RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jvHCSj/RM_10343.FriJan122036212024 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: 1705120578 Database = /dev/shm/rModeler.jvHCSj/GCA_031878655.1_mTapInd1.hap1 - Sequences = 259 - Bases = 2498393425 - N50 = 135063271 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 160663274-172138183 | [ 1 ] 149188366-160663274 | [ 3 ] 137713458-149188366 | [ 3 ] 126238549-137713457 | [ 3 ] 114763641-126238549 | [ 1 ] 103288733-114763641 | [ ] 91813825-103288733 | [ 2 ] 80338916-91813824 | [ 2 ] 68864008-80338916 | [ ] 57389100-68864008 | [ 2 ] 45914192-57389100 | [ 3 ] 34439283-45914191 | [ 4 ] 22964375-34439283 | [ 2 ] 11489467-22964375 | [ ] 14559-11489467 |************************************************** [ 233 ] Storage Throughput = excellent ( 1141.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027460 bp ( 40027060 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:02:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:49 (hh:mm:ss) Elapsed Time Round Time: 00:36:33 (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 : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10383 repeats masked totaling 2359788 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018885 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10018685 bp After Masking: 7629259 bp Masked: 23.85 % -- Input Database Coverage: 10018885 bp out of 2498393425 bp ( 0.40 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:16:22 (hh:mm:ss) Elapsed Time, 40842 HSPs Collected Number of families returned by RECON: 1067 Round Time: 00:18:21 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34145 repeats masked totaling 7960028 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008495 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30008295 bp After Masking: 21979014 bp Masked: 26.76 % -- Input Database Coverage: 40027380 bp out of 2498393425 bp ( 1.60 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:59:18 (hh:mm:ss) Elapsed Time, 303508 HSPs Collected Number of families returned by RECON: 2606 Round Time: 01:05:27 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113110 repeats masked totaling 26448428 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027929 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 90027529 bp After Masking: 63237920 bp Masked: 29.76 % -- Input Database Coverage: 130055309 bp out of 2498393425 bp ( 5.21 % ) Sampling Time: 00:10:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 04:56:43 (hh:mm:ss) Elapsed Time, 3206575 HSPs Collected Number of families returned by RECON: 10104 Round Time: 05:14:18 (hh:mm:ss) Elapsed Time : 196 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 387748 repeats masked totaling 91182865 bp(s). - TE Masking time 00:07:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020601 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 270019201 bp After Masking: 177994178 bp Masked: 34.08 % -- Input Database Coverage: 400075910 bp out of 2498393425 bp ( 16.01 % ) Sampling Time: 00:31:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 35:36:52 (hh:mm:ss) Elapsed Time, 32595251 HSPs Collected Number of families returned by RECON: 37651 Round Time: 37:01:51 (hh:mm:ss) Elapsed Time : 411 families discovered. RepeatScout/RECON discovery complete: 936 families found Classification Time: 00:50:42 (hh:mm:ss) Elapsed Time Program Time: 45:07:12 (hh:mm:ss) Elapsed Time