RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.xA9kZY/RM_2076696.TueMar41139552025 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: 1741117194 Database = /dev/shm/rModeler.xA9kZY/GCA_048164845.1_mCanLup2.hap2 - Sequences = 155 - Bases = 2336397564 - N50 = 65755526 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 114834726-123036378 | [ 1 ] 106633074-114834725 | [ ] 98431422-106633073 | [ ] 90229770-98431421 | [ 1 ] 82028119-90229770 |* [ 4 ] 73826467-82028118 |* [ 4 ] 65624815-73826466 |* [ 4 ] 57423163-65624814 |** [ 7 ] 49221511-57423162 |** [ 5 ] 41019860-49221511 |** [ 6 ] 32818208-41019859 |** [ 5 ] 24616556-32818207 | [ 1 ] 16414904-24616555 | [ ] 8213252-16414903 | [ ] 11601-8213252 |************************************************** [ 117 ] Storage Throughput = excellent ( 1822.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020382 bp ( 40020082 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:24 (hh:mm:ss) Elapsed Time Round Time: 00:11:53 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11392 repeats masked totaling 2148724 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001064 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10001064 bp After Masking: 7725314 bp Masked: 22.76 % -- Input Database Coverage: 10001064 bp out of 2336397564 bp ( 0.43 % ) Sampling Time: 00:00:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 29733 HSPs Collected Number of families returned by RECON: 853 Round Time: 00:03:40 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38706 repeats masked totaling 7444140 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019238 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30018938 bp After Masking: 22153117 bp Masked: 26.20 % -- Input Database Coverage: 40020302 bp out of 2336397564 bp ( 1.71 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:14:36 (hh:mm:ss) Elapsed Time, 168371 HSPs Collected Number of families returned by RECON: 2631 Round Time: 00:16:26 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125991 repeats masked totaling 25466859 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90007850 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90007050 bp After Masking: 63092498 bp Masked: 29.90 % -- Input Database Coverage: 130028152 bp out of 2336397564 bp ( 5.57 % ) Sampling Time: 00:04:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:29:34 (hh:mm:ss) Elapsed Time, 1686423 HSPs Collected Number of families returned by RECON: 9248 Round Time: 01:35:33 (hh:mm:ss) Elapsed Time : 154 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 408386 repeats masked totaling 84655024 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022063 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 270018663 bp After Masking: 181233051 bp Masked: 32.88 % -- Input Database Coverage: 400050215 bp out of 2336397564 bp ( 17.12 % ) Sampling Time: 00:13:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 10:36:26 (hh:mm:ss) Elapsed Time, 19148349 HSPs Collected Number of families returned by RECON: 39071 Round Time: 11:07:26 (hh:mm:ss) Elapsed Time : 309 families discovered. RepeatScout/RECON discovery complete: 713 families found Classification Time: 00:13:33 (hh:mm:ss) Elapsed Time Program Time: 13:28:31 (hh:mm:ss) Elapsed Time