RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kGflFH/RM_16176.SunJan151211492023 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: 1673813509 Database = /dev/shm/rModeler.kGflFH/GCF_015237465.2_rCheMyd1.pri.v2 - Sequences = 93 - Bases = 2134375114 Storage Throughput = excellent ( 1164.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40219768 bp ( 40019068 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:03:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:24 (hh:mm:ss) Elapsed Time Round Time: 00:25:38 (hh:mm:ss) Elapsed Time : 544 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13709 repeats masked totaling 2690090 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000594 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000494 bp After Masking: 7252531 bp Masked: 27.48 % -- Input Database Coverage: 10000594 bp out of 2134375114 bp ( 0.47 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 14913 HSPs Collected Number of families returned by RECON: 1772 Round Time: 00:07:53 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45879 repeats masked totaling 9248787 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30219094 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30018494 bp After Masking: 20611028 bp Masked: 31.34 % -- Input Database Coverage: 40219688 bp out of 2134375114 bp ( 1.88 % ) Sampling Time: 00:04:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:27:27 (hh:mm:ss) Elapsed Time, 69471 HSPs Collected Number of families returned by RECON: 5200 Round Time: 00:34:23 (hh:mm:ss) Elapsed Time : 140 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 156595 repeats masked totaling 31261200 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90459757 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90002839 bp After Masking: 58087712 bp Masked: 35.46 % -- Input Database Coverage: 130679445 bp out of 2134375114 bp ( 6.12 % ) Sampling Time: 00:13:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:38:10 (hh:mm:ss) Elapsed Time, 267170 HSPs Collected Number of families returned by RECON: 13805 Round Time: 03:04:21 (hh:mm:ss) Elapsed Time : 474 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:28:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 541048 repeats masked totaling 110704398 bp(s). - TE Masking time 00:10:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271653100 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 270026182 bp After Masking: 157503320 bp Masked: 41.67 % -- Input Database Coverage: 402332545 bp out of 2134375114 bp ( 18.85 % ) Sampling Time: 00:48:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 18:03:28 (hh:mm:ss) Elapsed Time, 536485 HSPs Collected Number of families returned by RECON: 45271 Round Time: 19:52:50 (hh:mm:ss) Elapsed Time : 1000 families discovered. RepeatScout/RECON discovery complete: 2185 families found Classification Time: 01:17:37 (hh:mm:ss) Elapsed Time Program Time: 25:22:42 (hh:mm:ss) Elapsed Time