RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.v1yffV/RM_13795.FriDec81724422023 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: 1702085081 Database = /dev/shm/rModeler.v1yffV/GCA_951394365.1_bTetUro1.1 - Sequences = 318 - Bases = 1013184029 - N50 = 76131576 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 180989477-193917226 | [ 1 ] 168061729-180989477 | [ ] 155133980-168061728 | [ ] 142206232-155133980 | [ ] 129278484-142206232 | [ ] 116350735-129278483 | [ ] 103422987-116350735 | [ 1 ] 90495238-103422986 | [ 1 ] 77567490-90495238 | [ ] 64639742-77567490 | [ 3 ] 51711993-64639741 | [ 2 ] 38784245-51711993 | [ ] 25856496-38784244 | [ 1 ] 12928748-25856496 |* [ 8 ] 1000-12928748 |************************************************** [ 301 ] Storage Throughput = excellent ( 1204.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038541 bp ( 40032774 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:17 (hh:mm:ss) Elapsed Time Round Time: 00:28:23 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3595 repeats masked totaling 875716 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015654 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10015254 bp After Masking: 9002094 bp Masked: 10.12 % -- Input Database Coverage: 10015654 bp out of 1013184029 bp ( 0.99 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:47 (hh:mm:ss) Elapsed Time, 482 HSPs Collected Number of families returned by RECON: 201 Round Time: 00:08:04 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11004 repeats masked totaling 2636165 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022807 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30017440 bp After Masking: 26840158 bp Masked: 10.58 % -- Input Database Coverage: 40038461 bp out of 1013184029 bp ( 3.95 % ) Sampling Time: 00:03:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:40:49 (hh:mm:ss) Elapsed Time, 5297 HSPs Collected Number of families returned by RECON: 1446 Round Time: 00:44:26 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34080 repeats masked totaling 8038419 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024593 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90007676 bp After Masking: 80739481 bp Masked: 10.30 % -- Input Database Coverage: 130063054 bp out of 1013184029 bp ( 12.84 % ) Sampling Time: 00:08:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 05:16:02 (hh:mm:ss) Elapsed Time, 34803 HSPs Collected Number of families returned by RECON: 9802 Round Time: 05:32:46 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109706 repeats masked totaling 25981668 bp(s). - TE Masking time 00:04:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270064959 bp Num Contigs Represented = 139 Non ambiguous bp: Initial: 270010683 bp After Masking: 239787616 bp Masked: 11.19 % -- Input Database Coverage: 400128013 bp out of 1013184029 bp ( 39.49 % ) Sampling Time: 00:30:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23089410 Comparison Time: 44:01:18 (hh:mm:ss) Elapsed Time, 190962 HSPs Collected Number of families returned by RECON: 66630 Round Time: 45:33:05 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatScout/RECON discovery complete: 336 families found Classification Time: 00:31:04 (hh:mm:ss) Elapsed Time Program Time: 52:57:48 (hh:mm:ss) Elapsed Time