RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hoH16Z/RM_13950.FriDec81951512023 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: 1702093909 Database = /dev/shm/rModeler.hoH16Z/GCA_951640355.1_mEptNil1.1 - Sequences = 207 - Bases = 2064119045 - N50 = 103318240 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 124240326-133114493 | [ 1 ] 115366160-124240326 | [ 2 ] 106491994-115366160 |* [ 4 ] 97617828-106491994 | [ 3 ] 88743662-97617828 | [ 2 ] 79869495-88743661 | [ 3 ] 70995329-79869495 | [ 1 ] 62121163-70995329 | [ 1 ] 53246997-62121163 | [ 2 ] 44372831-53246997 | [ 3 ] 35498664-44372830 | [ ] 26624498-35498664 | [ 1 ] 17750332-26624498 | [ 1 ] 8876166-17750332 | [ 2 ] 2000-8876166 |************************************************** [ 181 ] Storage Throughput = excellent ( 1101.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012808 bp ( 40006608 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:01:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:02 (hh:mm:ss) Elapsed Time Round Time: 00:31:47 (hh:mm:ss) Elapsed Time : 350 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15090 repeats masked totaling 2702499 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036006 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10034406 bp After Masking: 7085035 bp Masked: 29.39 % -- Input Database Coverage: 10036006 bp out of 2064119045 bp ( 0.49 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:55 (hh:mm:ss) Elapsed Time, 9175 HSPs Collected Number of families returned by RECON: 847 Round Time: 00:07:41 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46129 repeats masked totaling 8596869 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016722 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30012122 bp After Masking: 20211279 bp Masked: 32.66 % -- Input Database Coverage: 40052728 bp out of 2064119045 bp ( 1.94 % ) Sampling Time: 00:03:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:29:39 (hh:mm:ss) Elapsed Time, 176744 HSPs Collected Number of families returned by RECON: 2262 Round Time: 00:34:28 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 148235 repeats masked totaling 26915874 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028902 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90017973 bp After Masking: 59813291 bp Masked: 33.55 % -- Input Database Coverage: 130081630 bp out of 2064119045 bp ( 6.30 % ) Sampling Time: 00:10:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:20:24 (hh:mm:ss) Elapsed Time, 824582 HSPs Collected Number of families returned by RECON: 8597 Round Time: 03:36:22 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 482500 repeats masked totaling 88929913 bp(s). - TE Masking time 00:07:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270057440 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 270018094 bp After Masking: 171283137 bp Masked: 36.57 % -- Input Database Coverage: 400139070 bp out of 2064119045 bp ( 19.39 % ) Sampling Time: 00:33:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 25:49:27 (hh:mm:ss) Elapsed Time, 7592988 HSPs Collected Number of families returned by RECON: 33755 Round Time: 27:28:22 (hh:mm:ss) Elapsed Time : 455 families discovered. RepeatScout/RECON discovery complete: 1077 families found Classification Time: 00:46:18 (hh:mm:ss) Elapsed Time Program Time: 33:04:58 (hh:mm:ss) Elapsed Time