RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/013/358/685/GCA_013358685.1_fAntMac1.pri/trackData/repeatModeler/RM_3252.MonDec262134052022 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: 1672119242 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/013/358/685/GCA_013358685.1_fAntMac1.pri/trackData/repeatModeler/GCA_013358685.1_fAntMac1.pri - Sequences = 155 - Bases = 549949511 - N50 = 24806454 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29619366-31734190 | [ 1 ] 27504542-29619365 |* [ 3 ] 25389718-27504541 |* [ 3 ] 23274894-25389717 |* [ 3 ] 21160071-23274894 |* [ 3 ] 19045247-21160070 |* [ 5 ] 16930423-19045246 |* [ 3 ] 14815599-16930422 | [ 1 ] 12700775-14815598 | [ 1 ] 10585952-12700775 | [ 1 ] 8471128-10585951 | [ ] 6356304-8471127 | [ ] 4241480-6356303 | [ ] 2126656-4241479 | [ ] 11833-2126656 |************************************************** [ 131 ] Storage Throughput = good ( 720.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40070364 bp ( 40026589 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:15 (hh:mm:ss) Elapsed Time Round Time: 00:32:35 (hh:mm:ss) Elapsed Time : 381 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6045 repeats masked totaling 1511331 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018066 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10016966 bp After Masking: 7879273 bp Masked: 21.34 % -- Input Database Coverage: 10018066 bp out of 549949511 bp ( 1.82 % ) Sampling Time: 00:01:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:16 (hh:mm:ss) Elapsed Time, 2453 HSPs Collected Number of families returned by RECON: 736 Round Time: 00:08:27 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19783 repeats masked totaling 4981596 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30052297 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30009622 bp After Masking: 23533083 bp Masked: 21.58 % -- Input Database Coverage: 40070363 bp out of 549949511 bp ( 7.29 % ) Sampling Time: 00:04:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:33:42 (hh:mm:ss) Elapsed Time, 22088 HSPs Collected Number of families returned by RECON: 3306 Round Time: 00:41:41 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60734 repeats masked totaling 14656555 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90133590 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 90003666 bp After Masking: 70509119 bp Masked: 21.66 % -- Input Database Coverage: 130203953 bp out of 549949511 bp ( 23.68 % ) Sampling Time: 00:13:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:55:53 (hh:mm:ss) Elapsed Time, 133050 HSPs Collected Number of families returned by RECON: 12937 Round Time: 04:29:36 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 217450 repeats masked totaling 50858431 bp(s). - TE Masking time 00:06:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270487610 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 270016265 bp After Masking: 204533204 bp Masked: 24.25 % -- Input Database Coverage: 400691563 bp out of 549949511 bp ( 72.86 % ) Sampling Time: 00:42:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23089410 Comparison Time: 31:00:42 (hh:mm:ss) Elapsed Time, 742355 HSPs Collected Number of families returned by RECON: 57598 Round Time: 34:34:11 (hh:mm:ss) Elapsed Time : 693 families discovered. RepeatScout/RECON discovery complete: 1387 families found Classification Time: 01:05:18 (hh:mm:ss) Elapsed Time Program Time: 41:31:48 (hh:mm:ss) Elapsed Time