#Trim adapters java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ jgi.BBDuk -Xmx200g in=./input/CPB_metaDNA_1.fq in2=./input/CPB_metaDNA_2.fq out=./input/trimmed.fq ktrim=r k=23 mink=11 hdist=1 ref=/DATA/markop/bbmap/resources/adapters.fa tbo tpe maxns=0 trimq=20 qtrim=r maq=12 Executing jgi.BBDuk [-Xmx200g, in=./input/CPB_metaDNA_1.fq, in2=./input/CPB_metaDNA_2.fq, out=./input/trimmed.fq, ktrim=r, k=23, mink=11, hdist=1, ref=/DATA/markop/bbmap/resources/adapters.fa, tbo, tpe, maxns=0, trimq=20, qtrim=r, maq=12] Version 38.34 maskMiddle was disabled because useShortKmers=true 0.039 seconds. Initial: Memory: max=205800m, total=205800m, free=199358m, used=6442m Added 217045 kmers; time: 0.173 seconds. Memory: max=205800m, total=205800m, free=189694m, used=16106m Input is being processed as paired Started output streams: 0.022 seconds. Processing time: 11019.532 seconds. Input: 1417626672 reads 212644000800 bases. QTrimmed: 285623965 reads (20.15%) 8726094678 bases (4.10%) KTrimmed: 5754012 reads (0.41%) 176493446 bases (0.08%) Trimmed by overlap: 5463244 reads (0.39%) 147213420 bases (0.07%) Low quality discards: 20783600 reads (1.47%) 2786949082 bases (1.31%) Total Removed: 21978952 reads (1.55%) 11836750626 bases (5.57%) Result: 1395647720 reads (98.45%) 200807250174 bases (94.43%) Time: 11019.734 seconds. Reads Processed: 1417m 128.64k reads/sec Bases Processed: 212644m 19.30m bases/sec #Remove small contaminants java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBDuk -Xmx230g in=./input/trimmed.fq out=./input/filtered.fq k=31 ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa.gz,/DATA/markop/bbmap/resources/phix174_ill.ref.fa.gz Executing jgi.BBDuk [-Xmx230g, in=./input/trimmed.fq, out=./input/filtered.fq, k=31, ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa.gz,/DATA/markop/bbmap/resources/phix174_ill.ref.fa.gz] Version 38.34 0.043 seconds. Initial: Memory: max=236670m, total=236670m, free=228027m, used=8643m Added 92358 kmers; time: 0.185 seconds. Memory: max=236670m, total=236670m, free=215679m, used=20991m Input is being processed as paired Started output streams: 2.106 seconds. Processing time: 7304.720 seconds. Input: 1395647720 reads 200807250174 bases. Contaminants: 24 reads (0.00%) 3411 bases (0.00%) Total Removed: 24 reads (0.00%) 3411 bases (0.00%) Result: 1395647696 reads (100.00%) 200807246763 bases (100.00%) Time: 7307.017 seconds. Reads Processed: 1395m 191.00k reads/sec Bases Processed: 200807m 27.48m bases/sec #Error-correct 1 java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx230g in=./input/filtered.fq out=./input/ecco.fq ecco mix vstrict adapters=default Executing jgi.BBMerge [-Xmx230g, in=./input/filtered.fq, out=./input/ecco.fq, ecco, mix, vstrict, adapters=default] Version 38.34 Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in=./input/filtered.fq, out=./input/ecco.fq, ecco, mix, adapters=default] Writing mergable reads interleaved. Started output threads. Total time: 6970.063 seconds. Pairs: 697823848 Joined: 296974753 42.557% Ambiguous: 400595402 57.406% No Solution: 253693 0.036% Too Short: 0 0.000% Adapters Expected: 340027 0.024% Adapters Found: 43619 0.003% Errors Corrected: 8917295 Avg Insert: 240.2 Standard Deviation: 33.8 Mode: 270 Insert range: 35 - 289 90th percentile: 278 75th percentile: 266 50th percentile: 247 25th percentile: 221 10th percentile: 193 #Error-correct 2 java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ clump.Clumpify -Xmx200g in=./input/ecco.fq out=./input/eccc.fq ecc passes=6 minid=0.98 Executing clump.Clumpify [-Xmx200g, in=./input/ecco.fq, out=./input/eccc.fq, ecc, passes=6, minid=0.98] Version 38.34 Read Estimate: 1420540931 Memory Estimate: 900693 MB Memory Available: 160900 MB Set groups to 53 Executing clump.KmerSplit [in1=./input/ecco.fq, in2=, out=./input/eccc_clumpify_p1_temp%_4225c8f7a705d721.fq, out2=, groups=53, ecco=false, addname=f, shortname=f, unpair=false, repair=f, namesort=f, ow=true, ecc, passes=6] Input is being processed as paired Writing interleaved. Made a comparator with k=31, seed=1, border=1, hashes=4 Time: 6973.994 seconds. Reads Processed: 1395m 200.12k reads/sec Bases Processed: 200804m 28.79m bases/sec Executing clump.KmerSort3 [in1=./input/eccc_clumpify_p1_temp%_4225c8f7a705d721.fq, in2=, out=./input/eccc_clumpify_p2_temp%_4489df825fe74c2b.fq, out2=, groups=53, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6] Making comparator. Made a comparator with k=31, seed=1, border=1, hashes=4 Making 2 fetch threads. Starting threads. Fetching reads. Fetched 13074449 reads: 117.360 seconds. Making clumps. Clump time: 0.938 seconds. Correcting. Correct time: 13.536 seconds. Seed: 1 Reads: 13074449 Clumps: 874077 Corrections: 363666 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.383 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13127872 reads: 0.001 seconds. Making clumps. Clump time: 2.135 seconds. Correcting. Correct time: 91.165 seconds. Seed: 1 Reads: 13127872 Clumps: 871410 Corrections: 366609 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.274 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12831013 reads: 143.726 seconds. Making clumps. Clump time: 0.448 seconds. Correcting. Correct time: 16.870 seconds. Seed: 1 Reads: 12831013 Clumps: 873106 Corrections: 352506 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.139 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13321910 reads: 0.000 seconds. Making clumps. Clump time: 0.932 seconds. Correcting. Correct time: 42.532 seconds. Seed: 1 Reads: 13321910 Clumps: 873154 Corrections: 367849 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.072 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13215902 reads: 183.136 seconds. Making clumps. Clump time: 0.567 seconds. Correcting. Correct time: 31.856 seconds. Seed: 1 Reads: 13215902 Clumps: 872499 Corrections: 363006 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.187 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13332294 reads: 0.000 seconds. Making clumps. Clump time: 1.797 seconds. Correcting. Correct time: 64.040 seconds. Seed: 1 Reads: 13332294 Clumps: 872250 Corrections: 372335 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 1.959 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13180646 reads: 144.382 seconds. Making clumps. Clump time: 0.633 seconds. Correcting. Correct time: 17.670 seconds. Seed: 1 Reads: 13180646 Clumps: 871568 Corrections: 366508 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.315 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13173816 reads: 22.039 seconds. Making clumps. Clump time: 0.616 seconds. Correcting. Correct time: 29.758 seconds. Seed: 1 Reads: 13173816 Clumps: 872175 Corrections: 365429 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.025 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12819734 reads: 188.159 seconds. Making clumps. Clump time: 0.551 seconds. Correcting. Correct time: 11.913 seconds. Seed: 1 Reads: 12819734 Clumps: 871387 Corrections: 354249 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.269 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12996262 reads: 7.040 seconds. Making clumps. Clump time: 0.603 seconds. Correcting. Correct time: 12.161 seconds. Seed: 1 Reads: 12996262 Clumps: 872720 Corrections: 355018 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 1.984 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13074210 reads: 215.956 seconds. Making clumps. Clump time: 6.021 seconds. Correcting. Correct time: 92.846 seconds. Seed: 1 Reads: 13074210 Clumps: 872366 Corrections: 356568 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 1.976 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13473729 reads: 0.001 seconds. Making clumps. Clump time: 0.793 seconds. Correcting. Correct time: 22.397 seconds. Seed: 1 Reads: 13473729 Clumps: 872680 Corrections: 370920 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.076 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12847704 reads: 0.000 seconds. Making clumps. Clump time: 1.438 seconds. Correcting. Correct time: 11.526 seconds. Seed: 1 Reads: 12847704 Clumps: 874670 Corrections: 351810 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 3.824 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13218468 reads: 279.650 seconds. Making clumps. Clump time: 0.636 seconds. Correcting. Correct time: 15.281 seconds. Seed: 1 Reads: 13218468 Clumps: 872647 Corrections: 367029 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.255 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13054642 reads: 0.000 seconds. Making clumps. Clump time: 1.757 seconds. Correcting. Correct time: 10.970 seconds. Seed: 1 Reads: 13054642 Clumps: 872152 Corrections: 364410 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.196 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13408459 reads: 221.766 seconds. Making clumps. Clump time: 0.562 seconds. Correcting. Correct time: 45.977 seconds. Seed: 1 Reads: 13408459 Clumps: 871610 Corrections: 371236 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 3.394 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13134833 reads: 0.000 seconds. Making clumps. Clump time: 1.451 seconds. Correcting. Correct time: 11.974 seconds. Seed: 1 Reads: 13134833 Clumps: 873500 Corrections: 363999 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.064 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13015577 reads: 185.143 seconds. Making clumps. Clump time: 0.579 seconds. Correcting. Correct time: 13.361 seconds. Seed: 1 Reads: 13015577 Clumps: 872827 Corrections: 358110 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.135 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13266146 reads: 108.113 seconds. Making clumps. Clump time: 0.588 seconds. Correcting. Correct time: 14.232 seconds. Seed: 1 Reads: 13266146 Clumps: 872962 Corrections: 369956 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.193 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13272334 reads: 119.133 seconds. Making clumps. Clump time: 0.568 seconds. Correcting. Correct time: 11.822 seconds. Seed: 1 Reads: 13272334 Clumps: 873325 Corrections: 372376 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.380 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12962433 reads: 118.306 seconds. Making clumps. Clump time: 0.567 seconds. Correcting. Correct time: 29.250 seconds. Seed: 1 Reads: 12962433 Clumps: 872820 Corrections: 354998 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.116 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13231205 reads: 116.887 seconds. Making clumps. Clump time: 0.551 seconds. Correcting. Correct time: 11.606 seconds. Seed: 1 Reads: 13231205 Clumps: 871768 Corrections: 368033 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.193 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13242671 reads: 112.698 seconds. Making clumps. Clump time: 5.891 seconds. Correcting. Correct time: 22.101 seconds. Seed: 1 Reads: 13242671 Clumps: 872311 Corrections: 367470 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.272 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13210136 reads: 113.027 seconds. Making clumps. Clump time: 0.540 seconds. Correcting. Correct time: 56.250 seconds. Seed: 1 Reads: 13210136 Clumps: 872791 Corrections: 367120 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.882 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13474267 reads: 5.923 seconds. Making clumps. Clump time: 0.556 seconds. Correcting. Correct time: 72.793 seconds. Seed: 1 Reads: 13474267 Clumps: 871389 Corrections: 374932 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.279 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13088427 reads: 127.673 seconds. Making clumps. Clump time: 0.584 seconds. Correcting. Correct time: 29.267 seconds. Seed: 1 Reads: 13088427 Clumps: 872851 Corrections: 359280 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.266 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13321573 reads: 98.849 seconds. Making clumps. Clump time: 0.534 seconds. Correcting. Correct time: 23.236 seconds. Seed: 1 Reads: 13321573 Clumps: 870378 Corrections: 368426 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 6.341 seconds. Writing. Sent writable reads. Fetching reads. Fetched 14152233 reads: 125.644 seconds. Making clumps. Clump time: 0.640 seconds. Correcting. Correct time: 310.142 seconds. Seed: 1 Reads: 14152233 Clumps: 873407 Corrections: 387156 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.118 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13495583 reads: 0.001 seconds. Making clumps. Clump time: 1.651 seconds. Correcting. Correct time: 18.807 seconds. Seed: 1 Reads: 13495583 Clumps: 872495 Corrections: 368704 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.021 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13098767 reads: 0.000 seconds. Making clumps. Clump time: 1.655 seconds. Correcting. Correct time: 10.544 seconds. Seed: 1 Reads: 13098767 Clumps: 873366 Corrections: 365154 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.227 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13127909 reads: 299.256 seconds. Making clumps. Clump time: 0.555 seconds. Correcting. Correct time: 31.995 seconds. Seed: 1 Reads: 13127909 Clumps: 873436 Corrections: 358353 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.104 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13120522 reads: 0.001 seconds. Making clumps. Clump time: 1.030 seconds. Correcting. Correct time: 12.848 seconds. Seed: 1 Reads: 13120522 Clumps: 872856 Corrections: 363307 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 1.954 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13244396 reads: 214.848 seconds. Making clumps. Clump time: 0.580 seconds. Correcting. Correct time: 17.714 seconds. Seed: 1 Reads: 13244396 Clumps: 872349 Corrections: 369535 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.277 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13639823 reads: 88.118 seconds. Making clumps. Clump time: 1.070 seconds. Correcting. Correct time: 1419.051 seconds. Seed: 1 Reads: 13639823 Clumps: 874167 Corrections: 384407 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.079 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12770801 reads: 0.001 seconds. Making clumps. Clump time: 2.414 seconds. Correcting. Correct time: 19.128 seconds. Seed: 1 Reads: 12770801 Clumps: 872381 Corrections: 349291 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.077 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13193319 reads: 0.001 seconds. Making clumps. Clump time: 0.879 seconds. Correcting. Correct time: 28.352 seconds. Seed: 1 Reads: 13193319 Clumps: 873457 Corrections: 367221 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.180 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13350203 reads: 270.010 seconds. Making clumps. Clump time: 0.613 seconds. Correcting. Correct time: 541.053 seconds. Seed: 1 Reads: 13350203 Clumps: 872666 Corrections: 372564 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.129 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12752791 reads: 0.001 seconds. Making clumps. Clump time: 1.795 seconds. Correcting. Correct time: 10.335 seconds. Seed: 1 Reads: 12752791 Clumps: 873559 Corrections: 350692 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 1.995 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13014569 reads: 0.000 seconds. Making clumps. Clump time: 1.268 seconds. Correcting. Correct time: 11.581 seconds. Seed: 1 Reads: 13014569 Clumps: 873914 Corrections: 359607 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.078 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13275012 reads: 322.779 seconds. Making clumps. Clump time: 0.698 seconds. Correcting. Correct time: 37.012 seconds. Seed: 1 Reads: 13275012 Clumps: 871427 Corrections: 369615 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.202 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13263268 reads: 0.000 seconds. Making clumps. Clump time: 1.403 seconds. Correcting. Correct time: 32.647 seconds. Seed: 1 Reads: 13263268 Clumps: 872286 Corrections: 371325 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.081 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12803933 reads: 139.073 seconds. Making clumps. Clump time: 0.555 seconds. Correcting. Correct time: 13.592 seconds. Seed: 1 Reads: 12803933 Clumps: 871302 Corrections: 351041 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.143 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13111460 reads: 146.704 seconds. Making clumps. Clump time: 0.551 seconds. Correcting. Correct time: 19.233 seconds. Seed: 1 Reads: 13111460 Clumps: 871033 Corrections: 362742 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.773 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12898159 reads: 6.230 seconds. Making clumps. Clump time: 0.563 seconds. Correcting. Correct time: 43.613 seconds. Seed: 1 Reads: 12898159 Clumps: 873161 Corrections: 356833 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.008 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13412934 reads: 198.793 seconds. Making clumps. Clump time: 0.548 seconds. Correcting. Correct time: 50.315 seconds. Seed: 1 Reads: 13412934 Clumps: 874063 Corrections: 368896 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.036 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12871213 reads: 0.000 seconds. Making clumps. Clump time: 1.111 seconds. Correcting. Correct time: 17.806 seconds. Seed: 1 Reads: 12871213 Clumps: 871313 Corrections: 353002 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 1.992 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12977332 reads: 195.252 seconds. Making clumps. Clump time: 0.569 seconds. Correcting. Correct time: 12.172 seconds. Seed: 1 Reads: 12977332 Clumps: 873275 Corrections: 356040 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.160 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12914071 reads: 106.824 seconds. Making clumps. Clump time: 0.572 seconds. Correcting. Correct time: 10.919 seconds. Seed: 1 Reads: 12914071 Clumps: 872906 Corrections: 357173 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.038 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13247862 reads: 143.739 seconds. Making clumps. Clump time: 0.538 seconds. Correcting. Correct time: 9.354 seconds. Seed: 1 Reads: 13247862 Clumps: 872640 Corrections: 368757 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.142 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13440704 reads: 106.527 seconds. Making clumps. Clump time: 0.619 seconds. Correcting. Correct time: 11.652 seconds. Seed: 1 Reads: 13440704 Clumps: 874379 Corrections: 377555 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.256 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13202319 reads: 148.459 seconds. Making clumps. Clump time: 0.606 seconds. Correcting. Correct time: 16.628 seconds. Seed: 1 Reads: 13202319 Clumps: 873362 Corrections: 364674 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.181 seconds. Writing. Sent writable reads. Fetching reads. No more reads to fetch. Adding poison. Fetched 13121731 reads: 112.215 seconds. Making clumps. Clump time: 0.403 seconds. Correcting. Correct time: 7.937 seconds. Seed: 1 Reads: 13121731 Clumps: 872466 Corrections: 363047 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 2.229 seconds. Writing. Sent writable reads. Fetching reads. A fetch thread finished. Encountered poison; count=1 No more reads to fetch. Adding poison. Fetched 12952222 reads: 101.123 seconds. Making clumps. Clump time: 0.571 seconds. Correcting. Correct time: 13.229 seconds. Seed: 1 Reads: 12952222 Clumps: 871789 Corrections: 358142 Made a comparator with k=31, seed=2, border=0, hashes=4 Splitting. Split time: 1.900 seconds. Writing. Sent writable reads. Closing fetch threads. A fetch thread finished. Closed fetch threads. Waiting for writing to complete. Write time: 4.705 seconds. Time: 9278.802 seconds. Reads Processed: 1395m 150.41k reads/sec Bases Processed: 200804m 21.64m bases/sec Reads In: 1395647696 Clumps Formed: 46250848 Errors Corrected: 19308681 Executing clump.KmerSort3 [in1=./input/eccc_clumpify_p2_temp%_4489df825fe74c2b.fq, in2=, out=./input/eccc_clumpify_p3_temp%_1d5948f7662203ed.fq, out2=, groups=53, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6] Making comparator. Made a comparator with k=31, seed=2, border=0, hashes=4 Making 2 fetch threads. Starting threads. Fetching reads. Fetched 13084659 reads: 123.548 seconds. Making clumps. Clump time: 0.470 seconds. Correcting. Correct time: 20.700 seconds. Seed: 2 Reads: 13084659 Clumps: 804943 Corrections: 145876 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.129 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13117543 reads: 0.009 seconds. Making clumps. Clump time: 1.630 seconds. Correcting. Correct time: 16.077 seconds. Seed: 2 Reads: 13117543 Clumps: 807506 Corrections: 145152 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.877 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13070210 reads: 230.335 seconds. Making clumps. Clump time: 0.457 seconds. Correcting. Correct time: 14.593 seconds. Seed: 2 Reads: 13070210 Clumps: 806450 Corrections: 144606 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.108 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13226360 reads: 6.662 seconds. Making clumps. Clump time: 0.434 seconds. Correcting. Correct time: 56.792 seconds. Seed: 2 Reads: 13226360 Clumps: 806598 Corrections: 147822 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.980 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13039131 reads: 208.681 seconds. Making clumps. Clump time: 0.400 seconds. Correcting. Correct time: 17.452 seconds. Seed: 2 Reads: 13039131 Clumps: 805767 Corrections: 143870 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.975 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12949517 reads: 0.005 seconds. Making clumps. Clump time: 0.666 seconds. Correcting. Correct time: 11.822 seconds. Seed: 2 Reads: 12949517 Clumps: 803805 Corrections: 141639 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.898 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13131380 reads: 237.745 seconds. Making clumps. Clump time: 0.450 seconds. Correcting. Correct time: 18.142 seconds. Seed: 2 Reads: 13131380 Clumps: 805388 Corrections: 146726 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.174 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13342853 reads: 23.566 seconds. Making clumps. Clump time: 0.417 seconds. Correcting. Correct time: 30.070 seconds. Seed: 2 Reads: 13342853 Clumps: 806183 Corrections: 151296 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.110 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13103084 reads: 209.914 seconds. Making clumps. Clump time: 0.434 seconds. Correcting. Correct time: 53.870 seconds. Seed: 2 Reads: 13103084 Clumps: 805667 Corrections: 145490 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.132 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13241762 reads: 0.000 seconds. Making clumps. Clump time: 1.164 seconds. Correcting. Correct time: 26.898 seconds. Seed: 2 Reads: 13241762 Clumps: 806461 Corrections: 144946 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.027 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13530214 reads: 170.416 seconds. Making clumps. Clump time: 0.520 seconds. Correcting. Correct time: 82.991 seconds. Seed: 2 Reads: 13530214 Clumps: 806597 Corrections: 151333 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.192 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13071068 reads: 0.001 seconds. Making clumps. Clump time: 1.944 seconds. Correcting. Correct time: 14.973 seconds. Seed: 2 Reads: 13071068 Clumps: 804251 Corrections: 143892 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.915 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13251693 reads: 169.038 seconds. Making clumps. Clump time: 0.427 seconds. Correcting. Correct time: 14.108 seconds. Seed: 2 Reads: 13251693 Clumps: 806809 Corrections: 145388 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.179 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13462597 reads: 171.806 seconds. Making clumps. Clump time: 0.659 seconds. Correcting. Correct time: 117.010 seconds. Seed: 2 Reads: 13462597 Clumps: 805008 Corrections: 148382 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.926 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13201490 reads: 0.001 seconds. Making clumps. Clump time: 1.087 seconds. Correcting. Correct time: 14.840 seconds. Seed: 2 Reads: 13201490 Clumps: 805760 Corrections: 145295 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.091 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12892746 reads: 0.000 seconds. Making clumps. Clump time: 1.313 seconds. Correcting. Correct time: 6.454 seconds. Seed: 2 Reads: 12892746 Clumps: 805340 Corrections: 142583 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.015 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12655414 reads: 328.016 seconds. Making clumps. Clump time: 0.705 seconds. Correcting. Correct time: 17.079 seconds. Seed: 2 Reads: 12655414 Clumps: 805427 Corrections: 138783 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.981 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12920879 reads: 0.001 seconds. Making clumps. Clump time: 1.236 seconds. Correcting. Correct time: 21.042 seconds. Seed: 2 Reads: 12920879 Clumps: 805527 Corrections: 143517 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.963 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13269294 reads: 255.466 seconds. Making clumps. Clump time: 0.469 seconds. Correcting. Correct time: 30.065 seconds. Seed: 2 Reads: 13269294 Clumps: 805226 Corrections: 147466 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.561 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13139465 reads: 4.003 seconds. Making clumps. Clump time: 0.408 seconds. Correcting. Correct time: 14.058 seconds. Seed: 2 Reads: 13139465 Clumps: 806422 Corrections: 146413 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.958 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13113655 reads: 281.510 seconds. Making clumps. Clump time: 0.405 seconds. Correcting. Correct time: 20.728 seconds. Seed: 2 Reads: 13113655 Clumps: 806045 Corrections: 143753 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.130 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12918075 reads: 0.000 seconds. Making clumps. Clump time: 0.993 seconds. Correcting. Correct time: 15.658 seconds. Seed: 2 Reads: 12918075 Clumps: 807424 Corrections: 140455 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.916 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13509007 reads: 267.689 seconds. Making clumps. Clump time: 0.448 seconds. Correcting. Correct time: 58.579 seconds. Seed: 2 Reads: 13509007 Clumps: 806205 Corrections: 149085 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.059 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12902167 reads: 0.000 seconds. Making clumps. Clump time: 0.834 seconds. Correcting. Correct time: 16.739 seconds. Seed: 2 Reads: 12902167 Clumps: 805380 Corrections: 142574 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.014 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13438935 reads: 257.129 seconds. Making clumps. Clump time: 0.461 seconds. Correcting. Correct time: 38.669 seconds. Seed: 2 Reads: 13438935 Clumps: 806441 Corrections: 147793 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.223 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13117479 reads: 0.000 seconds. Making clumps. Clump time: 0.947 seconds. Correcting. Correct time: 93.425 seconds. Seed: 2 Reads: 13117479 Clumps: 806373 Corrections: 143111 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.141 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13089749 reads: 174.449 seconds. Making clumps. Clump time: 0.423 seconds. Correcting. Correct time: 92.356 seconds. Seed: 2 Reads: 13089749 Clumps: 806169 Corrections: 143310 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.138 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12965641 reads: 0.000 seconds. Making clumps. Clump time: 1.725 seconds. Correcting. Correct time: 13.060 seconds. Seed: 2 Reads: 12965641 Clumps: 806924 Corrections: 145491 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.921 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13332649 reads: 145.667 seconds. Making clumps. Clump time: 0.464 seconds. Correcting. Correct time: 30.976 seconds. Seed: 2 Reads: 13332649 Clumps: 806697 Corrections: 148545 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.033 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13049576 reads: 210.159 seconds. Making clumps. Clump time: 0.438 seconds. Correcting. Correct time: 20.246 seconds. Seed: 2 Reads: 13049576 Clumps: 805899 Corrections: 143897 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.052 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12706468 reads: 0.000 seconds. Making clumps. Clump time: 1.038 seconds. Correcting. Correct time: 53.456 seconds. Seed: 2 Reads: 12706468 Clumps: 805387 Corrections: 138236 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.987 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12867356 reads: 219.961 seconds. Making clumps. Clump time: 0.396 seconds. Correcting. Correct time: 26.567 seconds. Seed: 2 Reads: 12867356 Clumps: 805149 Corrections: 142662 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.221 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13231277 reads: 57.990 seconds. Making clumps. Clump time: 0.424 seconds. Correcting. Correct time: 11.480 seconds. Seed: 2 Reads: 13231277 Clumps: 804712 Corrections: 145131 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.010 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13329488 reads: 241.986 seconds. Making clumps. Clump time: 0.374 seconds. Correcting. Correct time: 114.944 seconds. Seed: 2 Reads: 13329488 Clumps: 806444 Corrections: 146974 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.062 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13224165 reads: 0.001 seconds. Making clumps. Clump time: 5.168 seconds. Correcting. Correct time: 12.695 seconds. Seed: 2 Reads: 13224165 Clumps: 805130 Corrections: 146697 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.115 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12863638 reads: 0.000 seconds. Making clumps. Clump time: 1.268 seconds. Correcting. Correct time: 13.800 seconds. Seed: 2 Reads: 12863638 Clumps: 806735 Corrections: 142006 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.959 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13098774 reads: 359.637 seconds. Making clumps. Clump time: 0.483 seconds. Correcting. Correct time: 28.835 seconds. Seed: 2 Reads: 13098774 Clumps: 804698 Corrections: 146166 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.575 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13769779 reads: 0.000 seconds. Making clumps. Clump time: 0.905 seconds. Correcting. Correct time: 45.737 seconds. Seed: 2 Reads: 13769779 Clumps: 805365 Corrections: 154073 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.173 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12765745 reads: 266.022 seconds. Making clumps. Clump time: 0.730 seconds. Correcting. Correct time: 12.706 seconds. Seed: 2 Reads: 12765745 Clumps: 805712 Corrections: 140289 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.079 seconds. Writing. Sent writable reads. Fetching reads. Fetched 14336198 reads: 0.000 seconds. Making clumps. Clump time: 1.418 seconds. Correcting. Correct time: 527.665 seconds. Seed: 2 Reads: 14336198 Clumps: 806641 Corrections: 160477 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.234 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13405589 reads: 0.000 seconds. Making clumps. Clump time: 2.392 seconds. Correcting. Correct time: 60.463 seconds. Seed: 2 Reads: 13405589 Clumps: 804903 Corrections: 149090 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.108 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13281617 reads: 0.000 seconds. Making clumps. Clump time: 0.420 seconds. Correcting. Correct time: 27.149 seconds. Seed: 2 Reads: 13281617 Clumps: 805264 Corrections: 146614 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.974 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12889768 reads: 313.149 seconds. Making clumps. Clump time: 0.390 seconds. Correcting. Correct time: 22.282 seconds. Seed: 2 Reads: 12889768 Clumps: 805994 Corrections: 141719 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.947 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13410386 reads: 0.034 seconds. Making clumps. Clump time: 1.261 seconds. Correcting. Correct time: 30.688 seconds. Seed: 2 Reads: 13410386 Clumps: 805871 Corrections: 150160 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.958 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13161771 reads: 258.324 seconds. Making clumps. Clump time: 6.197 seconds. Correcting. Correct time: 15.005 seconds. Seed: 2 Reads: 13161771 Clumps: 806811 Corrections: 144405 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.084 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13440721 reads: 50.912 seconds. Making clumps. Clump time: 0.464 seconds. Correcting. Correct time: 21.161 seconds. Seed: 2 Reads: 13440721 Clumps: 806716 Corrections: 148617 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.994 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13333164 reads: 231.685 seconds. Making clumps. Clump time: 0.436 seconds. Correcting. Correct time: 32.245 seconds. Seed: 2 Reads: 13333164 Clumps: 805984 Corrections: 147310 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.209 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12861725 reads: 0.000 seconds. Making clumps. Clump time: 1.233 seconds. Correcting. Correct time: 9.874 seconds. Seed: 2 Reads: 12861725 Clumps: 805369 Corrections: 142555 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.044 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13056235 reads: 263.032 seconds. Making clumps. Clump time: 0.491 seconds. Correcting. Correct time: 19.399 seconds. Seed: 2 Reads: 13056235 Clumps: 805838 Corrections: 142981 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.395 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13327943 reads: 123.898 seconds. Making clumps. Clump time: 0.465 seconds. Correcting. Correct time: 33.468 seconds. Seed: 2 Reads: 13327943 Clumps: 804881 Corrections: 147816 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.208 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13004891 reads: 149.688 seconds. Making clumps. Clump time: 0.448 seconds. Correcting. Correct time: 55.739 seconds. Seed: 2 Reads: 13004891 Clumps: 805836 Corrections: 143012 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.190 seconds. Writing. Sent writable reads. Fetching reads. No more reads to fetch. Adding poison. Fetched 13315147 reads: 55.732 seconds. Making clumps. Clump time: 0.425 seconds. Correcting. Correct time: 12.142 seconds. Seed: 2 Reads: 13315147 Clumps: 805350 Corrections: 146668 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 2.038 seconds. Writing. Sent writable reads. Fetching reads. A fetch thread finished. Encountered poison; count=1 No more reads to fetch. Adding poison. Fetched 13003711 reads: 175.990 seconds. Making clumps. Clump time: 0.442 seconds. Correcting. Correct time: 11.334 seconds. Seed: 2 Reads: 13003711 Clumps: 807910 Corrections: 143583 Made a comparator with k=31, seed=3, border=0, hashes=4 Splitting. Split time: 1.989 seconds. Writing. Sent writable reads. Closing fetch threads. A fetch thread finished. Closed fetch threads. Waiting for writing to complete. Write time: 6.397 seconds. Time: 8777.266 seconds. Reads Processed: 1395m 159.01k reads/sec Bases Processed: 200804m 22.88m bases/sec Reads In: 1395647696 Clumps Formed: 42711392 Errors Corrected: 27024411 Executing clump.KmerSort3 [in1=./input/eccc_clumpify_p3_temp%_1d5948f7662203ed.fq, in2=, out=./input/eccc_clumpify_p4_temp%_744d7777925266f1.fq, out2=, groups=53, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6] Making comparator. Made a comparator with k=31, seed=3, border=0, hashes=4 Making 2 fetch threads. Starting threads. Fetching reads. Fetched 13348629 reads: 160.262 seconds. Making clumps. Clump time: 0.514 seconds. Correcting. Correct time: 25.244 seconds. Seed: 3 Reads: 13348629 Clumps: 780124 Corrections: 67419 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.061 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13273032 reads: 0.000 seconds. Making clumps. Clump time: 0.897 seconds. Correcting. Correct time: 114.445 seconds. Seed: 3 Reads: 13273032 Clumps: 781665 Corrections: 66665 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.334 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13220308 reads: 187.367 seconds. Making clumps. Clump time: 0.441 seconds. Correcting. Correct time: 17.527 seconds. Seed: 3 Reads: 13220308 Clumps: 781159 Corrections: 66508 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.366 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13063882 reads: 122.724 seconds. Making clumps. Clump time: 0.452 seconds. Correcting. Correct time: 11.799 seconds. Seed: 3 Reads: 13063882 Clumps: 781133 Corrections: 64555 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.090 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12875903 reads: 193.206 seconds. Making clumps. Clump time: 0.451 seconds. Correcting. Correct time: 12.124 seconds. Seed: 3 Reads: 12875903 Clumps: 780520 Corrections: 63197 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.055 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13105873 reads: 140.655 seconds. Making clumps. Clump time: 0.473 seconds. Correcting. Correct time: 29.864 seconds. Seed: 3 Reads: 13105873 Clumps: 781008 Corrections: 65759 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.174 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13463502 reads: 177.564 seconds. Making clumps. Clump time: 0.417 seconds. Correcting. Correct time: 28.116 seconds. Seed: 3 Reads: 13463502 Clumps: 780955 Corrections: 67374 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.180 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12928087 reads: 126.252 seconds. Making clumps. Clump time: 0.431 seconds. Correcting. Correct time: 13.114 seconds. Seed: 3 Reads: 12928087 Clumps: 779864 Corrections: 64664 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.283 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12979716 reads: 200.748 seconds. Making clumps. Clump time: 0.427 seconds. Correcting. Correct time: 11.700 seconds. Seed: 3 Reads: 12979716 Clumps: 781204 Corrections: 63690 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.227 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13054192 reads: 138.253 seconds. Making clumps. Clump time: 0.452 seconds. Correcting. Correct time: 12.470 seconds. Seed: 3 Reads: 13054192 Clumps: 781552 Corrections: 64591 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.067 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13717512 reads: 200.615 seconds. Making clumps. Clump time: 0.572 seconds. Correcting. Correct time: 36.458 seconds. Seed: 3 Reads: 13717512 Clumps: 781042 Corrections: 69321 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.411 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13245925 reads: 66.355 seconds. Making clumps. Clump time: 0.423 seconds. Correcting. Correct time: 18.104 seconds. Seed: 3 Reads: 13245925 Clumps: 782587 Corrections: 65754 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.120 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13100671 reads: 246.707 seconds. Making clumps. Clump time: 0.467 seconds. Correcting. Correct time: 13.799 seconds. Seed: 3 Reads: 13100671 Clumps: 782811 Corrections: 65002 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.018 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13054050 reads: 125.486 seconds. Making clumps. Clump time: 0.421 seconds. Correcting. Correct time: 99.505 seconds. Seed: 3 Reads: 13054050 Clumps: 780490 Corrections: 64437 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.126 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12925309 reads: 134.053 seconds. Making clumps. Clump time: 0.445 seconds. Correcting. Correct time: 39.896 seconds. Seed: 3 Reads: 12925309 Clumps: 782860 Corrections: 64953 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 7.413 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13183077 reads: 0.000 seconds. Making clumps. Clump time: 1.549 seconds. Correcting. Correct time: 8.719 seconds. Seed: 3 Reads: 13183077 Clumps: 780871 Corrections: 65743 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 1.859 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13138350 reads: 314.144 seconds. Making clumps. Clump time: 0.378 seconds. Correcting. Correct time: 71.225 seconds. Seed: 3 Reads: 13138350 Clumps: 781299 Corrections: 64900 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.444 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12786418 reads: 0.003 seconds. Making clumps. Clump time: 1.682 seconds. Correcting. Correct time: 13.597 seconds. Seed: 3 Reads: 12786418 Clumps: 783258 Corrections: 64043 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 1.969 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13741901 reads: 234.174 seconds. Making clumps. Clump time: 0.395 seconds. Correcting. Correct time: 40.881 seconds. Seed: 3 Reads: 13741901 Clumps: 781363 Corrections: 69446 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.294 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13214915 reads: 195.901 seconds. Making clumps. Clump time: 0.413 seconds. Correcting. Correct time: 15.863 seconds. Seed: 3 Reads: 13214915 Clumps: 781733 Corrections: 65861 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.171 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13433050 reads: 145.166 seconds. Making clumps. Clump time: 0.434 seconds. Correcting. Correct time: 12.719 seconds. Seed: 3 Reads: 13433050 Clumps: 780973 Corrections: 67327 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.198 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12877334 reads: 206.381 seconds. Making clumps. Clump time: 0.434 seconds. Correcting. Correct time: 13.698 seconds. Seed: 3 Reads: 12877334 Clumps: 782450 Corrections: 64456 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.251 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13103182 reads: 153.657 seconds. Making clumps. Clump time: 0.457 seconds. Correcting. Correct time: 23.102 seconds. Seed: 3 Reads: 13103182 Clumps: 781290 Corrections: 65374 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.152 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12916003 reads: 182.122 seconds. Making clumps. Clump time: 0.440 seconds. Correcting. Correct time: 13.457 seconds. Seed: 3 Reads: 12916003 Clumps: 780903 Corrections: 65324 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.232 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13208466 reads: 170.536 seconds. Making clumps. Clump time: 0.403 seconds. Correcting. Correct time: 10.788 seconds. Seed: 3 Reads: 13208466 Clumps: 781954 Corrections: 65113 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.486 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13085617 reads: 205.145 seconds. Making clumps. Clump time: 0.399 seconds. Correcting. Correct time: 16.874 seconds. Seed: 3 Reads: 13085617 Clumps: 781666 Corrections: 65560 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.163 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13358762 reads: 159.009 seconds. Making clumps. Clump time: 0.435 seconds. Correcting. Correct time: 19.091 seconds. Seed: 3 Reads: 13358762 Clumps: 782566 Corrections: 65644 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.217 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12452885 reads: 187.256 seconds. Making clumps. Clump time: 0.457 seconds. Correcting. Correct time: 9.993 seconds. Seed: 3 Reads: 12452885 Clumps: 780201 Corrections: 62466 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.036 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13158489 reads: 130.599 seconds. Making clumps. Clump time: 0.450 seconds. Correcting. Correct time: 13.466 seconds. Seed: 3 Reads: 13158489 Clumps: 780559 Corrections: 65205 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.058 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13423810 reads: 156.223 seconds. Making clumps. Clump time: 0.446 seconds. Correcting. Correct time: 119.644 seconds. Seed: 3 Reads: 13423810 Clumps: 781324 Corrections: 69007 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.734 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13361028 reads: 0.000 seconds. Making clumps. Clump time: 1.908 seconds. Correcting. Correct time: 27.224 seconds. Seed: 3 Reads: 13361028 Clumps: 781334 Corrections: 67087 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 1.945 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13355097 reads: 0.000 seconds. Making clumps. Clump time: 1.352 seconds. Correcting. Correct time: 14.351 seconds. Seed: 3 Reads: 13355097 Clumps: 780032 Corrections: 66750 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.144 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13049200 reads: 299.236 seconds. Making clumps. Clump time: 0.467 seconds. Correcting. Correct time: 71.804 seconds. Seed: 3 Reads: 13049200 Clumps: 781369 Corrections: 65066 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.111 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13166344 reads: 0.000 seconds. Making clumps. Clump time: 1.982 seconds. Correcting. Correct time: 46.136 seconds. Seed: 3 Reads: 13166344 Clumps: 781913 Corrections: 65393 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 1.982 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12994806 reads: 13.019 seconds. Making clumps. Clump time: 0.419 seconds. Correcting. Correct time: 29.094 seconds. Seed: 3 Reads: 12994806 Clumps: 782121 Corrections: 65527 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.109 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13914073 reads: 255.323 seconds. Making clumps. Clump time: 0.602 seconds. Correcting. Correct time: 121.428 seconds. Seed: 3 Reads: 13914073 Clumps: 781138 Corrections: 72134 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.097 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12983724 reads: 0.001 seconds. Making clumps. Clump time: 2.008 seconds. Correcting. Correct time: 11.450 seconds. Seed: 3 Reads: 12983724 Clumps: 781077 Corrections: 65273 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.023 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13526268 reads: 0.000 seconds. Making clumps. Clump time: 1.390 seconds. Correcting. Correct time: 70.161 seconds. Seed: 3 Reads: 13526268 Clumps: 782014 Corrections: 69322 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.207 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13063098 reads: 261.468 seconds. Making clumps. Clump time: 0.420 seconds. Correcting. Correct time: 36.777 seconds. Seed: 3 Reads: 13063098 Clumps: 781171 Corrections: 65308 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.046 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13787481 reads: 0.000 seconds. Making clumps. Clump time: 0.881 seconds. Correcting. Correct time: 233.816 seconds. Seed: 3 Reads: 13787481 Clumps: 780906 Corrections: 69353 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.114 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12822929 reads: 0.000 seconds. Making clumps. Clump time: 1.110 seconds. Correcting. Correct time: 20.867 seconds. Seed: 3 Reads: 12822929 Clumps: 781633 Corrections: 63960 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.070 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12855398 reads: 0.000 seconds. Making clumps. Clump time: 0.821 seconds. Correcting. Correct time: 13.011 seconds. Seed: 3 Reads: 12855398 Clumps: 781689 Corrections: 63713 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 1.974 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13043052 reads: 316.206 seconds. Making clumps. Clump time: 0.432 seconds. Correcting. Correct time: 43.583 seconds. Seed: 3 Reads: 13043052 Clumps: 779099 Corrections: 65001 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.154 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13273686 reads: 0.000 seconds. Making clumps. Clump time: 0.607 seconds. Correcting. Correct time: 14.266 seconds. Seed: 3 Reads: 13273686 Clumps: 782031 Corrections: 66939 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.080 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13255166 reads: 246.484 seconds. Making clumps. Clump time: 0.524 seconds. Correcting. Correct time: 22.431 seconds. Seed: 3 Reads: 13255166 Clumps: 780875 Corrections: 66175 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 7.091 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13188953 reads: 4.666 seconds. Making clumps. Clump time: 0.405 seconds. Correcting. Correct time: 61.417 seconds. Seed: 3 Reads: 13188953 Clumps: 783673 Corrections: 65591 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.034 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13103221 reads: 198.218 seconds. Making clumps. Clump time: 0.440 seconds. Correcting. Correct time: 14.597 seconds. Seed: 3 Reads: 13103221 Clumps: 781532 Corrections: 65554 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 3.007 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13229965 reads: 4.310 seconds. Making clumps. Clump time: 0.401 seconds. Correcting. Correct time: 21.296 seconds. Seed: 3 Reads: 13229965 Clumps: 781339 Corrections: 65912 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.081 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13101757 reads: 240.200 seconds. Making clumps. Clump time: 0.481 seconds. Correcting. Correct time: 14.364 seconds. Seed: 3 Reads: 13101757 Clumps: 781543 Corrections: 65210 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.072 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13015267 reads: 0.001 seconds. Making clumps. Clump time: 0.935 seconds. Correcting. Correct time: 12.759 seconds. Seed: 3 Reads: 13015267 Clumps: 781818 Corrections: 64535 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 1.856 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13054402 reads: 258.090 seconds. Making clumps. Clump time: 0.408 seconds. Correcting. Correct time: 26.638 seconds. Seed: 3 Reads: 13054402 Clumps: 781770 Corrections: 66716 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 2.087 seconds. Writing. Sent writable reads. Fetching reads. No more reads to fetch. Adding poison. Fetched 13215456 reads: 0.000 seconds. Making clumps. Clump time: 1.069 seconds. Correcting. Correct time: 16.190 seconds. Seed: 3 Reads: 13215456 Clumps: 782662 Corrections: 65423 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 1.944 seconds. Writing. Sent writable reads. Fetching reads. A fetch thread finished. Encountered poison; count=1 No more reads to fetch. Adding poison. Fetched 13024627 reads: 170.544 seconds. Making clumps. Clump time: 0.404 seconds. Correcting. Correct time: 6.085 seconds. Seed: 3 Reads: 13024627 Clumps: 781742 Corrections: 64960 Made a comparator with k=31, seed=4, border=0, hashes=4 Splitting. Split time: 1.859 seconds. Writing. Sent writable reads. Closing fetch threads. A fetch thread finished. Closed fetch threads. Waiting for writing to complete. Write time: 6.003 seconds. Time: 9138.905 seconds. Reads Processed: 1395m 152.71k reads/sec Bases Processed: 200804m 21.97m bases/sec Reads In: 1395647696 Clumps Formed: 41415865 Errors Corrected: 30514671 Executing clump.KmerSort3 [in1=./input/eccc_clumpify_p4_temp%_744d7777925266f1.fq, in2=, out=./input/eccc_clumpify_p5_temp%_10f98d38aa7bd5b3.fq, out2=, groups=53, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6] Making comparator. Made a comparator with k=31, seed=4, border=0, hashes=4 Making 2 fetch threads. Starting threads. Fetching reads. Fetched 13462241 reads: 165.432 seconds. Making clumps. Clump time: 0.435 seconds. Correcting. Correct time: 46.269 seconds. Seed: 4 Reads: 13462241 Clumps: 770506 Corrections: 491377 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.064 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13699949 reads: 0.000 seconds. Making clumps. Clump time: 0.995 seconds. Correcting. Correct time: 648.957 seconds. Seed: 4 Reads: 13699949 Clumps: 770709 Corrections: 531884 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.123 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12894889 reads: 0.003 seconds. Making clumps. Clump time: 2.128 seconds. Correcting. Correct time: 15.480 seconds. Seed: 4 Reads: 12894889 Clumps: 770010 Corrections: 402784 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.833 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13028828 reads: 0.000 seconds. Making clumps. Clump time: 1.201 seconds. Correcting. Correct time: 12.408 seconds. Seed: 4 Reads: 13028828 Clumps: 771028 Corrections: 391222 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.072 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13015528 reads: 319.704 seconds. Making clumps. Clump time: 0.594 seconds. Correcting. Correct time: 17.477 seconds. Seed: 4 Reads: 13015528 Clumps: 770945 Corrections: 429016 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.163 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12915093 reads: 0.000 seconds. Making clumps. Clump time: 1.550 seconds. Correcting. Correct time: 39.956 seconds. Seed: 4 Reads: 12915093 Clumps: 768579 Corrections: 359993 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.872 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13440133 reads: 211.159 seconds. Making clumps. Clump time: 0.435 seconds. Correcting. Correct time: 32.002 seconds. Seed: 4 Reads: 13440133 Clumps: 769703 Corrections: 401333 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.137 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13085401 reads: 0.001 seconds. Making clumps. Clump time: 2.430 seconds. Correcting. Correct time: 119.377 seconds. Seed: 4 Reads: 13085401 Clumps: 769874 Corrections: 414644 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 5.845 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13339664 reads: 130.757 seconds. Making clumps. Clump time: 9.859 seconds. Correcting. Correct time: 22.945 seconds. Seed: 4 Reads: 13339664 Clumps: 768619 Corrections: 462126 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.734 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12718343 reads: 3.931 seconds. Making clumps. Clump time: 0.411 seconds. Correcting. Correct time: 11.722 seconds. Seed: 4 Reads: 12718343 Clumps: 770426 Corrections: 379304 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.894 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13133415 reads: 251.398 seconds. Making clumps. Clump time: 0.378 seconds. Correcting. Correct time: 30.692 seconds. Seed: 4 Reads: 13133415 Clumps: 770249 Corrections: 373626 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.242 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13382326 reads: 24.974 seconds. Making clumps. Clump time: 2.925 seconds. Correcting. Correct time: 62.257 seconds. Seed: 4 Reads: 13382326 Clumps: 769522 Corrections: 417398 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.166 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13209204 reads: 193.796 seconds. Making clumps. Clump time: 0.427 seconds. Correcting. Correct time: 56.117 seconds. Seed: 4 Reads: 13209204 Clumps: 770457 Corrections: 457330 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.106 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13330536 reads: 0.001 seconds. Making clumps. Clump time: 1.745 seconds. Correcting. Correct time: 21.329 seconds. Seed: 4 Reads: 13330536 Clumps: 769321 Corrections: 427323 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.075 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13245447 reads: 146.832 seconds. Making clumps. Clump time: 0.513 seconds. Correcting. Correct time: 60.887 seconds. Seed: 4 Reads: 13245447 Clumps: 768618 Corrections: 500190 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.153 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12928435 reads: 120.591 seconds. Making clumps. Clump time: 0.432 seconds. Correcting. Correct time: 21.609 seconds. Seed: 4 Reads: 12928435 Clumps: 769006 Corrections: 370368 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.162 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12996603 reads: 95.724 seconds. Making clumps. Clump time: 0.402 seconds. Correcting. Correct time: 50.860 seconds. Seed: 4 Reads: 12996603 Clumps: 770245 Corrections: 445524 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.409 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13950223 reads: 139.706 seconds. Making clumps. Clump time: 0.672 seconds. Correcting. Correct time: 139.366 seconds. Seed: 4 Reads: 13950223 Clumps: 769879 Corrections: 723041 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.198 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12988228 reads: 0.001 seconds. Making clumps. Clump time: 1.110 seconds. Correcting. Correct time: 20.092 seconds. Seed: 4 Reads: 12988228 Clumps: 768074 Corrections: 418944 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.060 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12983883 reads: 0.001 seconds. Making clumps. Clump time: 1.246 seconds. Correcting. Correct time: 9.770 seconds. Seed: 4 Reads: 12983883 Clumps: 769691 Corrections: 377542 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.098 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13295787 reads: 322.392 seconds. Making clumps. Clump time: 0.429 seconds. Correcting. Correct time: 71.884 seconds. Seed: 4 Reads: 13295787 Clumps: 769333 Corrections: 445203 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.186 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13036851 reads: 0.000 seconds. Making clumps. Clump time: 1.125 seconds. Correcting. Correct time: 14.770 seconds. Seed: 4 Reads: 13036851 Clumps: 768930 Corrections: 399766 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.949 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13110895 reads: 147.555 seconds. Making clumps. Clump time: 4.532 seconds. Correcting. Correct time: 10.712 seconds. Seed: 4 Reads: 13110895 Clumps: 770690 Corrections: 385446 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 5.151 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13001718 reads: 181.280 seconds. Making clumps. Clump time: 0.457 seconds. Correcting. Correct time: 12.416 seconds. Seed: 4 Reads: 13001718 Clumps: 770682 Corrections: 389625 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.157 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13142995 reads: 70.275 seconds. Making clumps. Clump time: 0.416 seconds. Correcting. Correct time: 14.130 seconds. Seed: 4 Reads: 13142995 Clumps: 769314 Corrections: 436769 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.097 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12938053 reads: 202.753 seconds. Making clumps. Clump time: 0.413 seconds. Correcting. Correct time: 30.172 seconds. Seed: 4 Reads: 12938053 Clumps: 769187 Corrections: 427521 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.972 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13267576 reads: 0.000 seconds. Making clumps. Clump time: 0.887 seconds. Correcting. Correct time: 34.594 seconds. Seed: 4 Reads: 13267576 Clumps: 769531 Corrections: 461031 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.994 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12688696 reads: 237.450 seconds. Making clumps. Clump time: 0.399 seconds. Correcting. Correct time: 12.681 seconds. Seed: 4 Reads: 12688696 Clumps: 769538 Corrections: 375310 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.370 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13002183 reads: 10.276 seconds. Making clumps. Clump time: 0.421 seconds. Correcting. Correct time: 12.511 seconds. Seed: 4 Reads: 13002183 Clumps: 767569 Corrections: 388636 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.982 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13228429 reads: 260.654 seconds. Making clumps. Clump time: 0.412 seconds. Correcting. Correct time: 22.000 seconds. Seed: 4 Reads: 13228429 Clumps: 770274 Corrections: 362419 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.099 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13330610 reads: 0.001 seconds. Making clumps. Clump time: 1.157 seconds. Correcting. Correct time: 14.654 seconds. Seed: 4 Reads: 13330610 Clumps: 768640 Corrections: 562024 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.950 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13086332 reads: 256.525 seconds. Making clumps. Clump time: 0.375 seconds. Correcting. Correct time: 21.441 seconds. Seed: 4 Reads: 13086332 Clumps: 770386 Corrections: 389439 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.153 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12964698 reads: 51.463 seconds. Making clumps. Clump time: 0.440 seconds. Correcting. Correct time: 42.666 seconds. Seed: 4 Reads: 12964698 Clumps: 769179 Corrections: 449387 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.129 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12832587 reads: 183.524 seconds. Making clumps. Clump time: 0.457 seconds. Correcting. Correct time: 35.775 seconds. Seed: 4 Reads: 12832587 Clumps: 769447 Corrections: 347915 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.217 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12853697 reads: 0.000 seconds. Making clumps. Clump time: 1.171 seconds. Correcting. Correct time: 24.720 seconds. Seed: 4 Reads: 12853697 Clumps: 769288 Corrections: 404026 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.956 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13305522 reads: 195.364 seconds. Making clumps. Clump time: 0.442 seconds. Correcting. Correct time: 21.637 seconds. Seed: 4 Reads: 13305522 Clumps: 768701 Corrections: 463667 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.145 seconds. Writing. Sent writable reads. Fetching reads. Fetched 14472564 reads: 134.541 seconds. Making clumps. Clump time: 0.515 seconds. Correcting. Correct time: 762.395 seconds. Seed: 4 Reads: 14472564 Clumps: 770079 Corrections: 700239 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.168 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13155398 reads: 0.008 seconds. Making clumps. Clump time: 2.183 seconds. Correcting. Correct time: 28.861 seconds. Seed: 4 Reads: 13155398 Clumps: 769442 Corrections: 351172 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.006 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13154495 reads: 0.000 seconds. Making clumps. Clump time: 1.427 seconds. Correcting. Correct time: 21.766 seconds. Seed: 4 Reads: 13154495 Clumps: 767486 Corrections: 464629 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.322 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13112398 reads: 307.130 seconds. Making clumps. Clump time: 0.471 seconds. Correcting. Correct time: 60.655 seconds. Seed: 4 Reads: 13112398 Clumps: 770837 Corrections: 408631 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.220 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13448776 reads: 0.000 seconds. Making clumps. Clump time: 2.132 seconds. Correcting. Correct time: 18.514 seconds. Seed: 4 Reads: 13448776 Clumps: 768755 Corrections: 518960 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.024 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13821309 reads: 154.092 seconds. Making clumps. Clump time: 0.380 seconds. Correcting. Correct time: 104.574 seconds. Seed: 4 Reads: 13821309 Clumps: 769224 Corrections: 603698 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.359 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12944765 reads: 91.381 seconds. Making clumps. Clump time: 0.410 seconds. Correcting. Correct time: 23.605 seconds. Seed: 4 Reads: 12944765 Clumps: 769576 Corrections: 377131 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.157 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12869279 reads: 74.084 seconds. Making clumps. Clump time: 0.404 seconds. Correcting. Correct time: 12.428 seconds. Seed: 4 Reads: 12869279 Clumps: 769178 Corrections: 424174 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.031 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13411259 reads: 195.968 seconds. Making clumps. Clump time: 0.447 seconds. Correcting. Correct time: 36.939 seconds. Seed: 4 Reads: 13411259 Clumps: 769059 Corrections: 475620 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.208 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13112398 reads: 0.000 seconds. Making clumps. Clump time: 1.286 seconds. Correcting. Correct time: 15.343 seconds. Seed: 4 Reads: 13112398 Clumps: 769841 Corrections: 476490 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.984 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13178227 reads: 246.726 seconds. Making clumps. Clump time: 0.438 seconds. Correcting. Correct time: 25.897 seconds. Seed: 4 Reads: 13178227 Clumps: 771488 Corrections: 443641 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.269 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13077142 reads: 74.494 seconds. Making clumps. Clump time: 0.374 seconds. Correcting. Correct time: 10.594 seconds. Seed: 4 Reads: 13077142 Clumps: 769968 Corrections: 370870 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.186 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12908143 reads: 207.787 seconds. Making clumps. Clump time: 0.398 seconds. Correcting. Correct time: 12.704 seconds. Seed: 4 Reads: 12908143 Clumps: 769231 Corrections: 354925 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 8.853 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13000777 reads: 0.000 seconds. Making clumps. Clump time: 0.761 seconds. Correcting. Correct time: 18.205 seconds. Seed: 4 Reads: 13000777 Clumps: 770489 Corrections: 382315 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.926 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12950307 reads: 260.453 seconds. Making clumps. Clump time: 0.436 seconds. Correcting. Correct time: 15.565 seconds. Seed: 4 Reads: 12950307 Clumps: 769314 Corrections: 407371 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 2.965 seconds. Writing. Sent writable reads. Fetching reads. No more reads to fetch. Adding poison. Fetched 13228412 reads: 3.997 seconds. Making clumps. Clump time: 0.431 seconds. Correcting. Correct time: 19.943 seconds. Seed: 4 Reads: 13228412 Clumps: 769866 Corrections: 446457 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.991 seconds. Writing. Sent writable reads. Fetching reads. A fetch thread finished. Encountered poison; count=1 No more reads to fetch. Adding poison. Fetched 13143201 reads: 184.281 seconds. Making clumps. Clump time: 0.428 seconds. Correcting. Correct time: 30.881 seconds. Seed: 4 Reads: 13143201 Clumps: 769317 Corrections: 367446 Made a comparator with k=31, seed=5, border=0, hashes=4 Splitting. Split time: 1.891 seconds. Writing. Sent writable reads. Closing fetch threads. A fetch thread finished. Closed fetch threads. Waiting for writing to complete. Write time: 4.207 seconds. Time: 9273.075 seconds. Reads Processed: 1395m 150.51k reads/sec Bases Processed: 200804m 21.65m bases/sec Reads In: 1395647696 Clumps Formed: 40789300 Errors Corrected: 53551593 Executing clump.KmerSort3 [in1=./input/eccc_clumpify_p5_temp%_10f98d38aa7bd5b3.fq, in2=, out=./input/eccc_clumpify_p6_temp%_62d549150519411a.fq, out2=, groups=53, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6] Making comparator. Made a comparator with k=31, seed=5, border=0, hashes=4 Making 2 fetch threads. Starting threads. Fetching reads. Fetched 12846031 reads: 140.146 seconds. Making clumps. Clump time: 0.396 seconds. Correcting. Correct time: 30.625 seconds. Seed: 5 Reads: 12846031 Clumps: 736929 Corrections: 190428 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.205 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13259236 reads: 0.000 seconds. Making clumps. Clump time: 1.707 seconds. Correcting. Correct time: 15.325 seconds. Seed: 5 Reads: 13259236 Clumps: 737326 Corrections: 226284 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.939 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13593683 reads: 179.848 seconds. Making clumps. Clump time: 0.443 seconds. Correcting. Correct time: 185.837 seconds. Seed: 5 Reads: 13593683 Clumps: 736329 Corrections: 258370 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.997 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12986116 reads: 0.000 seconds. Making clumps. Clump time: 1.081 seconds. Correcting. Correct time: 7.769 seconds. Seed: 5 Reads: 12986116 Clumps: 737148 Corrections: 230561 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.050 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12805635 reads: 0.000 seconds. Making clumps. Clump time: 1.035 seconds. Correcting. Correct time: 28.131 seconds. Seed: 5 Reads: 12805635 Clumps: 737688 Corrections: 205383 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.940 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12904418 reads: 272.924 seconds. Making clumps. Clump time: 0.537 seconds. Correcting. Correct time: 14.033 seconds. Seed: 5 Reads: 12904418 Clumps: 737939 Corrections: 245235 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.068 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13078489 reads: 0.000 seconds. Making clumps. Clump time: 1.028 seconds. Correcting. Correct time: 12.944 seconds. Seed: 5 Reads: 13078489 Clumps: 737865 Corrections: 232155 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.017 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13191897 reads: 226.519 seconds. Making clumps. Clump time: 0.434 seconds. Correcting. Correct time: 39.035 seconds. Seed: 5 Reads: 13191897 Clumps: 737228 Corrections: 246827 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.015 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13143698 reads: 0.001 seconds. Making clumps. Clump time: 0.678 seconds. Correcting. Correct time: 15.247 seconds. Seed: 5 Reads: 13143698 Clumps: 738135 Corrections: 244725 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.976 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12949973 reads: 160.237 seconds. Making clumps. Clump time: 0.412 seconds. Correcting. Correct time: 16.339 seconds. Seed: 5 Reads: 12949973 Clumps: 736719 Corrections: 216276 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.058 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13308154 reads: 127.633 seconds. Making clumps. Clump time: 0.462 seconds. Correcting. Correct time: 155.525 seconds. Seed: 5 Reads: 13308154 Clumps: 735320 Corrections: 219183 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.105 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13281250 reads: 0.003 seconds. Making clumps. Clump time: 2.064 seconds. Correcting. Correct time: 68.178 seconds. Seed: 5 Reads: 13281250 Clumps: 736352 Corrections: 243907 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.137 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13365950 reads: 0.002 seconds. Making clumps. Clump time: 1.973 seconds. Correcting. Correct time: 27.311 seconds. Seed: 5 Reads: 13365950 Clumps: 737207 Corrections: 248256 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.050 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13044626 reads: 219.194 seconds. Making clumps. Clump time: 0.397 seconds. Correcting. Correct time: 13.474 seconds. Seed: 5 Reads: 13044626 Clumps: 735618 Corrections: 221611 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.103 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13184776 reads: 0.000 seconds. Making clumps. Clump time: 0.849 seconds. Correcting. Correct time: 19.722 seconds. Seed: 5 Reads: 13184776 Clumps: 736616 Corrections: 224989 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.103 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13111965 reads: 223.808 seconds. Making clumps. Clump time: 0.413 seconds. Correcting. Correct time: 39.696 seconds. Seed: 5 Reads: 13111965 Clumps: 737278 Corrections: 243842 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.115 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13042844 reads: 0.000 seconds. Making clumps. Clump time: 1.563 seconds. Correcting. Correct time: 40.495 seconds. Seed: 5 Reads: 13042844 Clumps: 736870 Corrections: 192972 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.054 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12902195 reads: 137.601 seconds. Making clumps. Clump time: 0.430 seconds. Correcting. Correct time: 14.357 seconds. Seed: 5 Reads: 12902195 Clumps: 736678 Corrections: 202021 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.126 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12861062 reads: 124.616 seconds. Making clumps. Clump time: 0.430 seconds. Correcting. Correct time: 17.965 seconds. Seed: 5 Reads: 12861062 Clumps: 736983 Corrections: 257215 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 6.817 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13177699 reads: 96.353 seconds. Making clumps. Clump time: 0.435 seconds. Correcting. Correct time: 25.680 seconds. Seed: 5 Reads: 13177699 Clumps: 737635 Corrections: 242549 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.196 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13408389 reads: 114.701 seconds. Making clumps. Clump time: 0.451 seconds. Correcting. Correct time: 47.377 seconds. Seed: 5 Reads: 13408389 Clumps: 738553 Corrections: 284721 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.160 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13386674 reads: 90.470 seconds. Making clumps. Clump time: 0.435 seconds. Correcting. Correct time: 17.167 seconds. Seed: 5 Reads: 13386674 Clumps: 738099 Corrections: 240563 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.162 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13075734 reads: 112.022 seconds. Making clumps. Clump time: 0.424 seconds. Correcting. Correct time: 13.448 seconds. Seed: 5 Reads: 13075734 Clumps: 737302 Corrections: 208378 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.969 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12808348 reads: 122.561 seconds. Making clumps. Clump time: 0.426 seconds. Correcting. Correct time: 16.424 seconds. Seed: 5 Reads: 12808348 Clumps: 736567 Corrections: 200578 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.286 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13338554 reads: 112.140 seconds. Making clumps. Clump time: 5.717 seconds. Correcting. Correct time: 14.673 seconds. Seed: 5 Reads: 13338554 Clumps: 736977 Corrections: 258608 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 7.285 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13285928 reads: 105.274 seconds. Making clumps. Clump time: 0.433 seconds. Correcting. Correct time: 41.147 seconds. Seed: 5 Reads: 13285928 Clumps: 736290 Corrections: 234196 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.460 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12876558 reads: 83.201 seconds. Making clumps. Clump time: 0.397 seconds. Correcting. Correct time: 14.567 seconds. Seed: 5 Reads: 12876558 Clumps: 736104 Corrections: 220054 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.448 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13117669 reads: 114.202 seconds. Making clumps. Clump time: 0.426 seconds. Correcting. Correct time: 14.267 seconds. Seed: 5 Reads: 13117669 Clumps: 736009 Corrections: 262460 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.099 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13031787 reads: 118.056 seconds. Making clumps. Clump time: 0.434 seconds. Correcting. Correct time: 100.711 seconds. Seed: 5 Reads: 13031787 Clumps: 738091 Corrections: 223331 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.967 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12936586 reads: 0.002 seconds. Making clumps. Clump time: 0.922 seconds. Correcting. Correct time: 11.861 seconds. Seed: 5 Reads: 12936586 Clumps: 737893 Corrections: 257429 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 7.667 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13237067 reads: 0.001 seconds. Making clumps. Clump time: 0.803 seconds. Correcting. Correct time: 48.244 seconds. Seed: 5 Reads: 13237067 Clumps: 737957 Corrections: 251896 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 5.484 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13219697 reads: 253.855 seconds. Making clumps. Clump time: 0.526 seconds. Correcting. Correct time: 36.062 seconds. Seed: 5 Reads: 13219697 Clumps: 738395 Corrections: 228017 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.079 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13564204 reads: 0.000 seconds. Making clumps. Clump time: 0.652 seconds. Correcting. Correct time: 32.864 seconds. Seed: 5 Reads: 13564204 Clumps: 738831 Corrections: 253964 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.994 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13475183 reads: 215.538 seconds. Making clumps. Clump time: 0.442 seconds. Correcting. Correct time: 32.231 seconds. Seed: 5 Reads: 13475183 Clumps: 737369 Corrections: 304732 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.255 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13186101 reads: 0.001 seconds. Making clumps. Clump time: 0.659 seconds. Correcting. Correct time: 19.289 seconds. Seed: 5 Reads: 13186101 Clumps: 737089 Corrections: 240179 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.983 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12967268 reads: 199.019 seconds. Making clumps. Clump time: 0.406 seconds. Correcting. Correct time: 35.465 seconds. Seed: 5 Reads: 12967268 Clumps: 738460 Corrections: 225775 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.082 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13027628 reads: 41.169 seconds. Making clumps. Clump time: 0.437 seconds. Correcting. Correct time: 26.328 seconds. Seed: 5 Reads: 13027628 Clumps: 736975 Corrections: 220284 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.976 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12724923 reads: 158.448 seconds. Making clumps. Clump time: 0.400 seconds. Correcting. Correct time: 11.036 seconds. Seed: 5 Reads: 12724923 Clumps: 737035 Corrections: 188591 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.059 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13592464 reads: 112.900 seconds. Making clumps. Clump time: 0.531 seconds. Correcting. Correct time: 65.487 seconds. Seed: 5 Reads: 13592464 Clumps: 735917 Corrections: 343623 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.424 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13178534 reads: 9.944 seconds. Making clumps. Clump time: 0.447 seconds. Correcting. Correct time: 25.415 seconds. Seed: 5 Reads: 13178534 Clumps: 738582 Corrections: 215698 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.963 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12819741 reads: 164.302 seconds. Making clumps. Clump time: 0.427 seconds. Correcting. Correct time: 17.830 seconds. Seed: 5 Reads: 12819741 Clumps: 736482 Corrections: 213547 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.286 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13281713 reads: 128.282 seconds. Making clumps. Clump time: 0.406 seconds. Correcting. Correct time: 42.481 seconds. Seed: 5 Reads: 13281713 Clumps: 736694 Corrections: 235160 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.217 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13347276 reads: 104.089 seconds. Making clumps. Clump time: 0.498 seconds. Correcting. Correct time: 28.501 seconds. Seed: 5 Reads: 13347276 Clumps: 736522 Corrections: 283592 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 7.226 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13256103 reads: 120.691 seconds. Making clumps. Clump time: 0.429 seconds. Correcting. Correct time: 31.814 seconds. Seed: 5 Reads: 13256103 Clumps: 738300 Corrections: 265861 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.298 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13360453 reads: 100.280 seconds. Making clumps. Clump time: 0.376 seconds. Correcting. Correct time: 18.153 seconds. Seed: 5 Reads: 13360453 Clumps: 737880 Corrections: 236349 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.198 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13338575 reads: 128.109 seconds. Making clumps. Clump time: 0.438 seconds. Correcting. Correct time: 47.814 seconds. Seed: 5 Reads: 13338575 Clumps: 737079 Corrections: 262364 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.980 seconds. Writing. Sent writable reads. Fetching reads. Fetched 12843914 reads: 0.001 seconds. Making clumps. Clump time: 0.617 seconds. Correcting. Correct time: 7.859 seconds. Seed: 5 Reads: 12843914 Clumps: 738527 Corrections: 234962 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.031 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13106851 reads: 216.468 seconds. Making clumps. Clump time: 4.370 seconds. Correcting. Correct time: 8.224 seconds. Seed: 5 Reads: 13106851 Clumps: 737269 Corrections: 244092 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.246 seconds. Writing. Sent writable reads. Fetching reads. Fetched 14213006 reads: 116.007 seconds. Making clumps. Clump time: 0.646 seconds. Correcting. Correct time: 251.599 seconds. Seed: 5 Reads: 14213006 Clumps: 736999 Corrections: 452668 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.108 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13124388 reads: 0.001 seconds. Making clumps. Clump time: 0.592 seconds. Correcting. Correct time: 10.826 seconds. Seed: 5 Reads: 13124388 Clumps: 738649 Corrections: 229429 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.056 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13283545 reads: 0.000 seconds. Making clumps. Clump time: 5.345 seconds. Correcting. Correct time: 15.348 seconds. Seed: 5 Reads: 13283545 Clumps: 738417 Corrections: 203451 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.025 seconds. Writing. Sent writable reads. Fetching reads. Fetched 13246554 reads: 325.590 seconds. Making clumps. No more reads to fetch. Adding poison. Clump time: 0.880 seconds. Correcting. Correct time: 90.236 seconds. Seed: 5 Reads: 13246554 Clumps: 737742 Corrections: 259329 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 2.072 seconds. Writing. Sent writable reads. Fetching reads. No more reads to fetch. Adding poison. Fetched 13122736 reads: 0.000 seconds. Making clumps. Clump time: 0.890 seconds. Correcting. Correct time: 11.547 seconds. Seed: 5 Reads: 13122736 Clumps: 738111 Corrections: 232128 Made a comparator with k=31, seed=6, border=0, hashes=4 Splitting. Split time: 1.984 seconds. Writing. Sent writable reads. Closing fetch threads. A fetch thread finished. A fetch thread finished. Closed fetch threads. Waiting for writing to complete. Write time: 51.262 seconds. Time: 7669.664 seconds. Reads Processed: 1395m 181.97k reads/sec Bases Processed: 200804m 26.18m bases/sec Reads In: 1395647696 Clumps Formed: 39077029 Errors Corrected: 66360391 Executing clump.KmerSort3 [in1=./input/eccc_clumpify_p6_temp%_62d549150519411a.fq, in2=, out=./input/eccc.fq, out2=, groups=53, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6] Making comparator. Made a comparator with k=31, seed=6, border=0, hashes=4 Making 2 fetch threads. Starting threads. Fetching reads. Fetched 13055603 reads: 158.221 seconds. Making clumps. Clump time: 0.764 seconds. Correcting. Correct time: 17.167 seconds. Seed: 6 Reads: 13055603 Clumps: 722056 Corrections: 141660 Writing. Fetching reads. Fetched 13262010 reads: 0.000 seconds. Making clumps. Clump time: 0.460 seconds. Correcting. Correct time: 29.341 seconds. Seed: 6 Reads: 13262010 Clumps: 721588 Corrections: 181789 Writing. Fetching reads. Fetched 13162214 reads: 233.108 seconds. Making clumps. Clump time: 0.438 seconds. Correcting. Correct time: 17.337 seconds. Seed: 6 Reads: 13162214 Clumps: 720334 Corrections: 158862 Writing. Fetching reads. Fetched 12996764 reads: 0.000 seconds. Making clumps. Clump time: 35.293 seconds. Correcting. Correct time: 19.111 seconds. Seed: 6 Reads: 12996764 Clumps: 721392 Corrections: 138129 Writing. Fetching reads. Fetched 13253991 reads: 257.738 seconds. Making clumps. Clump time: 0.449 seconds. Correcting. Correct time: 36.861 seconds. Seed: 6 Reads: 13253991 Clumps: 720450 Corrections: 151211 Writing. Fetching reads. Fetched 13154759 reads: 0.000 seconds. Making clumps. Clump time: 0.475 seconds. Correcting. Correct time: 15.473 seconds. Seed: 6 Reads: 13154759 Clumps: 721679 Corrections: 136511 Writing. Fetching reads. Fetched 13057263 reads: 222.100 seconds. Making clumps. Clump time: 6.493 seconds. Correcting. Correct time: 7.208 seconds. Seed: 6 Reads: 13057263 Clumps: 721863 Corrections: 143215 Writing. Fetching reads. Fetched 13064004 reads: 123.953 seconds. Making clumps. Clump time: 0.460 seconds. Correcting. Correct time: 11.464 seconds. Seed: 6 Reads: 13064004 Clumps: 721732 Corrections: 131858 Writing. Fetching reads. Fetched 13069655 reads: 155.123 seconds. Making clumps. Clump time: 0.427 seconds. Correcting. Correct time: 54.518 seconds. Seed: 6 Reads: 13069655 Clumps: 719994 Corrections: 146052 Writing. Fetching reads. Fetched 12987596 reads: 20.470 seconds. Making clumps. Clump time: 0.483 seconds. Correcting. Correct time: 13.892 seconds. Seed: 6 Reads: 12987596 Clumps: 720636 Corrections: 117921 Writing. Fetching reads. Fetched 12915400 reads: 216.504 seconds. Making clumps. Clump time: 0.362 seconds. Correcting. Correct time: 36.881 seconds. Seed: 6 Reads: 12915400 Clumps: 721063 Corrections: 148479 Writing. Fetching reads. Fetched 13494637 reads: 121.536 seconds. Making clumps. Clump time: 0.445 seconds. Correcting. Correct time: 72.491 seconds. Seed: 6 Reads: 13494637 Clumps: 721597 Corrections: 234456 Writing. Fetching reads. Fetched 13328117 reads: 5.802 seconds. Making clumps. Clump time: 0.433 seconds. Correcting. Correct time: 15.070 seconds. Seed: 6 Reads: 13328117 Clumps: 722115 Corrections: 133513 Writing. Fetching reads. Fetched 13065220 reads: 222.281 seconds. Making clumps. Clump time: 0.437 seconds. Correcting. Correct time: 12.954 seconds. Seed: 6 Reads: 13065220 Clumps: 721303 Corrections: 151503 Writing. Fetching reads. Fetched 12775404 reads: 137.897 seconds. Making clumps. Clump time: 0.489 seconds. Correcting. Correct time: 21.628 seconds. Seed: 6 Reads: 12775404 Clumps: 721011 Corrections: 132342 Writing. Fetching reads. Fetched 13393488 reads: 155.538 seconds. Making clumps. Clump time: 0.440 seconds. Correcting. Correct time: 106.697 seconds. Seed: 6 Reads: 13393488 Clumps: 721026 Corrections: 187119 Writing. Fetching reads. Fetched 13033010 reads: 0.000 seconds. Making clumps. Clump time: 0.441 seconds. Correcting. Correct time: 16.936 seconds. Seed: 6 Reads: 13033010 Clumps: 721196 Corrections: 145793 Writing. Fetching reads. Fetched 13281441 reads: 0.000 seconds. Making clumps. Clump time: 0.729 seconds. Correcting. Correct time: 12.681 seconds. Seed: 6 Reads: 13281441 Clumps: 720991 Corrections: 165334 Writing. Fetching reads. Fetched 13161042 reads: 360.696 seconds. Making clumps. Clump time: 0.962 seconds. Correcting. Correct time: 14.774 seconds. Seed: 6 Reads: 13161042 Clumps: 721381 Corrections: 142021 Writing. Fetching reads. Fetched 12711379 reads: 0.000 seconds. Making clumps. Clump time: 0.281 seconds. Correcting. Correct time: 11.104 seconds. Seed: 6 Reads: 12711379 Clumps: 720845 Corrections: 156758 Writing. Fetching reads. Fetched 13020258 reads: 301.016 seconds. Making clumps. Clump time: 4.089 seconds. Correcting. Correct time: 10.683 seconds. Seed: 6 Reads: 13020258 Clumps: 721018 Corrections: 143411 Writing. Fetching reads. Fetched 13119705 reads: 0.000 seconds. Making clumps. Clump time: 0.342 seconds. Correcting. Correct time: 11.446 seconds. Seed: 6 Reads: 13119705 Clumps: 720173 Corrections: 148336 Writing. Fetching reads. Fetched 12967480 reads: 278.825 seconds. Making clumps. Clump time: 0.456 seconds. Correcting. Correct time: 23.628 seconds. Seed: 6 Reads: 12967480 Clumps: 722463 Corrections: 141916 Writing. Fetching reads. Fetched 13232119 reads: 0.000 seconds. Making clumps. Clump time: 0.788 seconds. Correcting. Correct time: 28.972 seconds. Seed: 6 Reads: 13232119 Clumps: 720639 Corrections: 167744 Writing. Fetching reads. Fetched 13033275 reads: 246.564 seconds. Making clumps. Clump time: 0.537 seconds. Correcting. Correct time: 7.480 seconds. Seed: 6 Reads: 13033275 Clumps: 721895 Corrections: 147842 Writing. Fetching reads. Fetched 12867944 reads: 140.438 seconds. Making clumps. Clump time: 0.481 seconds. Correcting. Correct time: 17.553 seconds. Seed: 6 Reads: 12867944 Clumps: 720737 Corrections: 148432 Writing. Fetching reads. Fetched 13659379 reads: 165.770 seconds. Making clumps. Clump time: 0.509 seconds. Correcting. Correct time: 49.535 seconds. Seed: 6 Reads: 13659379 Clumps: 722193 Corrections: 157853 Writing. Fetching reads. Fetched 13491003 reads: 0.000 seconds. Making clumps. Clump time: 0.431 seconds. Correcting. Correct time: 102.985 seconds. Seed: 6 Reads: 13491003 Clumps: 722937 Corrections: 164553 Writing. Fetching reads. Fetched 13128617 reads: 152.521 seconds. Making clumps. Clump time: 0.436 seconds. Correcting. Correct time: 39.199 seconds. Seed: 6 Reads: 13128617 Clumps: 722414 Corrections: 177578 Writing. Fetching reads. Fetched 13279737 reads: 123.400 seconds. Making clumps. Clump time: 0.403 seconds. Correcting. Correct time: 23.831 seconds. Seed: 6 Reads: 13279737 Clumps: 719948 Corrections: 159639 Writing. Fetching reads. Fetched 13338721 reads: 142.670 seconds. Making clumps. Clump time: 0.470 seconds. Correcting. Correct time: 44.589 seconds. Seed: 6 Reads: 13338721 Clumps: 720970 Corrections: 170420 Writing. Fetching reads. Fetched 12932374 reads: 54.988 seconds. Making clumps. Clump time: 0.432 seconds. Correcting. Correct time: 7.188 seconds. Seed: 6 Reads: 12932374 Clumps: 722233 Corrections: 140599 Writing. Fetching reads. Fetched 13110852 reads: 217.471 seconds. Making clumps. Clump time: 0.428 seconds. Correcting. Correct time: 33.556 seconds. Seed: 6 Reads: 13110852 Clumps: 721347 Corrections: 144613 Writing. Fetching reads. Fetched 13139476 reads: 122.688 seconds. Making clumps. Clump time: 0.437 seconds. Correcting. Correct time: 10.959 seconds. Seed: 6 Reads: 13139476 Clumps: 722062 Corrections: 136384 Writing. Fetching reads. Fetched 13009985 reads: 169.118 seconds. Making clumps. Clump time: 0.411 seconds. Correcting. Correct time: 13.438 seconds. Seed: 6 Reads: 13009985 Clumps: 720572 Corrections: 126961 Writing. Fetching reads. Fetched 14309998 reads: 142.963 seconds. Making clumps. Clump time: 0.779 seconds. Correcting. Correct time: 45.404 seconds. Seed: 6 Reads: 14309998 Clumps: 722589 Corrections: 311813 Writing. Fetching reads. Fetched 13384947 reads: 137.633 seconds. Making clumps. Clump time: 0.350 seconds. Correcting. Correct time: 7.863 seconds. Seed: 6 Reads: 13384947 Clumps: 722502 Corrections: 161603 Writing. Fetching reads. Fetched 13593760 reads: 138.920 seconds. Making clumps. Clump time: 0.446 seconds. Correcting. Correct time: 104.543 seconds. Seed: 6 Reads: 13593760 Clumps: 720306 Corrections: 199624 Writing. Fetching reads. Fetched 13350160 reads: 0.000 seconds. Making clumps. Clump time: 0.954 seconds. Correcting. Correct time: 17.298 seconds. Seed: 6 Reads: 13350160 Clumps: 722632 Corrections: 179660 Writing. Fetching reads. Fetched 13230504 reads: 0.000 seconds. Making clumps. Clump time: 0.706 seconds. Correcting. Correct time: 13.899 seconds. Seed: 6 Reads: 13230504 Clumps: 721271 Corrections: 133837 Writing. Fetching reads. Fetched 12998173 reads: 364.980 seconds. Making clumps. Clump time: 0.445 seconds. Correcting. Correct time: 14.000 seconds. Seed: 6 Reads: 12998173 Clumps: 722338 Corrections: 136130 Writing. Fetching reads. Fetched 12915105 reads: 5.066 seconds. Making clumps. Clump time: 0.403 seconds. Correcting. Correct time: 12.590 seconds. Seed: 6 Reads: 12915105 Clumps: 720411 Corrections: 142901 Writing. Fetching reads. Fetched 13011136 reads: 286.788 seconds. Making clumps. Clump time: 0.450 seconds. Correcting. Correct time: 13.440 seconds. Seed: 6 Reads: 13011136 Clumps: 721134 Corrections: 137221 Writing. Fetching reads. Fetched 13321288 reads: 0.000 seconds. Making clumps. Clump time: 0.680 seconds. Correcting. Correct time: 37.391 seconds. Seed: 6 Reads: 13321288 Clumps: 720994 Corrections: 157193 Writing. Fetching reads. Fetched 13256631 reads: 272.202 seconds. Making clumps. Clump time: 0.359 seconds. Correcting. Correct time: 14.999 seconds. Seed: 6 Reads: 13256631 Clumps: 721271 Corrections: 148269 Writing. Fetching reads. Fetched 13011843 reads: 5.023 seconds. Making clumps. Clump time: 0.415 seconds. Correcting. Correct time: 6.367 seconds. Seed: 6 Reads: 13011843 Clumps: 721158 Corrections: 129947 Writing. Fetching reads. Fetched 13024978 reads: 303.829 seconds. Making clumps. Clump time: 0.404 seconds. Correcting. Correct time: 61.983 seconds. Seed: 6 Reads: 13024978 Clumps: 721202 Corrections: 131482 Writing. Fetching reads. Fetched 13312177 reads: 0.000 seconds. Making clumps. Clump time: 0.434 seconds. Correcting. Correct time: 19.664 seconds. Seed: 6 Reads: 13312177 Clumps: 720102 Corrections: 167961 Writing. Fetching reads. Fetched 13181308 reads: 162.675 seconds. Making clumps. Clump time: 0.438 seconds. Correcting. Correct time: 14.335 seconds. Seed: 6 Reads: 13181308 Clumps: 720534 Corrections: 130523 Writing. Fetching reads. Fetched 13217358 reads: 238.562 seconds. Making clumps. Clump time: 0.462 seconds. Correcting. Correct time: 21.820 seconds. Seed: 6 Reads: 13217358 Clumps: 720906 Corrections: 154013 Writing. Fetching reads. Fetched 13480332 reads: 0.000 seconds. Making clumps. Clump time: 0.419 seconds. Correcting. Correct time: 20.129 seconds. Seed: 6 Reads: 13480332 Clumps: 720732 Corrections: 176109 Writing. Fetching reads. No more reads to fetch. Adding poison. Fetched 13019381 reads: 283.645 seconds. Making clumps. Clump time: 0.469 seconds. Correcting. Correct time: 45.842 seconds. Seed: 6 Reads: 13019381 Clumps: 720648 Corrections: 134770 Writing. Fetching reads. No more reads to fetch. Adding poison. Fetched 12650847 reads: 0.000 seconds. Making clumps. Clump time: 0.394 seconds. Correcting. Correct time: 24.746 seconds. Seed: 6 Reads: 12650847 Clumps: 720666 Corrections: 130352 Writing. Closing fetch threads. A fetch thread finished. A fetch thread finished. Closed fetch threads. Waiting for writing to complete. Write time: 57.101 seconds. Done! Time: 8635.616 seconds. Reads Processed: 1395m 161.62k reads/sec Bases Processed: 200804m 23.25m bases/sec Reads In: 1395647696 Clumps Formed: 38227249 Errors Corrected: 74544606 Total time: 60275.162 seconds. #Error-correct 3 java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ assemble.Tadpole -Xmx200g in=./input/eccc.fq out=./input/ecct.fq ecc Executing assemble.Tadpole1 [-Xmx200g, in=./input/eccc.fq, out=./input/ecct.fq, ecc] Version 38.34 Switching to correct mode because ecc=t. Using 32 threads. Executing kmer.KmerTableSet [-Xmx200g, in=./input/eccc.fq, out=./input/ecct.fq, ecc] Initial: Ways=83, initialSize=128000, prefilter=f, prealloc=f Memory: max=205800m, total=205800m, free=201505m, used=4295m Initialization Time: 0.067 seconds. Loading kmers. Estimated kmer capacity: 9967382606 0.110 seconds. After table allocation: Memory: max=205800m, total=205800m, free=198284m, used=7516m After loading: Memory: max=190887m, total=190887m, free=54700m, used=136187m Input: 1395647696 reads 200804772348 bases. Unique Kmers: 4322776654 Load Time: 4033.779 seconds. Reads Processed: 1395m 345.99k reads/sec Bases Processed: 200804m 49.78m bases/sec Extending/error-correcting/discarding. After extending reads: Memory: max=190887m, total=190887m, free=47289m, used=143598m Input: 1395647696 reads 200804772348 bases. Output: 1395647696 reads 200804772348 bases. Errors detected: 820494831 Errors corrected: 157930743 (157930743 reassemble) Reads with errors detected: 240021986 (17.20%) Reads fully corrected: 96911535 (40.38% of detected) Reads partly corrected: 24128659 (10.05% of detected) Rollbacks: 9249336 (3.85% of detected) Extend/error-correct time: 7972.651 seconds. Total Time: 12006.520 seconds. Reads Processed: 1395m 116.24k reads/sec Bases Processed: 200804m 16.72m bases/sec #Merge java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx200g in=./input/ecct.fq out=./input/merged.fq outu=unmerged.fq rem k=62 extend2=50 adapters=default Executing jgi.BBMerge [-Xmx200g, in=./input/ecct.fq, out=./input/merged.fq, outu=unmerged.fq, rem, k=62, extend2=50, adapters=default] Version 38.34 Executing assemble.Tadpole2 [in=./input/ecct.fq, branchlower=3, branchmult1=20.0, branchmult2=3.0, mincountseed=3, mincountextend=2, minprob=0.5, k=62, prealloc=false, prefilter=0, ecctail=false, eccpincer=false, eccreassemble=true] Version 38.34 Using 32 threads. Executing ukmer.KmerTableSetU [in=./input/ecct.fq, branchlower=3, branchmult1=20.0, branchmult2=3.0, mincountseed=3, mincountextend=2, minprob=0.5, k=62, prealloc=false, prefilter=0, ecctail=false, eccpincer=false, eccreassemble=true] Initial: Ways=83, initialSize=128000, prefilter=f, prealloc=f Memory: max=205800m, total=205800m, free=200432m, used=5368m Estimated kmer capacity: 4784343650 After table allocation: Memory: max=205800m, total=205800m, free=198284m, used=7516m After loading: Memory: max=205781m, total=205781m, free=101241m, used=104540m Input: 1395647696 reads 200804772348 bases. Unique Kmers: 3944479191 Load Time: 3087.142 seconds. Writing mergable reads merged. Started output threads. Total time: 11569.460 seconds. Pairs: 697823848 Joined: 562502607 80.608% Ambiguous: 134756731 19.311% No Solution: 564510 0.081% Too Short: 0 0.000% Fully Extended: 933318715 66.917% Partly Extended: 368678835 26.433% Not Extended: 92753356 6.650% Adapters Expected: 753400 0.054% Adapters Found: 65056 0.005% Avg Insert: 275.3 Standard Deviation: 49.1 Mode: 280 Insert range: 35 - 391 90th percentile: 338 75th percentile: 309 50th percentile: 277 25th percentile: 243 10th percentile: 211 #Split unmerged into two files java -ea -Xmx200m -cp /DATA/markop/bbmap/current/ jgi.ReformatReads in=./input/unmerged.fq out1=./input/unmerged_1.fq out2=./input/unmerged_2.fq overwrite=true Executing jgi.ReformatReads [in=./input/unmerged.fq, out1=./input/unmerged_1.fq, out2=./input/unmerged_2.fq, overwrite=true] Set INTERLEAVED to true Input is being processed as paired Input: 270642482 reads 35009673124 bases Output: 270642482 reads (100.00%) 35009673124 bases (100.00%) Time: 414.441 seconds. Reads Processed: 270m 653.03k reads/sec Bases Processed: 35009m 84.47m bases/sec #run metaSPAdes see ./output/spades.log #Evaluate /DATA/markop/CPB_metaSpades $ /DATA/markop/bbmap/stats.sh -Xmx200g in=./output/contigs.fasta A C G T N IUPAC Other GC GC_stdev 0.3152 0.1814 0.1821 0.3213 0.0000 0.0000 0.0000 0.3635 0.0716 Main genome scaffold total: 5789416 Main genome contig total: 5789416 Main genome scaffold sequence total: 2176.773 MB Main genome contig sequence total: 2176.773 MB 0.000% gap Main genome scaffold N/L50: 900730/621 Main genome contig N/L50: 900730/621 Main genome scaffold N/L90: 3825451/131 Main genome contig N/L90: 3825451/131 Max scaffold length: 529.641 KB Max contig length: 529.641 KB Number of scaffolds > 50 KB: 211 % main genome in scaffolds > 50 KB: 1.09% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 5,789,416 5,789,416 2,176,773,479 2,176,773,479 100.00% 100 5,789,416 5,789,416 2,176,773,479 2,176,773,479 100.00% 250 2,372,908 2,372,908 1,695,643,255 1,695,643,255 100.00% 500 1,294,480 1,294,480 1,307,344,216 1,307,344,216 100.00% 1 KB 352,910 352,910 667,154,387 667,154,387 100.00% 2.5 KB 45,772 45,772 230,537,262 230,537,262 100.00% 5 KB 9,637 9,637 112,098,886 112,098,886 100.00% 10 KB 2,608 2,608 65,451,762 65,451,762 100.00% 25 KB 573 573 36,298,983 36,298,983 100.00% 50 KB 211 211 23,786,478 23,786,478 100.00% 100 KB 70 70 13,952,831 13,952,831 100.00% 250 KB 16 16 6,101,723 6,101,723 100.00% 500 KB 1 1 529,641 529,641 100.00% #filter contigs java -ea -Xmx200m -cp /DATA/markop/bbmap/current/ jgi.ReformatReads in=./output/contigs.fasta out=./output/contigs1to5k.fasta minlength=1000 maxlength=5999 Executing jgi.ReformatReads [in=./output/contigs.fasta, out=./output/contigs1to5k.fasta, minlength=1000, maxlength=5999] Input is being processed as unpaired Input: 5789416 reads 2176773479 bases Short Read Discards: 5443207 reads (94.02%) 1605718146 bases (73.77%) Output: 346209 reads (5.98%) 571055333 bases (26.23%) Time: 8.486 seconds. Reads Processed: 5789k 682.26k reads/sec Bases Processed: 2176m 256.52m bases/sec java -ea -Xmx200m -cp /DATA/markop/bbmap/current/ jgi.ReformatReads in=./output/contigs.fasta out=./output/contigs5kup.fasta minlength=5000 Executing jgi.ReformatReads [in=./output/contigs.fasta, out=./output/contigs5kup.fasta, minlength=5000] Input is being processed as unpaired Input: 5789416 reads 2176773479 bases Short Read Discards: 5779779 reads (99.83%) 2064674593 bases (94.85%) Output: 9637 reads (0.17%) 112098886 bases (5.15%) Time: 8.923 seconds. Reads Processed: 5789k 648.84k reads/sec Bases Processed: 2176m 243.96m bases/sec