RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.G9W6E0/RM_21914.SatJul62310222024 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: 1720332620 Database = /dev/shm/rModeler.G9W6E0/GCF_001443285.1_P_latipinna-1.0 - Sequences = 17986 - Bases = 815142410 - N50 = 279238 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1756502-1881953 | [ 1 ] 1631052-1756502 | [ 1 ] 1505602-1631052 | [ ] 1380152-1505602 | [ 4 ] 1254702-1380152 | [ 4 ] 1129251-1254701 | [ 4 ] 1003801-1129251 | [ 5 ] 878351-1003801 | [ 16 ] 752901-878351 | [ 34 ] 627451-752901 | [ 59 ] 502000-627450 | [ 129 ] 376550-502000 | [ 257 ] 251100-376550 |* [ 503 ] 125650-251100 |*** [ 1022 ] 200-125650 |************************************************** [ 15947 ] Storage Throughput = excellent ( 1021.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 48368060 bp ( 40027559 non ambiguous ) - Num Contigs Represented = 1880 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:34 (hh:mm:ss) Elapsed Time Round Time: 00:24:11 (hh:mm:ss) Elapsed Time : 500 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9530 repeats masked totaling 1110985 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 12100227 bp Num Contigs Represented = 520 Non ambiguous bp: Initial: 10023579 bp After Masking: 8821398 bp Masked: 11.99 % -- Input Database Coverage: 12100227 bp out of 815142410 bp ( 1.48 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 144991 Comparison Time: 00:08:58 (hh:mm:ss) Elapsed Time, 13394 HSPs Collected Number of families returned by RECON: 1701 Round Time: 00:10:09 (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 : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32745 repeats masked totaling 4153900 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 36267772 bp Num Contigs Represented = 1440 Non ambiguous bp: Initial: 30003919 bp After Masking: 25579566 bp Masked: 14.75 % -- Input Database Coverage: 48367999 bp out of 815142410 bp ( 5.93 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1252153 Comparison Time: 00:52:11 (hh:mm:ss) Elapsed Time, 54383 HSPs Collected Number of families returned by RECON: 5050 Round Time: 00:55:37 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115003 repeats masked totaling 15259670 bp(s). - TE Masking time 00:01:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 108136706 bp Num Contigs Represented = 3611 Non ambiguous bp: Initial: 90035668 bp After Masking: 73953782 bp Masked: 17.86 % -- Input Database Coverage: 156504705 bp out of 815142410 bp ( 19.20 % ) Sampling Time: 00:04:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 10453878 Comparison Time: 06:12:19 (hh:mm:ss) Elapsed Time, 209102 HSPs Collected Number of families returned by RECON: 17968 Round Time: 06:29:55 (hh:mm:ss) Elapsed Time : 414 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 401021 repeats masked totaling 57292636 bp(s). - TE Masking time 00:11:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 323492148 bp Num Contigs Represented = 8855 Non ambiguous bp: Initial: 270000197 bp After Masking: 210314827 bp Masked: 22.11 % -- Input Database Coverage: 479996853 bp out of 815142410 bp ( 58.89 % ) Sampling Time: 00:20:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 98623990 Comparison Time: 49:56:15 (hh:mm:ss) Elapsed Time, 640755 HSPs Collected Number of families returned by RECON: 67612 Round Time: 52:14:10 (hh:mm:ss) Elapsed Time : 988 families discovered. RepeatScout/RECON discovery complete: 2044 families found Classification Time: 01:30:05 (hh:mm:ss) Elapsed Time Program Time: 61:44:07 (hh:mm:ss) Elapsed Time