RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IT7Tmd/RM_64187.FriApr250714132025 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: 1745590452 Database = /dev/shm/rModeler.IT7Tmd/GCA_048544225.1_fCoiMys1.hap2 - Sequences = 184 - Bases = 854254650 - N50 = 35291789 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 42048226-45051600 | [ 1 ] 39044853-42048226 | [ 1 ] 36041480-39044853 |* [ 5 ] 33038106-36041479 |*** [ 12 ] 30034733-33038106 | [ 2 ] 27031360-30034733 | [ 3 ] 24027986-27031359 | [ ] 21024613-24027986 | [ ] 18021240-21024613 | [ ] 15017866-18021239 | [ ] 12014493-15017866 | [ ] 9011120-12014493 | [ ] 6007746-9011119 | [ 1 ] 3004373-6007746 | [ ] 1000-3004373 |************************************************** [ 159 ] Storage Throughput = excellent ( 1806.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043718 bp ( 40037118 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:53 (hh:mm:ss) Elapsed Time Round Time: 00:19:29 (hh:mm:ss) Elapsed Time : 491 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8060 repeats masked totaling 1429737 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008353 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10006753 bp After Masking: 7379940 bp Masked: 26.25 % -- Input Database Coverage: 10008353 bp out of 854254650 bp ( 1.17 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:10 (hh:mm:ss) Elapsed Time, 7639 HSPs Collected Number of families returned by RECON: 1223 Round Time: 00:04:50 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26137 repeats masked totaling 4471481 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035349 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30030349 bp After Masking: 21381897 bp Masked: 28.80 % -- Input Database Coverage: 40043702 bp out of 854254650 bp ( 4.69 % ) Sampling Time: 00:04:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:14:37 (hh:mm:ss) Elapsed Time, 30249 HSPs Collected Number of families returned by RECON: 4274 Round Time: 00:22:38 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 83806 repeats masked totaling 14064514 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036288 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90025468 bp After Masking: 63493747 bp Masked: 29.47 % -- Input Database Coverage: 130079990 bp out of 854254650 bp ( 15.23 % ) Sampling Time: 00:14:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:30:52 (hh:mm:ss) Elapsed Time, 232184 HSPs Collected Number of families returned by RECON: 16374 Round Time: 01:49:09 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 307031 repeats masked totaling 53824330 bp(s). - TE Masking time 00:05:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270048468 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 270011268 bp After Masking: 180367511 bp Masked: 33.20 % -- Input Database Coverage: 400128458 bp out of 854254650 bp ( 46.84 % ) Sampling Time: 00:43:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 10:35:09 (hh:mm:ss) Elapsed Time, 784738 HSPs Collected Number of families returned by RECON: 57916 Round Time: 12:12:43 (hh:mm:ss) Elapsed Time : 1092 families discovered. RepeatScout/RECON discovery complete: 2080 families found Classification Time: 00:49:33 (hh:mm:ss) Elapsed Time Program Time: 15:38:22 (hh:mm:ss) Elapsed Time