RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3oZ8Ni/RM_3637.MonJan90612142023 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: 1673273533 Database = /dev/shm/rModeler.3oZ8Ni/GCA_020745775.1_bTheCae1.pri.cur - Sequences = 88 - Bases = 1203372763 Storage Throughput = excellent ( 1135.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014452 bp ( 40013029 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:20 (hh:mm:ss) Elapsed Time Round Time: 00:26:39 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1152 repeats masked totaling 534104 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004834 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10004834 bp After Masking: 9443810 bp Masked: 5.61 % -- Input Database Coverage: 10004834 bp out of 1203372763 bp ( 0.83 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:02 (hh:mm:ss) Elapsed Time, 827 HSPs Collected Number of families returned by RECON: 292 Round Time: 00:08:04 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:36 (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... 3327 repeats masked totaling 1477647 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009616 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30008193 bp After Masking: 28355353 bp Masked: 5.51 % -- Input Database Coverage: 40014450 bp out of 1203372763 bp ( 3.33 % ) Sampling Time: 00:02:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:39:16 (hh:mm:ss) Elapsed Time, 7201 HSPs Collected Number of families returned by RECON: 1674 Round Time: 00:42:21 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12677 repeats masked totaling 5071464 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90156752 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90012090 bp After Masking: 84448399 bp Masked: 6.18 % -- Input Database Coverage: 130171202 bp out of 1203372763 bp ( 10.82 % ) Sampling Time: 00:07:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 04:51:35 (hh:mm:ss) Elapsed Time, 33648 HSPs Collected Number of families returned by RECON: 9138 Round Time: 05:02:21 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49853 repeats masked totaling 18099804 bp(s). - TE Masking time 00:01:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270540220 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 270027212 bp After Masking: 250448133 bp Masked: 7.25 % -- Input Database Coverage: 400711422 bp out of 1203372763 bp ( 33.30 % ) Sampling Time: 00:24:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 39:43:12 (hh:mm:ss) Elapsed Time, 191715 HSPs Collected Number of families returned by RECON: 60562 Round Time: 41:02:12 (hh:mm:ss) Elapsed Time : 233 families discovered. RepeatScout/RECON discovery complete: 356 families found Classification Time: 00:21:28 (hh:mm:ss) Elapsed Time Program Time: 47:43:05 (hh:mm:ss) Elapsed Time