RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.dCzXif/RM_11061.MonDec21728192024 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: 1733189297 Database = /scratch/tmp/rModeler.dCzXif/GCA_028885475.2_NHGRI_mGorGor1-v2.0_pat - Sequences = 24 - Bases = 3351856267 Storage Throughput = fair ( 619.15 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001483 bp ( 40001483 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:37 (hh:mm:ss) Elapsed Time Round Time: 00:56:22 (hh:mm:ss) Elapsed Time : 232 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11138 repeats masked totaling 2594379 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000253 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000253 bp After Masking: 5352043 bp Masked: 46.48 % -- Input Database Coverage: 10000253 bp out of 3351856267 bp ( 0.30 % ) Sampling Time: 00:08:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:42 (hh:mm:ss) Elapsed Time, 5385 HSPs Collected Number of families returned by RECON: 768 Round Time: 00:14:02 (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 : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38137 repeats masked totaling 8586004 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001150 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30001150 bp After Masking: 16334561 bp Masked: 45.55 % -- Input Database Coverage: 40001403 bp out of 3351856267 bp ( 1.19 % ) Sampling Time: 00:24:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:23:56 (hh:mm:ss) Elapsed Time, 22644 HSPs Collected Number of families returned by RECON: 1965 Round Time: 00:50:04 (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 : 00:03:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:10:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118513 repeats masked totaling 27171815 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90070140 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90030140 bp After Masking: 45975330 bp Masked: 48.93 % -- Input Database Coverage: 130071543 bp out of 3351856267 bp ( 3.88 % ) Sampling Time: 01:15:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:29:09 (hh:mm:ss) Elapsed Time, 88084 HSPs Collected Number of families returned by RECON: 6472 Round Time: 03:52:30 (hh:mm:ss) Elapsed Time : 184 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:18:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 388089 repeats masked totaling 89217888 bp(s). - TE Masking time 00:06:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270198692 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270038692 bp After Masking: 131406688 bp Masked: 51.34 % -- Input Database Coverage: 400270235 bp out of 3351856267 bp ( 11.94 % ) Sampling Time: 03:37:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 18:51:46 (hh:mm:ss) Elapsed Time, 270814 HSPs Collected Number of families returned by RECON: 25067 Round Time: 23:03:58 (hh:mm:ss) Elapsed Time : 337 families discovered. RepeatScout/RECON discovery complete: 828 families found Classification Time: 00:40:28 (hh:mm:ss) Elapsed Time Program Time: 29:37:24 (hh:mm:ss) Elapsed Time