RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JyhWds/RM_2509945.SatMar91754122024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1710035651 Database = /dev/shm/rModeler.JyhWds/GCA_003287225.2_phaCin_HiC - Sequences = 1246 - Bases = 3192631935 - N50 = 480246837 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 681730675-730425699 | [ 1 ] 633035652-681730675 | [ ] 584340629-633035652 | [ ] 535645606-584340629 | [ ] 486950583-535645606 | [ ] 438255560-486950583 | [ 1 ] 389560537-438255560 | [ 2 ] 340865514-389560537 | [ ] 292170491-340865514 | [ 1 ] 243475468-292170491 | [ 2 ] 194780445-243475468 | [ 1 ] 146085422-194780445 | [ ] 97390399-146085422 | [ ] 48695376-97390399 | [ 1 ] 353-48695376 |************************************************** [ 1237 ] Storage Throughput = excellent ( 1194.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010179 bp ( 40009679 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:08:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:08 (hh:mm:ss) Elapsed Time Round Time: 00:27:51 (hh:mm:ss) Elapsed Time : 329 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27418 repeats masked totaling 3835475 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012808 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10012608 bp After Masking: 6038707 bp Masked: 39.69 % -- Input Database Coverage: 10012808 bp out of 3192631935 bp ( 0.31 % ) Sampling Time: 00:02:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:02 (hh:mm:ss) Elapsed Time, 11197 HSPs Collected Number of families returned by RECON: 1137 Round Time: 00:09:34 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 83911 repeats masked totaling 12929938 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037291 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30036991 bp After Masking: 16681641 bp Masked: 44.46 % -- Input Database Coverage: 40050099 bp out of 3192631935 bp ( 1.25 % ) Sampling Time: 00:09:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:27:17 (hh:mm:ss) Elapsed Time, 33740 HSPs Collected Number of families returned by RECON: 3002 Round Time: 00:37:18 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:19:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 266979 repeats masked totaling 41465128 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010516 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90008516 bp After Masking: 47292608 bp Masked: 47.46 % -- Input Database Coverage: 130060615 bp out of 3192631935 bp ( 4.07 % ) Sampling Time: 00:25:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:33:43 (hh:mm:ss) Elapsed Time, 101108 HSPs Collected Number of families returned by RECON: 9962 Round Time: 03:02:40 (hh:mm:ss) Elapsed Time : 214 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:58:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 876423 repeats masked totaling 135003796 bp(s). - TE Masking time 00:06:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012628 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 270006927 bp After Masking: 131212501 bp Masked: 51.40 % -- Input Database Coverage: 400073243 bp out of 3192631935 bp ( 12.53 % ) Sampling Time: 01:17:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23191455 Comparison Time: 17:06:17 (hh:mm:ss) Elapsed Time, 247577 HSPs Collected Number of families returned by RECON: 35390 Round Time: 18:56:48 (hh:mm:ss) Elapsed Time : 529 families discovered. RepeatScout/RECON discovery complete: 1164 families found Classification Time: 00:35:00 (hh:mm:ss) Elapsed Time Program Time: 23:49:11 (hh:mm:ss) Elapsed Time