RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.klA2BW/RM_1884604.SunJan212004392024 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: 1705896278 Database = /dev/shm/rModeler.klA2BW/GCA_028858845.2_NHGRI_mPanPan1-v2.0_mat - Sequences = 32 - Bases = 3210032406 Storage Throughput = excellent ( 1298.46 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001434 bp ( 40001434 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:17 (hh:mm:ss) Elapsed Time Round Time: 00:28:48 (hh:mm:ss) Elapsed Time : 246 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12148 repeats masked totaling 2864993 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000247 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000247 bp After Masking: 6097522 bp Masked: 39.03 % -- Input Database Coverage: 10000247 bp out of 3210032406 bp ( 0.31 % ) Sampling Time: 00:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:21 (hh:mm:ss) Elapsed Time, 5621 HSPs Collected Number of families returned by RECON: 824 Round Time: 00:08:46 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40703 repeats masked totaling 9423100 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001107 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30001107 bp After Masking: 17332812 bp Masked: 42.23 % -- Input Database Coverage: 40001354 bp out of 3210032406 bp ( 1.25 % ) Sampling Time: 00:10:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:26:49 (hh:mm:ss) Elapsed Time, 25937 HSPs Collected Number of families returned by RECON: 2438 Round Time: 00:38:12 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128958 repeats masked totaling 29566724 bp(s). - TE Masking time 00:01:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90164528 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90004524 bp After Masking: 50235421 bp Masked: 44.19 % -- Input Database Coverage: 130165882 bp out of 3210032406 bp ( 4.05 % ) Sampling Time: 00:32:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:32:30 (hh:mm:ss) Elapsed Time, 111632 HSPs Collected Number of families returned by RECON: 8046 Round Time: 03:08:08 (hh:mm:ss) Elapsed Time : 213 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:24:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 435361 repeats masked totaling 98331167 bp(s). - TE Masking time 00:06:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270247214 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270036628 bp After Masking: 143011378 bp Masked: 47.04 % -- Input Database Coverage: 400413096 bp out of 3210032406 bp ( 12.47 % ) Sampling Time: 01:39:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 22:21:39 (hh:mm:ss) Elapsed Time, 266851 HSPs Collected Number of families returned by RECON: 28035 Round Time: 24:22:47 (hh:mm:ss) Elapsed Time : 387 families discovered. RepeatScout/RECON discovery complete: 922 families found Classification Time: 00:41:17 (hh:mm:ss) Elapsed Time Program Time: 29:27:58 (hh:mm:ss) Elapsed Time