input/log.txt

Version 1

#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