RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3DKaRt/RM_176846.MonJan160510572023 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: 1673874655 Database = /dev/shm/rModeler.3DKaRt/GCF_004115215.2_mOrnAna1.pri.v4 - Sequences = 322 - Bases = 1859281927 - N50 = 110293030 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 174073029-186506016 | [ 1 ] 161640043-174073029 | [ 1 ] 149207057-161640043 | [ ] 136774071-149207057 | [ 1 ] 124341085-136774071 | [ 2 ] 111908099-124341085 | [ ] 99475113-111908099 | [ 1 ] 87042126-99475112 | [ ] 74609140-87042126 | [ 1 ] 62176154-74609140 | [ 3 ] 49743168-62176154 | [ 5 ] 37310182-49743168 | [ 4 ] 24877196-37310182 | [ 5 ] 12444210-24877196 | [ 1 ] 11224-12444210 |************************************************** [ 297 ] Storage Throughput = excellent ( 1679.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40358040 bp ( 40036985 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:35 (hh:mm:ss) Elapsed Time Round Time: 00:22:28 (hh:mm:ss) Elapsed Time : 264 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 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34712 repeats masked totaling 4683854 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040885 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10000676 bp After Masking: 5110967 bp Masked: 48.89 % -- Input Database Coverage: 10040885 bp out of 1859281927 bp ( 0.54 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:56 (hh:mm:ss) Elapsed Time, 33130 HSPs Collected Number of families returned by RECON: 447 Round Time: 00:07:22 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112628 repeats masked totaling 14637465 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30317141 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30036295 bp After Masking: 14941543 bp Masked: 50.26 % -- Input Database Coverage: 40358026 bp out of 1859281927 bp ( 2.17 % ) Sampling Time: 00:03:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:23:52 (hh:mm:ss) Elapsed Time, 88006 HSPs Collected Number of families returned by RECON: 1380 Round Time: 00:27:49 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 344517 repeats masked totaling 44882221 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90419596 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90022276 bp After Masking: 43929387 bp Masked: 51.20 % -- Input Database Coverage: 130777622 bp out of 1859281927 bp ( 7.03 % ) Sampling Time: 00:08:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 01:57:04 (hh:mm:ss) Elapsed Time, 761509 HSPs Collected Number of families returned by RECON: 5439 Round Time: 02:07:31 (hh:mm:ss) Elapsed Time : 112 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1042555 repeats masked totaling 136839169 bp(s). - TE Masking time 00:07:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272108807 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 270024217 bp After Masking: 129127681 bp Masked: 52.18 % -- Input Database Coverage: 402886429 bp out of 1859281927 bp ( 21.67 % ) Sampling Time: 00:30:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23259610 Comparison Time: 13:25:34 (hh:mm:ss) Elapsed Time, 5913107 HSPs Collected Number of families returned by RECON: 23257 Round Time: 14:08:20 (hh:mm:ss) Elapsed Time : 287 families discovered. RepeatScout/RECON discovery complete: 701 families found Classification Time: 00:12:23 (hh:mm:ss) Elapsed Time Program Time: 17:25:53 (hh:mm:ss) Elapsed Time