RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UPaEdv/RM_226924.SunJan150852362023 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: 1673801555 Database = /dev/shm/rModeler.UPaEdv/GCF_009764565.3_rDerCor1.pri.v4 - Sequences = 40 - Bases = 2164762090 Storage Throughput = excellent ( 1137.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40202733 bp ( 40018408 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:41 (hh:mm:ss) Elapsed Time Round Time: 00:24:39 (hh:mm:ss) Elapsed Time : 490 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14415 repeats masked totaling 3019131 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10120717 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10031649 bp After Masking: 6934125 bp Masked: 30.88 % -- Input Database Coverage: 10120717 bp out of 2164762090 bp ( 0.47 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:53 (hh:mm:ss) Elapsed Time, 16841 HSPs Collected Number of families returned by RECON: 1807 Round Time: 00:07:19 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46487 repeats masked totaling 9846684 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30121857 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30026600 bp After Masking: 20020439 bp Masked: 33.32 % -- Input Database Coverage: 40242574 bp out of 2164762090 bp ( 1.86 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:23:45 (hh:mm:ss) Elapsed Time, 67006 HSPs Collected Number of families returned by RECON: 4962 Round Time: 00:28:49 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157746 repeats masked totaling 33852958 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90085883 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 90036612 bp After Masking: 55681496 bp Masked: 38.16 % -- Input Database Coverage: 130328457 bp out of 2164762090 bp ( 6.02 % ) Sampling Time: 00:09:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 02:00:39 (hh:mm:ss) Elapsed Time, 207332 HSPs Collected Number of families returned by RECON: 13467 Round Time: 02:16:17 (hh:mm:ss) Elapsed Time : 395 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:25:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 526291 repeats masked totaling 113879818 bp(s). - TE Masking time 00:05:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270719957 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 270009973 bp After Masking: 154418128 bp Masked: 42.81 % -- Input Database Coverage: 401048414 bp out of 2164762090 bp ( 18.53 % ) Sampling Time: 00:40:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 12:49:31 (hh:mm:ss) Elapsed Time, 497352 HSPs Collected Number of families returned by RECON: 43653 Round Time: 14:09:02 (hh:mm:ss) Elapsed Time : 978 families discovered. RepeatScout/RECON discovery complete: 2053 families found Classification Time: 00:52:59 (hh:mm:ss) Elapsed Time Program Time: 18:19:05 (hh:mm:ss) Elapsed Time