RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.b0tlLM/RM_16236.MonDec21728322024 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: 1733189309 Database = /scratch/tmp/rModeler.b0tlLM/GCA_028858825.2_NHGRI_mPanPan1-v2.0_pat - Sequences = 38 - Bases = 3076853215 Storage Throughput = fair ( 653.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40078810 bp ( 40038803 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:02 (hh:mm:ss) Elapsed Time Round Time: 00:32:41 (hh:mm:ss) Elapsed Time : 234 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14452 repeats masked totaling 2888476 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040193 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000186 bp After Masking: 6402867 bp Masked: 35.97 % -- Input Database Coverage: 10040193 bp out of 3076853215 bp ( 0.33 % ) Sampling Time: 00:02:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:01 (hh:mm:ss) Elapsed Time, 7586 HSPs Collected Number of families returned by RECON: 750 Round Time: 00:08:10 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42553 repeats masked totaling 8802873 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038537 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30038537 bp After Masking: 17634341 bp Masked: 41.29 % -- Input Database Coverage: 40078730 bp out of 3076853215 bp ( 1.30 % ) Sampling Time: 00:13:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:24:59 (hh:mm:ss) Elapsed Time, 21304 HSPs Collected Number of families returned by RECON: 2141 Round Time: 00:40:41 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 139163 repeats masked totaling 29181389 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90131744 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90015059 bp After Masking: 50442275 bp Masked: 43.96 % -- Input Database Coverage: 130210474 bp out of 3076853215 bp ( 4.23 % ) Sampling Time: 00:41:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:46:51 (hh:mm:ss) Elapsed Time, 102848 HSPs Collected Number of families returned by RECON: 7478 Round Time: 03:36:33 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:49:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 455046 repeats masked totaling 95197898 bp(s). - TE Masking time 00:07:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270383868 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270001920 bp After Masking: 144357360 bp Masked: 46.53 % -- Input Database Coverage: 400594342 bp out of 3076853215 bp ( 13.02 % ) Sampling Time: 02:08:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 21:17:05 (hh:mm:ss) Elapsed Time, 299765 HSPs Collected Number of families returned by RECON: 30648 Round Time: 24:47:34 (hh:mm:ss) Elapsed Time : 405 families discovered. RepeatScout/RECON discovery complete: 901 families found Classification Time: 00:42:49 (hh:mm:ss) Elapsed Time Program Time: 30:28:28 (hh:mm:ss) Elapsed Time