RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.87myqq/RM_298703.ThuJul251625042024 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: 1721949802 Database = /dev/shm/rModeler.87myqq/GCF_022458985.1_CIBA_Mcephalus_1.1 - Sequences = 24 - Bases = 634849760 Storage Throughput = good ( 955.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047193 bp ( 40035370 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:53 (hh:mm:ss) Elapsed Time Round Time: 00:48:52 (hh:mm:ss) Elapsed Time : 511 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8788 repeats masked totaling 1099022 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041720 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10038720 bp After Masking: 8778134 bp Masked: 12.56 % -- Input Database Coverage: 10041720 bp out of 634849760 bp ( 1.58 % ) Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 02:00:12 (hh:mm:ss) Elapsed Time, 5429 HSPs Collected Number of families returned by RECON: 1341 Round Time: 02:05:45 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26624 repeats masked totaling 3366095 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045388 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30036565 bp After Masking: 26156686 bp Masked: 12.92 % -- Input Database Coverage: 40087108 bp out of 634849760 bp ( 6.31 % ) Sampling Time: 00:04:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 05:17:55 (hh:mm:ss) Elapsed Time, 48467 HSPs Collected Number of families returned by RECON: 5572 Round Time: 05:32:45 (hh:mm:ss) Elapsed Time : 129 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92848 repeats masked totaling 11960764 bp(s). - TE Masking time 00:01:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90051055 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90023404 bp After Masking: 76707612 bp Masked: 14.79 % -- Input Database Coverage: 130138163 bp out of 634849760 bp ( 20.50 % ) Sampling Time: 00:06:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 14:31:17 (hh:mm:ss) Elapsed Time, 229125 HSPs Collected Number of families returned by RECON: 18290 Round Time: 15:10:25 (hh:mm:ss) Elapsed Time : 436 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 337980 repeats masked totaling 47179720 bp(s). - TE Masking time 00:07:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270142164 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270037705 bp After Masking: 218269615 bp Masked: 19.17 % -- Input Database Coverage: 400280327 bp out of 634849760 bp ( 63.05 % ) Sampling Time: 00:23:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 32:16:37 (hh:mm:ss) Elapsed Time, 785232 HSPs Collected Number of families returned by RECON: 73411 Round Time: 34:12:26 (hh:mm:ss) Elapsed Time : 1066 families discovered. RepeatScout/RECON discovery complete: 2149 families found Classification Time: 01:30:14 (hh:mm:ss) Elapsed Time Program Time: 59:20:27 (hh:mm:ss) Elapsed Time