RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.iyJOG0/RM_7452.SunDec81312122024 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: 1733692331 Database = /scratch/tmp/rModeler.iyJOG0/GCA_039656995.1_mGloMut1.hap2 - Sequences = 71 - Bases = 2156622230 Storage Throughput = fair ( 595.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035934 bp ( 40035434 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:03:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:43 (hh:mm:ss) Elapsed Time Round Time: 00:32:24 (hh:mm:ss) Elapsed Time : 209 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8936 repeats masked totaling 2565809 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032586 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10032386 bp After Masking: 7425552 bp Masked: 25.98 % -- Input Database Coverage: 10032586 bp out of 2156622230 bp ( 0.47 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:07 (hh:mm:ss) Elapsed Time, 5537 HSPs Collected Number of families returned by RECON: 844 Round Time: 00:07:08 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:35 (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... 29675 repeats masked totaling 8004467 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003341 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 30003041 bp After Masking: 21895711 bp Masked: 27.02 % -- Input Database Coverage: 40035927 bp out of 2156622230 bp ( 1.86 % ) Sampling Time: 00:03:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:27:55 (hh:mm:ss) Elapsed Time, 23262 HSPs Collected Number of families returned by RECON: 2554 Round Time: 00:34:29 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99844 repeats masked totaling 27005293 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027320 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 90026720 bp After Masking: 62656607 bp Masked: 30.40 % -- Input Database Coverage: 130063247 bp out of 2156622230 bp ( 6.03 % ) Sampling Time: 00:11:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 03:20:07 (hh:mm:ss) Elapsed Time, 108375 HSPs Collected Number of families returned by RECON: 8180 Round Time: 03:42:06 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 335437 repeats masked totaling 88417972 bp(s). - TE Masking time 00:06:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270008802 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 270007502 bp After Masking: 180594089 bp Masked: 33.12 % -- Input Database Coverage: 400072049 bp out of 2156622230 bp ( 18.55 % ) Sampling Time: 00:37:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 25:44:46 (hh:mm:ss) Elapsed Time, 369587 HSPs Collected Number of families returned by RECON: 36431 Round Time: 27:26:10 (hh:mm:ss) Elapsed Time : 384 families discovered. RepeatScout/RECON discovery complete: 850 families found Classification Time: 00:42:39 (hh:mm:ss) Elapsed Time Program Time: 33:04:56 (hh:mm:ss) Elapsed Time