RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.swWN3d/RM_141206.TueJan101726262023 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: 1673400385 Database = /dev/shm/rModeler.swWN3d/GCA_017639555.1_bCicMag1.pri - Sequences = 153 - Bases = 1239437416 - N50 = 128636905 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 205676087-220367150 | [ 1 ] 190985024-205676086 | [ ] 176293961-190985023 | [ ] 161602898-176293960 | [ 1 ] 146911836-161602898 | [ ] 132220773-146911835 | [ ] 117529710-132220772 | [ 1 ] 102838647-117529709 | [ ] 88147584-102838646 | [ ] 73456522-88147584 | [ 2 ] 58765459-73456521 |* [ 3 ] 44074396-58765458 | [ 2 ] 29383333-44074395 | [ ] 14692270-29383332 |** [ 6 ] 1208-14692270 |************************************************* [ 137 ] Storage Throughput = fair ( 659.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40841422 bp ( 40032703 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:02:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:12 (hh:mm:ss) Elapsed Time Round Time: 00:26:32 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1037 repeats masked totaling 535260 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10302685 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10036230 bp After Masking: 9466919 bp Masked: 5.67 % -- Input Database Coverage: 10302685 bp out of 1239437416 bp ( 0.83 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:08:21 (hh:mm:ss) Elapsed Time, 819 HSPs Collected Number of families returned by RECON: 271 Round Time: 00:09:52 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3306 repeats masked totaling 1639440 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30578737 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30036473 bp After Masking: 28291288 bp Masked: 5.81 % -- Input Database Coverage: 40881422 bp out of 1239437416 bp ( 3.30 % ) Sampling Time: 00:04:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:43:46 (hh:mm:ss) Elapsed Time, 5829 HSPs Collected Number of families returned by RECON: 1594 Round Time: 00:48:16 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11554 repeats masked totaling 5109994 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91442751 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90035800 bp After Masking: 84617420 bp Masked: 6.02 % -- Input Database Coverage: 132324173 bp out of 1239437416 bp ( 10.68 % ) Sampling Time: 00:09:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2632365 Comparison Time: 04:39:05 (hh:mm:ss) Elapsed Time, 37244 HSPs Collected Number of families returned by RECON: 9576 Round Time: 04:52:03 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49711 repeats masked totaling 18650804 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274528208 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 270012789 bp After Masking: 250440852 bp Masked: 7.25 % -- Input Database Coverage: 406852381 bp out of 1239437416 bp ( 32.83 % ) Sampling Time: 00:29:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23650003 Comparison Time: 34:16:29 (hh:mm:ss) Elapsed Time, 167174 HSPs Collected Number of families returned by RECON: 60524 Round Time: 35:27:24 (hh:mm:ss) Elapsed Time : 214 families discovered. RepeatScout/RECON discovery complete: 340 families found Classification Time: 00:18:40 (hh:mm:ss) Elapsed Time Program Time: 42:02:47 (hh:mm:ss) Elapsed Time