holtgrew@sequoia /group/agabi/read_correction/data/dmelanogaster/SRR049254/fiona/SRR049254.fasta.d
15:01:20 SRR049254.fasta.d $ head -1000 step1.{cmd,stderr,stdout}
==> step1.cmd <==
command line: /group/agabi/read_correction/bin/fiona -id 1 -e 0.01 -or 1 -g 139731881 -i 1000 -os 0.5 -l 22 29 /group/agabi/read_correction/data/dmelanogaster/SRR049254/original/SRR049254.fasta /group/agabi/read_correction/data/dmelanogaster/SRR049254/fiona/SRR049254.fasta

==> step1.stderr <==
(pos:1)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 830.621 --1.90094e-11)
(pos:2)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 830.621 --1.90094e-11)
(pos:3)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 826.461 --1.88797e-11)
(pos:4)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 822.087 --1.87145e-11)
(pos:5)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 817.54 --1.85385e-11)
(pos:6)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 812.819 --1.83583e-11)
(pos:7)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 807.925 --1.81756e-11)
(pos:8)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 802.858 --1.79908e-11)
(pos:9)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 797.617 --1.78041e-11)
(pos:10)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 792.203 --1.76154e-11)
(pos:11)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 786.616 --1.74248e-11)
(pos:12)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 780.855 --1.72324e-11)
(pos:13)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 774.921 --1.7038e-11)
(pos:14)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 768.814 --1.68417e-11)
(pos:15)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 762.533 --1.66436e-11)
(pos:16)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 756.079 --1.64435e-11)
(pos:17)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 749.451 --1.62415e-11)
(pos:18)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 742.65 --1.60376e-11)
(pos:19)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 735.676 --1.58318e-11)
(pos:20)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 728.529 --1.56241e-11)
(pos:21)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 721.208 --1.54145e-11)
(pos:22)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 713.714 --1.5203e-11)
(pos:23)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 723.421 --1.53096e-11)
(pos:24)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 732.782 --1.54124e-11)
(pos:25)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 741.796 --1.55114e-11)
(pos:26)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 750.463 --1.56066e-11)
(pos:27)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 758.784 --1.5698e-11)
(pos:28)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 766.758 --1.57856e-11)
(pos:29)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 774.385 --1.58694e-11)
(pos:30)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 781.666 --1.59493e-11)
(pos:31)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 788.6 --1.60255e-11)
(pos:32)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 795.187 --1.60978e-11)
(pos:33)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 801.427 --1.61664e-11)
(pos:34)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 807.321 --1.62311e-11)
(pos:35)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 812.868 --1.6292e-11)
(pos:36)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 818.069 --1.63492e-11)
(pos:37)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 822.923 --1.64025e-11)
(pos:38)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 827.43 --1.6452e-11)
(pos:39)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 831.59 --1.64977e-11)
(pos:40)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 835.404 --1.65396e-11)
(pos:41)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 838.871 --1.65776e-11)
(pos:42)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 841.991 --1.66119e-11)
(pos:43)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 844.764 --1.66424e-11)
(pos:44)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 847.191 --1.6669e-11)
(pos:45)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 849.271 --1.66919e-11)
(pos:46)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 851.005 --1.67109e-11)
(pos:47)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 852.392 --1.67261e-11)
(pos:48)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 853.432 --1.67376e-11)
(pos:49)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 854.125 --1.67452e-11)
(pos:50)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 854.472 --1.6749e-11)
(pos:51)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 854.472 --1.6749e-11)
(pos:52)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 854.125 --1.67452e-11)
(pos:53)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 853.432 --1.67376e-11)
(pos:54)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 852.392 --1.67261e-11)
(pos:55)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 851.005 --1.67109e-11)
(pos:56)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 849.271 --1.66919e-11)
(pos:57)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 847.191 --1.6669e-11)
(pos:58)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 844.764 --1.66424e-11)
(pos:59)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 841.991 --1.66119e-11)
(pos:60)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 838.871 --1.65776e-11)
(pos:61)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 835.404 --1.65396e-11)
(pos:62)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 831.59 --1.64977e-11)
(pos:63)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 827.43 --1.6452e-11)
(pos:64)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 822.923 --1.64025e-11)
(pos:65)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 818.069 --1.63492e-11)
(pos:66)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 812.868 --1.6292e-11)
(pos:67)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 807.321 --1.62311e-11)
(pos:68)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 801.427 --1.61664e-11)
(pos:69)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 795.187 --1.60978e-11)
(pos:70)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 788.6 --1.60255e-11)
(pos:71)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 781.666 --1.59493e-11)
(pos:72)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 774.385 --1.58694e-11)
(pos:73)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 766.758 --1.57856e-11)
(pos:74)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 758.784 --1.5698e-11)
(pos:75)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 750.463 --1.56066e-11)
(pos:76)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 741.796 --1.55114e-11)
(pos:77)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 732.782 --1.54124e-11)
(pos:78)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 723.421 --1.53096e-11)
(pos:79)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 713.714 --1.5203e-11)
(pos:80)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 721.208 --1.54145e-11)
(pos:81)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 728.529 --1.56241e-11)
(pos:82)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 735.676 --1.58318e-11)
(pos:83)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 742.65 --1.60376e-11)
(pos:84)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 749.451 --1.62415e-11)
(pos:85)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 756.079 --1.64435e-11)
(pos:86)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 762.533 --1.66436e-11)
(pos:87)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 768.814 --1.68417e-11)
(pos:88)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 774.921 --1.7038e-11)
(pos:89)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 780.855 --1.72324e-11)
(pos:90)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 786.616 --1.74248e-11)
(pos:91)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 792.203 --1.76154e-11)
(pos:92)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 797.617 --1.78041e-11)
(pos:93)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 802.858 --1.79908e-11)
(pos:94)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 807.925 --1.81756e-11)
(pos:95)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 812.819 --1.83583e-11)
(pos:96)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 817.54 --1.85385e-11)
(pos:97)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 822.087 --1.87145e-11)
(pos:98)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 826.461 --1.88797e-11)
(pos:99)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 830.621 --1.90094e-11)
(pos:100)(rl:100-22) -- lambda - OvSum noerror/errors: (0.220634 , 830.621 --1.90094e-11)

==> step1.stdout <==
Genome length:139731881
Loaded 30829636 reads.
number iters: 1000

Cycle 1
Length of the reads:100
 run the multiple-Correction-per-Round Fiona method

Log-odds method assuming a Poisson coverage distribution
Error rate provided: 0.01
Expected number of erroneous reads (percent): 1.9545e+07 (63)
Odds of erroneous/correct reads: 1.732
Expected coverage of k-mers before sequencing (k, coverage):
(22 , 17.4301)  (23 , 17.2095)  (24 , 16.9888)  (25 , 16.7682)  (26 , 16.5476)  (27 , 16.3269)  (28 , 16.1063)  (29 , 15.8857)
Computed cutoffs for errors (level, cutoff):
(22 , 4)  (23 , 4)  (24 , 4)  (25 , 4)  (26 , 4)  (27 , 4)  (28 , 4)  (29 , 3)
Computed cutoffs for repeats (level, cutoff):
(22 , 145)  (23 , 146)  (24 , 147)  (25 , 147)  (26 , 148)  (27 , 149)  (28 , 149)  (29 , 150)

Computed cutoffs for nb overlap bp (pos, cutoff)
(1 , 416)  (2 , 416)  (3 , 414)  (4 , 412)  (5 , 409)  (6 , 407)  (7 , 404)  (8 , 402)  (9 , 399)  (10 , 397)  (11 , 394)  (12 , 391)  (13 , 388)  (14 , 385)  (15 , 382)  (16 , 379)  (17 , 375)  (18 , 372)  (19 , 368)  (20 , 365)  (21 , 361)  (22 , 357)  (23 , 362)  (24 , 367)  (25 , 371)  (26 , 376)  (27 , 380)  (28 , 384)  (29 , 388)  (30 , 391)  (31 , 395)  (32 , 398)  (33 , 401)  (34 , 404)  (35 , 407)  (36 , 410)  (37 , 412)  (38 , 414)  (39 , 416)  (40 , 418)  (41 , 420)  (42 , 421)  (43 , 423)  (44 , 424)  (45 , 425)  (46 , 426)  (47 , 427)  (48 , 427)  (49 , 428)  (50 , 428)  (51 , 428)  (52 , 428)  (53 , 427)  (54 , 427)  (55 , 426)  (56 , 425)  (57 , 424)  (58 , 423)  (59 , 421)  (60 , 420)  (61 , 418)  (62 , 416)  (63 , 414)  (64 , 412)  (65 , 410)  (66 , 407)  (67 , 404)  (68 , 401)  (69 , 398)  (70 , 395)  (71 , 391)  (72 , 388)  (73 , 384)  (74 , 380)  (75 , 376)  (76 , 371)  (77 , 367)  (78 , 362)  (79 , 357)  (80 , 361)  (81 , 365)  (82 , 368)  (83 , 372)  (84 , 375)  (85 , 379)  (86 , 382)  (87 , 385)  (88 , 388)  (89 , 391)  (90 , 394)  (91 , 397)  (92 , 399)  (93 , 402)  (94 , 404)  (95 , 407)  (96 , 409)  (97 , 412)  (98 , 414)  (99 , 416)  (100 , 416)
Searching...
Construct external q-gram index ... done. (1014.49 seconds)
Suffix tree traversal ............. holtgrew@sequoia /group/agabi/read_correction/data/dmelanogaster/SRR049254/fiona/SRR049254.fasta.d
15:01:22 SRR049254.fasta.d $