RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UKkJSe/RM_31375.WedMay101034182023 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: 1683740057 Database = /dev/shm/rModeler.UKkJSe/GCA_027887145.1_bAmmCau1.pri - Sequences = 282 - Bases = 1241209685 - N50 = 78532051 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146676973-157152855 | [ 1 ] 136201092-146676973 | [ ] 125725211-136201092 | [ ] 115249330-125725211 | [ 2 ] 104773449-115249330 | [ ] 94297568-104773449 | [ ] 83821687-94297568 | [ 1 ] 73345806-83821687 | [ 2 ] 62869925-73345806 | [ 1 ] 52394044-62869925 | [ ] 41918163-52394044 | [ 2 ] 31442282-41918163 | [ 1 ] 20966401-31442282 | [ 4 ] 10490520-20966401 |* [ 9 ] 14639-10490520 |************************************************** [ 259 ] Storage Throughput = excellent ( 1144.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027246 bp ( 40005020 non ambiguous ) - Num Contigs Represented = 85 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:28:45 (hh:mm:ss) Elapsed Time Round Time: 00:36:09 (hh:mm:ss) Elapsed Time : 155 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2959 repeats masked totaling 725853 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028670 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10007770 bp After Masking: 8034378 bp Masked: 19.72 % -- Input Database Coverage: 10028670 bp out of 1241209685 bp ( 0.81 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:08 (hh:mm:ss) Elapsed Time, 1078 HSPs Collected Number of families returned by RECON: 315 Round Time: 00:08:58 (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 : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8050 repeats masked totaling 2167028 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038652 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 30037326 bp After Masking: 24053425 bp Masked: 19.92 % -- Input Database Coverage: 40067322 bp out of 1241209685 bp ( 3.23 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:36:36 (hh:mm:ss) Elapsed Time, 7545 HSPs Collected Number of families returned by RECON: 1579 Round Time: 00:42:31 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25208 repeats masked totaling 6863255 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90294816 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 90010122 bp After Masking: 72493809 bp Masked: 19.46 % -- Input Database Coverage: 130362138 bp out of 1241209685 bp ( 10.50 % ) Sampling Time: 00:15:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 04:21:03 (hh:mm:ss) Elapsed Time, 98114 HSPs Collected Number of families returned by RECON: 10104 Round Time: 04:59:14 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 91756 repeats masked totaling 27784696 bp(s). - TE Masking time 00:06:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270591374 bp Num Contigs Represented = 191 Non ambiguous bp: Initial: 270023951 bp After Masking: 208879653 bp Masked: 22.64 % -- Input Database Coverage: 400953512 bp out of 1241209685 bp ( 32.30 % ) Sampling Time: 00:45:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 33:28:01 (hh:mm:ss) Elapsed Time, 463551 HSPs Collected Number of families returned by RECON: 63205 Round Time: 35:19:54 (hh:mm:ss) Elapsed Time : 262 families discovered. RepeatScout/RECON discovery complete: 546 families found Classification Time: 00:46:12 (hh:mm:ss) Elapsed Time Program Time: 42:32:58 (hh:mm:ss) Elapsed Time