RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TA3UMm/RM_13567.WedJan110637432023 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: 1673447862 Database = /dev/shm/rModeler.TA3UMm/GCA_016128335.1_ZJU1.0 - Sequences = 802 - Bases = 1247468792 - N50 = 129390489 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201854500-216272475 | [ 1 ] 187436525-201854499 | [ ] 173018550-187436524 | [ ] 158600575-173018549 | [ 1 ] 144182600-158600574 | [ ] 129764625-144182599 | [ ] 115346650-129764624 | [ 1 ] 100928675-115346649 | [ ] 86510700-100928674 | [ ] 72092725-86510699 | [ 3 ] 57674750-72092724 | [ ] 43256775-57674749 | [ 1 ] 28838800-43256774 | [ 3 ] 14420825-28838799 | [ 9 ] 2851-14420825 |************************************************** [ 783 ] Storage Throughput = excellent ( 1199.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009606 bp ( 40007944 non ambiguous ) - Num Contigs Represented = 69 - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:47 (hh:mm:ss) Elapsed Time Round Time: 00:30:25 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 773 repeats masked totaling 296633 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009152 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10008452 bp After Masking: 9504939 bp Masked: 5.03 % -- Input Database Coverage: 10009152 bp out of 1247468792 bp ( 0.80 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:22 (hh:mm:ss) Elapsed Time, 1575 HSPs Collected Number of families returned by RECON: 351 Round Time: 00:09:27 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2562 repeats masked totaling 932533 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040374 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30039412 bp After Masking: 28463068 bp Masked: 5.25 % -- Input Database Coverage: 40049526 bp out of 1247468792 bp ( 3.21 % ) Sampling Time: 00:03:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:42:16 (hh:mm:ss) Elapsed Time, 8992 HSPs Collected Number of families returned by RECON: 1863 Round Time: 00:46:01 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10074 repeats masked totaling 3206033 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010519 bp Num Contigs Represented = 145 Non ambiguous bp: Initial: 90006731 bp After Masking: 84584411 bp Masked: 6.02 % -- Input Database Coverage: 130060045 bp out of 1247468792 bp ( 10.43 % ) Sampling Time: 00:10:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2604903 Comparison Time: 05:16:30 (hh:mm:ss) Elapsed Time, 56555 HSPs Collected Number of families returned by RECON: 10040 Round Time: 05:30:51 (hh:mm:ss) Elapsed Time : 85 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45784 repeats masked totaling 12972840 bp(s). - TE Masking time 00:02:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022075 bp Num Contigs Represented = 292 Non ambiguous bp: Initial: 270010471 bp After Masking: 251280686 bp Masked: 6.94 % -- Input Database Coverage: 400082120 bp out of 1247468792 bp ( 32.07 % ) Sampling Time: 00:31:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23492085 Comparison Time: 40:49:25 (hh:mm:ss) Elapsed Time, 218290 HSPs Collected Number of families returned by RECON: 62010 Round Time: 42:26:27 (hh:mm:ss) Elapsed Time : 298 families discovered. RepeatScout/RECON discovery complete: 447 families found Classification Time: 00:40:42 (hh:mm:ss) Elapsed Time Program Time: 50:03:53 (hh:mm:ss) Elapsed Time