RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.LYgev9/RM_1689313.FriApr180439132025 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: 1744976352 Database = /data/tmp/rModeler.LYgev9/GCA_964341485.1_mMesMir1.hap2.1 - Sequences = 1384 - Bases = 2956530355 - N50 = 115648949 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 213238520-228469772 | [ 1 ] 198007269-213238520 | [ ] 182776017-198007268 | [ 3 ] 167544766-182776017 | [ ] 152313514-167544765 | [ ] 137082263-152313514 | [ 3 ] 121851011-137082262 | [ ] 106619760-121851011 | [ 4 ] 91388508-106619759 | [ 3 ] 76157257-91388508 | [ 4 ] 60926005-76157256 | [ 2 ] 45694754-60926005 | [ ] 30463502-45694753 | [ 1 ] 15232251-30463502 | [ ] 1000-15232251 |************************************************** [ 1363 ] Storage Throughput = excellent ( 1257.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018342 bp ( 40015542 non ambiguous ) - Num Contigs Represented = 150 - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:02 (hh:mm:ss) Elapsed Time Round Time: 00:38:46 (hh:mm:ss) Elapsed Time : 201 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10552 repeats masked totaling 3025896 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011245 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10010045 bp After Masking: 6351239 bp Masked: 36.55 % -- Input Database Coverage: 10011245 bp out of 2956530355 bp ( 0.34 % ) Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:19 (hh:mm:ss) Elapsed Time, 56169 HSPs Collected Number of families returned by RECON: 658 Round Time: 00:09:06 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33446 repeats masked totaling 9771567 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007093 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 30005493 bp After Masking: 17966374 bp Masked: 40.12 % -- Input Database Coverage: 40018338 bp out of 2956530355 bp ( 1.35 % ) Sampling Time: 00:04:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:23:36 (hh:mm:ss) Elapsed Time, 60402 HSPs Collected Number of families returned by RECON: 2384 Round Time: 00:31:56 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114060 repeats masked totaling 32377541 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012689 bp Num Contigs Represented = 261 Non ambiguous bp: Initial: 90006089 bp After Masking: 52673331 bp Masked: 41.48 % -- Input Database Coverage: 130031027 bp out of 2956530355 bp ( 4.40 % ) Sampling Time: 00:13:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2598060 Comparison Time: 02:19:12 (hh:mm:ss) Elapsed Time, 686091 HSPs Collected Number of families returned by RECON: 7842 Round Time: 02:43:10 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 379039 repeats masked totaling 106383945 bp(s). - TE Masking time 00:05:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020961 bp Num Contigs Represented = 578 Non ambiguous bp: Initial: 270000086 bp After Masking: 145150743 bp Masked: 46.24 % -- Input Database Coverage: 400051988 bp out of 2956530355 bp ( 13.53 % ) Sampling Time: 00:47:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23259610 Comparison Time: 18:24:48 (hh:mm:ss) Elapsed Time, 1430058 HSPs Collected Number of families returned by RECON: 27122 Round Time: 20:00:40 (hh:mm:ss) Elapsed Time : 393 families discovered. RepeatScout/RECON discovery complete: 848 families found Classification Time: 01:00:58 (hh:mm:ss) Elapsed Time Program Time: 25:04:36 (hh:mm:ss) Elapsed Time