RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.pkUq1Z/RM_2115053.FriApr110714382025 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: 1744380877 Database = /data/tmp/rModeler.pkUq1Z/GCA_964662115.1_mMusNiv2.hap1.1 - Sequences = 3180 - Bases = 3437873602 - N50 = 120177077 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201339684-215721019 | [ 1 ] 186958349-201339683 | [ 1 ] 172577015-186958349 | [ 1 ] 158195680-172577014 | [ 1 ] 143814346-158195680 | [ 3 ] 129433011-143814345 | [ 2 ] 115051676-129433010 | [ 2 ] 100670342-115051676 | [ 2 ] 86289007-100670341 | [ 3 ] 71907673-86289007 | [ ] 57526338-71907672 | [ 3 ] 43145003-57526337 | [ 1 ] 28763669-43145003 | [ 2 ] 14382334-28763668 | [ ] 1000-14382334 |************************************************** [ 3158 ] Storage Throughput = excellent ( 1118.15 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015461 bp ( 40010061 non ambiguous ) - Num Contigs Represented = 260 - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:06 (hh:mm:ss) Elapsed Time Round Time: 00:30:47 (hh:mm:ss) Elapsed Time : 122 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 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11653 repeats masked totaling 4226792 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037408 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 10037008 bp After Masking: 5776620 bp Masked: 42.45 % -- Input Database Coverage: 10037408 bp out of 3437873602 bp ( 0.29 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:21 (hh:mm:ss) Elapsed Time, 3754 HSPs Collected Number of families returned by RECON: 546 Round Time: 00:09:55 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36390 repeats masked totaling 14180740 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018107 bp Num Contigs Represented = 212 Non ambiguous bp: Initial: 30013107 bp After Masking: 15701875 bp Masked: 47.68 % -- Input Database Coverage: 40055515 bp out of 3437873602 bp ( 1.17 % ) Sampling Time: 00:03:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:22:02 (hh:mm:ss) Elapsed Time, 120728 HSPs Collected Number of families returned by RECON: 1717 Round Time: 00:28:52 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116901 repeats masked totaling 43911827 bp(s). - TE Masking time 00:02:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030836 bp Num Contigs Represented = 521 Non ambiguous bp: Initial: 90016228 bp After Masking: 45765459 bp Masked: 49.16 % -- Input Database Coverage: 130086351 bp out of 3437873602 bp ( 3.78 % ) Sampling Time: 00:10:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 02:28:43 (hh:mm:ss) Elapsed Time, 1398786 HSPs Collected Number of families returned by RECON: 6035 Round Time: 02:47:21 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 386925 repeats masked totaling 136938912 bp(s). - TE Masking time 00:09:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046418 bp Num Contigs Represented = 1093 Non ambiguous bp: Initial: 270001270 bp After Masking: 131980212 bp Masked: 51.12 % -- Input Database Coverage: 400132769 bp out of 3437873602 bp ( 11.64 % ) Sampling Time: 00:36:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23711941 Comparison Time: 17:47:56 (hh:mm:ss) Elapsed Time, 9271644 HSPs Collected Number of families returned by RECON: 22641 Round Time: 19:02:41 (hh:mm:ss) Elapsed Time : 268 families discovered. RepeatScout/RECON discovery complete: 581 families found Classification Time: 00:40:39 (hh:mm:ss) Elapsed Time Program Time: 23:40:15 (hh:mm:ss) Elapsed Time