RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Nr2Co2/RM_1391549.TueDec51744332023 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: 1701827073 Database = /dev/shm/rModeler.Nr2Co2/GCF_003957555.1_bCalAnn1_v1.p - Sequences = 159 - Bases = 1059687259 - N50 = 114810999 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 184381261-197551010 | [ 1 ] 171211512-184381260 | [ ] 158041763-171211511 | [ ] 144872014-158041762 | [ 1 ] 131702265-144872013 | [ ] 118532516-131702264 | [ ] 105362767-118532515 | [ 1 ] 92193019-105362767 | [ ] 79023270-92193018 | [ ] 65853521-79023269 | [ 1 ] 52683772-65853520 | [ ] 39514023-52683771 | [ 2 ] 26344274-39514022 |* [ 4 ] 13174525-26344273 |*** [ 11 ] 4777-13174525 |************************************************** [ 138 ] Storage Throughput = excellent ( 1348.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40847087 bp ( 40039318 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:19 (hh:mm:ss) Elapsed Time Round Time: 00:21:09 (hh:mm:ss) Elapsed Time : 91 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 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3009 repeats masked totaling 838241 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10265525 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10005765 bp After Masking: 9080485 bp Masked: 9.25 % -- Input Database Coverage: 10265525 bp out of 1059687259 bp ( 0.97 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:07:03 (hh:mm:ss) Elapsed Time, 604 HSPs Collected Number of families returned by RECON: 298 Round Time: 00:08:13 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:38 (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... 8546 repeats masked totaling 2460903 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30581560 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30033551 bp After Masking: 27270994 bp Masked: 9.20 % -- Input Database Coverage: 40847085 bp out of 1059687259 bp ( 3.85 % ) Sampling Time: 00:03:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:39:02 (hh:mm:ss) Elapsed Time, 5091 HSPs Collected Number of families returned by RECON: 1805 Round Time: 00:42:42 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24974 repeats masked totaling 7191446 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91415287 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 90027435 bp After Masking: 82069963 bp Masked: 8.84 % -- Input Database Coverage: 132262372 bp out of 1059687259 bp ( 12.48 % ) Sampling Time: 00:09:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2618616 Comparison Time: 04:49:55 (hh:mm:ss) Elapsed Time, 45705 HSPs Collected Number of families returned by RECON: 11844 Round Time: 05:02:23 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85986 repeats masked totaling 25036645 bp(s). - TE Masking time 00:02:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274821803 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 270038384 bp After Masking: 242780319 bp Masked: 10.09 % -- Input Database Coverage: 407084175 bp out of 1059687259 bp ( 38.42 % ) Sampling Time: 00:26:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23746386 Comparison Time: 34:52:10 (hh:mm:ss) Elapsed Time, 211918 HSPs Collected Number of families returned by RECON: 78471 Round Time: 36:19:19 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatScout/RECON discovery complete: 336 families found Classification Time: 00:21:46 (hh:mm:ss) Elapsed Time Program Time: 42:55:32 (hh:mm:ss) Elapsed Time