RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.j7UidH/RM_24523.SatDec21958012023 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: 1701575880 Database = /dev/shm/rModeler.j7UidH/GCA_030412105.1_rCycPin1.hap1 - Sequences = 30 - Bases = 1983631412 Storage Throughput = excellent ( 1190.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001684 bp ( 40001684 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:05:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:20 (hh:mm:ss) Elapsed Time Round Time: 00:32:07 (hh:mm:ss) Elapsed Time : 438 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16513 repeats masked totaling 3090333 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000479 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10000479 bp After Masking: 6777625 bp Masked: 32.23 % -- Input Database Coverage: 10000479 bp out of 1983631412 bp ( 0.50 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:36 (hh:mm:ss) Elapsed Time, 13367 HSPs Collected Number of families returned by RECON: 1414 Round Time: 00:08:38 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54860 repeats masked totaling 10471493 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001204 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30001204 bp After Masking: 19358495 bp Masked: 35.47 % -- Input Database Coverage: 40001683 bp out of 1983631412 bp ( 2.02 % ) Sampling Time: 00:05:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:28:20 (hh:mm:ss) Elapsed Time, 43106 HSPs Collected Number of families returned by RECON: 3907 Round Time: 00:35:42 (hh:mm:ss) Elapsed Time : 110 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:12:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 176949 repeats masked totaling 34234864 bp(s). - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90163369 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 90027633 bp After Masking: 55208753 bp Masked: 38.68 % -- Input Database Coverage: 130165052 bp out of 1983631412 bp ( 6.56 % ) Sampling Time: 00:16:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:17:06 (hh:mm:ss) Elapsed Time, 177747 HSPs Collected Number of families returned by RECON: 12866 Round Time: 03:43:13 (hh:mm:ss) Elapsed Time : 337 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:36:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 580823 repeats masked totaling 113285512 bp(s). - TE Masking time 00:09:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270267569 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 270022453 bp After Masking: 154866587 bp Masked: 42.65 % -- Input Database Coverage: 400432621 bp out of 1983631412 bp ( 20.19 % ) Sampling Time: 00:53:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 23:21:51 (hh:mm:ss) Elapsed Time, 455099 HSPs Collected Number of families returned by RECON: 45441 Round Time: 25:19:53 (hh:mm:ss) Elapsed Time : 804 families discovered. RepeatScout/RECON discovery complete: 1729 families found Classification Time: 01:07:07 (hh:mm:ss) Elapsed Time Program Time: 31:26:40 (hh:mm:ss) Elapsed Time