RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3GuMhy/RM_24196.SunDec30321212023 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: 1701602480 Database = /dev/shm/rModeler.3GuMhy/GCA_030463535.1_fSalBra1.hap2 - Sequences = 104 - Bases = 1066501646 - N50 = 41637409 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 92763597-99388286 | [ 1 ] 86138909-92763597 | [ ] 79514220-86138908 | [ ] 72889532-79514220 | [ ] 66264843-72889531 | [ ] 59640155-66264843 | [ 1 ] 53015466-59640154 | [ ] 46390778-53015466 |** [ 4 ] 39766089-46390777 |*** [ 6 ] 33141401-39766089 |****** [ 10 ] 26516712-33141400 |* [ 3 ] 19892024-26516712 | [ ] 13267335-19892023 | [ ] 6642647-13267335 | [ ] 17959-6642647 |************************************************** [ 79 ] Storage Throughput = excellent ( 1134.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40381355 bp ( 40027635 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:02 (hh:mm:ss) Elapsed Time Round Time: 00:31:10 (hh:mm:ss) Elapsed Time : 729 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16400 repeats masked totaling 2403073 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10116438 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10037511 bp After Masking: 6606122 bp Masked: 34.19 % -- Input Database Coverage: 10116438 bp out of 1066501646 bp ( 0.95 % ) Sampling Time: 00:02:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:24 (hh:mm:ss) Elapsed Time, 10274 HSPs Collected Number of families returned by RECON: 1589 Round Time: 00:07:54 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51396 repeats masked totaling 7306553 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30304834 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30030041 bp After Masking: 19367328 bp Masked: 35.51 % -- Input Database Coverage: 40421272 bp out of 1066501646 bp ( 3.79 % ) Sampling Time: 00:06:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:28:26 (hh:mm:ss) Elapsed Time, 74772 HSPs Collected Number of families returned by RECON: 5909 Round Time: 00:39:22 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 169685 repeats masked totaling 23901753 bp(s). - TE Masking time 00:02:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90813231 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90031179 bp After Masking: 56701578 bp Masked: 37.02 % -- Input Database Coverage: 131234503 bp out of 1066501646 bp ( 12.31 % ) Sampling Time: 00:16:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 03:27:25 (hh:mm:ss) Elapsed Time, 347118 HSPs Collected Number of families returned by RECON: 17751 Round Time: 04:04:50 (hh:mm:ss) Elapsed Time : 475 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 598789 repeats masked totaling 87146738 bp(s). - TE Masking time 00:13:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272323400 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 270031498 bp After Masking: 152235000 bp Masked: 43.62 % -- Input Database Coverage: 403557903 bp out of 1066501646 bp ( 37.84 % ) Sampling Time: 00:59:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23239153 Comparison Time: 23:25:00 (hh:mm:ss) Elapsed Time, 851096 HSPs Collected Number of families returned by RECON: 54915 Round Time: 26:00:32 (hh:mm:ss) Elapsed Time : 1059 families discovered. RepeatScout/RECON discovery complete: 2448 families found Classification Time: 01:37:44 (hh:mm:ss) Elapsed Time Program Time: 33:01:32 (hh:mm:ss) Elapsed Time