285] Initial preNode count 586132
[7.977306] Destroyed 307167 preNodes
[7.977315] Concatenation over!
[7.977317] Clipping short tips off preGraph
[8.133477] Concatenation...
[8.242390] Renumbering preNodes
[8.242402] Initial preNode count 278965
[8.268963] Destroyed 124007 preNodes
[8.269043] Concatenation over!
[8.269045] 93472 tips cut off
[8.269046] 154958 nodes left
[8.269119] Writing into pregraph file hsv.beforedigipe.35/PreGraph...
[9.098949] Reading read set file hsv.beforedigipe.35/Sequences
..
imming read tips
[23.317718] Renumbering nodes
[23.317719] Initial node count 947
[23.317722] Removed 0 null nodes
[23.317723] Confronted to 0 multiple hits and 0 null over 0
[23.317725] Read coherency over!
[23.328491] Starting pebble resolution...
[23.336831] Computing read to node mapping array sizes
[23.352789] Computing read to node mappings
[23.402607] Estimating library insert lengths...
[23.412737] Done
[23.412776] Computing direct node to node mappings
[23.415765] Scaffolding node 0
[23.418851]  === Nodes Scaffolded in 0.006072 s
[23.419832] Preparing to correct graph with cutoff 0.200000
[23.428181] Cleaning memory
[23.428186] Deactivating local correction settings
[23.428209] Pebble done.
[23.428211] Starting pebble resolution...
[23.460587] Computing read to node mapping array sizes
[23.476483] Computing read to node mappings
[23.526613] Estimating library insert lengths...
[23.536850] Done
[23.536866] Computing direct node to node mappings
[23.539470] Scaffolding node 0
[23.541921]  === Nodes Scaffolded in 0.005052 s
[23.542494] Preparing to correct graph with cutoff 0.200000
[23.547302] Cleaning memory
[23.547310] Deactivating local correction settings
[23.547332] Pebble done.
[23.547335] Concatenation...
[23.548030] Renumbering nodes
[23.548032] Initial node count 947
[23.548058] Removed 198 null nodes
[23.548067] Concatenation over!
[23.548068] Removing reference contigs with coverage < 2.859459...
[23.548102] Concatenation...
[23.548133] Renumbering nodes
[23.548135] Initial node count 749
[23.548137] Removed 0 null nodes
[23.548145] Concatenation over!
[23.579111] Writing contigs into hsv.beforedigipe.55/contigs.fa...
[23.701842] Writing into stats file hsv.beforedigipe.55/stats.txt...
[23.707168] Writing into graph file hsv.beforedigipe.55/LastGraph...
[23.894273] Estimated Coverage = 5.718919
[23.894284] Estimated Coverage cutoff = 2.859459
Final graph has 749 nodes and n50 of 2272, max 11085, total 236264, using 232838/1172427 reads
[0.000001] Reading file 'afterdiginorm.pe.fasta' using 'Raw read' as FastA
[2.507621] 858038 sequences found
[2.507625] Done
[2.507678] Reading file 'afterdiginorm.se.fasta' using 'Raw read' as FastA
[3.216319] 314389 sequences found
[3.216322] Done
[3.216419] Reading read set file hsv.beforedigipe.65/Sequences;
[3.587389] 1172427 sequences found
[5.592384] Done
[5.592393] 1172427 sequences in total.
[5.592464] Writing into roadmap file hsv.beforedigipe.65/Roadmaps...
[6.374598] Inputting sequences...
[6.374608] Inputting sequence 0 / 1172427
[11.391028] Inputting sequence 1000000 / 1172427
[11.686373]  === Sequences loaded in 5.393373 s
[11.686430] Done inputting sequences
[11.686433] Destroying splay table
[11.858534] Splay table destroyed
[0.000000] Reading roadmap file hsv.beforedigipe.65/Roadmaps
[1.349741] 1172427 roadmaps read
[1.354378] Creating insertion markers
[1.484428] Ordering insertion markers
[1.787699] Counting preNodes
[1.840182] 224824 preNodes counted, creating them now
[4.334236] Sequence 1000000 / 1172427
[4.574199] Adjusting marker info...
[4.612337] Connecting preNodes
[4.955743] Connecting 1000000 / 1172427
[4.960211] Cleaning up memory
[4.965472] Done creating preGraph
[4.965478] Concatenation...
[5.069530] Renumbering preNodes
[5.069542] Initial preNode count 224824
[5.082662] Destroyed 160824 preNodes
[5.082673] Concatenation over!
[5.082675] Clipping short tips off preGraph
[5.104432] Concatenation...
[5.120154] Renumbering preNodes
[5.120164] Initial preNode count 64000
[5.121573] Destroyed 59287 preNodes
[5.121577] Concatenation over!
[5.121578] 53330 tips cut off
[5.121580] 4713 nodes left
[5.121657] Writing into pregraph file hsv.beforedigipe.65/PreGraph...
[5.203253] Reading read set file hsv.beforedigipe.65/Sequences;
[5.559168] 1172427 sequences found
[7.489759] Done
[8.271532] Reading pre-graph file hsv.beforedigipe.65/PreGraph
[8.271617] Graph has 4713 nodes and 1172427 sequences
[8.291591] Scanning pre-graph file hsv.beforedigipe.65/PreGraph for k-mers
[8.343277] 291651 kmers found
[8.376114] Sorting kmer occurence table ... 
[8.582519] Sorting done.
[8.582528] Computing acceleration table... 
[8.604360] Computing offsets... 
[8.607653] Ghost Threading through reads 0 / 1172427
[12.637265] Ghost Threading through reads 1000000 / 1172427
[12.796853]  === Ghost-Threaded in 4.189201 s
[12.796862] Threading through reads 0 / 1172427
[17.155775] Threading through reads 1000000 / 1172427
[17.333275]  === Threaded in 4.536413 s
[17.358874] Correcting graph with cutoff 0.200000
[17.359280] Determining eligible starting points
[17.363475] Done listing starting nodes
[17.363477] Initializing todo lists
[17.363865] Done with initilization
[17.363867] Activating arc lookup table
[17.364267] Done activating arc lookup table
[17.433637] Concatenation...
[17.433927] Renumbering nodes
[17.433929] Initial node count 4713
[17.434040] Removed 767 null nodes
[17.434042] Concatenation over!
[17.434043] Clipping short tips off graph, drastic
[17.437199] Concatenation...
[17.442751] Renumbering nodes
[17.442759] Initial node count 3946
[17.442809] Removed 2936 null nodes
[17.442811] Concatenation over!
[17.442812] 1010 nodes left
[17.442909] Writing into graph file hsv.beforedigipe.65/Graph2...
[17.620029] Measuring median coverage depth...
[17.620415] Median coverage depth = 28.646829
[17.620470] Removing contigs with coverage < 14.323414...
[17.622232] Concatenation...
[17.627539] Renumbering nodes
[17.627545] Initial node count 1010
[17.627553] Removed 932 null nodes
[17.627554] Concatenation over!
[17.627558] Concatenation...
[17.627560] Renumbering nodes
[17.627561] Initial node count 78
[17.627562] Removed 0 null nodes
[17.627564] Concatenation over!
[17.627582] Clipping short tips off graph, drastic
[17.627594] Concatenation...
[17.627623] Renumbering nodes
[17.627624] Initial node count 78
[17.627626] Removed 7 null nodes
[17.627627] Concatenation over!
[17.627628] 71 nodes left
[17.627630] Read coherency...
[17.627631] Identifying unique nodes
[17.627634] Done, 51 unique nodes counted
[17.627636] Trimming read tips
[17.627639] Renumbering nodes
[17.627640] Initial node count 71
[17.627641] Removed 0 null nodes
[17.627642] Confronted to 0 multiple hits and 0 null over 0
[17.627644] Read coherency over!
[17.638094] Starting pebble resolution...
[17.646297] Computing read to node mapping array sizes
[17.658024] Computing read to node mappings
[17.688679] Estimating library insert lengths...
[17.698822] Done
[17.698856] Computing direct node to node mappings
[17.732302] Scaffolding node 0
[17.742588]  === Nodes Scaffolded in 0.043728 s
[17.745280] Preparing to correct graph with cutoff 0.200000
[17.747000] Cleaning memory
[17.747006] Deactivating local correction settings
[17.747016] Pebble done.
[17.747018] Starting pebble resolution...
[17.756661] Computing read to node mapping array sizes
[17.770105] Computing read to node mappings
[17.800608] Estimating library insert lengths...
[17.810755] Done
[17.810766] Computing direct node to node mappings
[17.820022] Scaffolding node 0
[17.829830]  === Nodes Scaffolded in 0.019061 s
[17.831995] Preparing to correct graph with cutoff 0.200000
[17.832092] Cleaning memory
[17.832095] Deactivating local correction settings
[17.832102] Pebble done.
[17.832104] Concatenation...
[17.832109] Renumbering nodes
[17.832110] Initial node count 71
[17.832114] Removed 11 null nodes
[17.832116] Concatenation over!
[17.832117] Removing reference contigs with coverage < 14.323414...
[17.832124] Concatenation...
[17.832126] Renumbering nodes
[17.832127] Initial node count 60
[17.832129] Removed 0 null nodes
[17.832130] Concatenation over!
[17.838996] Writing contigs into hsv.beforedigipe.65/contigs.fa...
[17.935267] Writing into stats file hsv.beforedigipe.65/stats.txt...
[17.937051] Writing into graph file hsv.beforedigipe.65/LastGraph...
[18.049513] Estimated Coverage = 28.646829
[18.049525] Estimated Coverage cutoff = 14.323414
Final graph has 60 nodes and n50 of 4484, max 12319, total 123743, using 186038/1172427 reads
Your inserted inputs on [SSPACE_Basic_v2.0_linux] at Wed Aug 27 02:10:20 2014:
Required inputs: 
	-l = library.txt
	-s = /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/draft_genome.fasta
	-b = sspace.tmp

Optional inputs:
	-x = 1
	-z = 0
	-k = 5
	-a = 0.7
	-n = 15
	-T = 1
	-p = 0

Contig extension inputs:
	-o = 20
	-t = 0
	-m = 32
	-r = 0.9


=>Wed Aug 27 02:10:20 2014: Reading, filtering and converting input sequences of library file initiated

Reading read-pairs Lib1.1 @ 0       
Reading read-pairs Lib1.1 @ 1000000         
Reading read-pairs Lib1.1 @ 2000000         
Reading read-pairs Lib1.1 @ 3000000         
Reading read-pairs Lib1.1 @ 4000000         
Reading read-pairs Lib1.1 @ 5000000         
Reading read-pairs Lib1.1 @ 6000000         
Reading read-pairs Lib1.1 @ 7000000         
Reading read-pairs Lib1.1 @ 8000000         
Reading read-pairs Lib1.1 @ 9000000         
Reading read-pairs Lib1.1 @ 10000000         
Reading read-pairs Lib1.1 @ 11000000         
Reading read-pairs Lib1.1 @ 12000000         
Reading read-pairs Lib1.1 @ 13000000         
Reading read-pairs Lib1.1 @ 14000000         
Reading read-pairs Lib1.1 @ 15000000         
Reading read-pairs Lib1.1 @ 16000000         

                                        
------------------------------------------------------------

=>Wed Aug 27 02:13:12 2014: Building Bowtie index for contigs

=>Wed Aug 27 02:13:13 2014: Mapping reads to Bowtie index

100000
200000
300000
400000
500000
600000
700000
800000
900000
1000000
1100000
1200000
1300000
1400000
1500000
1600000
1700000
1800000
1900000
2000000
2100000
2200000
2300000
2400000
2500000
2600000
2700000
2800000
2900000
3000000
3100000
3200000
3300000
3400000
3500000
3600000
3700000
3800000
3900000
4000000
4100000
4200000
4300000
4400000
4500000
4600000
4700000
4800000
4900000
5000000
5100000
5200000
5300000
5400000
5500000
5600000
5700000
5800000
5900000
       
=>Wed Aug 27 02:34:45 2014: Contig extension initiated

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
                
LIBRARY Lib1
------------------------------------------------------------

=>Wed Aug 27 02:34:48 2014: Reading contig file

                
=>Wed Aug 27 02:34:48 2014: Building Bowtie index for contigs

=>Wed Aug 27 02:34:48 2014: Mapping reads to contigs. Reading bowtie output and pairing contigs

1000000
                
=>Wed Aug 27 02:37:52 2014: Building scaffolds file

1
2
3
4
5
6
7
8
                
=>Wed Aug 27 02:37:52 2014: Merging contigs and creating fasta file of scaffolds

                
------------------------------------------------------------

=>Wed Aug 27 02:37:52 2014: Creating summary file
**************************************************

Process run succesfully on Wed Aug 27 02:37:52 2014 in 27 minutes and 32 seconds


/mnt/src/quast-2.2/quast.py -R /mnt/galaxy/galaxy-dist/database/files/000/dataset_35.dat -o /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files sspace.fasta

Version 2.2, build 31.07.2013 02:04


System information:
  OS: Linux-3.2.0-40-virtual-x86_64-with-Ubuntu-12.04-precise
  Python version: 2.7.3
  CPUs number: 1

Started: 2014-08-27 02:37:53

Logging to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/quast.log

NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

Reference:
  /mnt/galaxy/galaxy-dist/database/files/000/dataset_35.dat ==> dataset_35

Contigs:
  sspace.fasta ==> sspace

2014-08-27 02:37:54
Running Basic statistics processor...
  Reference genome:
    dataset_35.dat, Reference length = 136376, Reference GC % = 67.53
  Contig files: 
    sspace
  Calculating N50 and L50...
    sspace, N50 = 71400, L50 = 1, Total length = 133500, GC % = 67.22, # N's per 100 kbp =  114.61
  Drawing cumulative plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/basic_stats/GC_content_plot.pdf
  Drawing Nx plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/basic_stats/NGx_plot.pdf
Done.

2014-08-27 02:37:55
Running Contig analyzer...
  sspace
  Logging to files /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/contigs_reports/contigs_report_sspace.stdout and contigs_report_sspace.stderr...
  Running Nucmer... 
/mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/contigs_reports/alignments_sspace.tsv
  Analysis is finished.
  Creating total report...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Creating total report...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
Done.

2014-08-27 02:37:56
Running NA-NGA calculation...
  Calculating NA50 and NGA50...
    sspace, Largest alignment = 71313, NA50 = 71313, NGA50 = 71313, LA50 = 1, LGA50 = 1
  Drawing cumulative plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/aligned_stats/NGAx_plot.pdf
  Done.

2014-08-27 02:37:57
Running Genome analyzer...
  NOTICE: Annotated genes file was not provided. Use -G option to specify it.
  NOTICE: Annotated operons file was not provided. Use -O option to specify it.
  sspace
  Drawing Genome fraction, % histogram...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/genome_stats/genome_fraction_histogram.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it.

2014-08-27 02:37:57
Summarizing...
  Creating total report...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/report.txt, report.tsv, and report.tex
  Transposed version of total report...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/report.html
  All pdf files are merged to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/plots.pdf
Log saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/dataset_1089_files/quast.log

Finished: 2014-08-27 02:37:57
Elapsed time: 0:00:04.062887
debuggroup summary 0.16s welcome to circos v0.64 2 May 2013
debuggroup summary 0.16s loading configuration from file comparison_circos.conf
debuggroup summary 0.16s found conf file comparison_circos.conf
debuggroup summary 0.52s debug will appear for these features: summary
debuggroup summary 0.52s parsing karyotype and organizing ideograms
debuggroup summary 0.53s applying global and local scaling
debuggroup summary 0.59s allocating image, colors and brushes
debuggroup summary 2.36s drawing highlights and ideograms
debuggroup summary 2.90s found conf file /mnt/src/circos-0.64/bin/../etc/tracks/link.conf
debuggroup summary 2.91s reading data and processing link id track_0 track from /mnt/galaxy/galaxy-dist/database/job_working_directory/000/491/comparison_circos_links.txt
debuggroup summary 2.93s drawing links track_0 z 0
debuggroup summary,output 3.01s generating output
debuggroup summary,output 3.01s created SVG image ./comparison_circos.svg (108 kb)
Trimming /mnt/galaxy/galaxy-dist/database/files/000/dataset_184.dat ...
Trimming /mnt/galaxy/galaxy-dist/database/files/000/dataset_185.dat ...
Merging left.fastq and right.fastq ...