RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4iYC6S/RM_4013036.SatJun291545282024 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: 1719701128 Database = /dev/shm/rModeler.4iYC6S/GCF_904425465.1_Colossoma_macropomum - Sequences = 1269 - Bases = 1221847006 - N50 = 42604281 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 59562707-63817184 | [ 1 ] 55308230-59562706 | [ ] 51053754-55308230 | [ 1 ] 46799277-51053753 | [ 2 ] 42544801-46799277 | [ 8 ] 38290324-42544800 | [ 2 ] 34035848-38290324 | [ 9 ] 29781371-34035847 | [ 2 ] 25526895-29781371 | [ ] 21272418-25526894 | [ 2 ] 17017942-21272418 | [ ] 12763465-17017941 | [ ] 8508989-12763465 | [ ] 4254512-8508988 | [ 1 ] 36-4254512 |************************************************** [ 1241 ] Storage Throughput = excellent ( 1228.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011722 bp ( 40010031 non ambiguous ) - Num Contigs Represented = 143 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:39 (hh:mm:ss) Elapsed Time Round Time: 00:22:06 (hh:mm:ss) Elapsed Time : 811 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19953 repeats masked totaling 2941341 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013680 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10012719 bp After Masking: 6533839 bp Masked: 34.74 % -- Input Database Coverage: 10013680 bp out of 1221847006 bp ( 0.82 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:05:29 (hh:mm:ss) Elapsed Time, 16800 HSPs Collected Number of families returned by RECON: 2200 Round Time: 00:07:46 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62701 repeats masked totaling 9360516 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038044 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 30037314 bp After Masking: 19400224 bp Masked: 35.41 % -- Input Database Coverage: 40051724 bp out of 1221847006 bp ( 3.28 % ) Sampling Time: 00:05:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303031 Comparison Time: 00:27:07 (hh:mm:ss) Elapsed Time, 107311 HSPs Collected Number of families returned by RECON: 6695 Round Time: 00:35:37 (hh:mm:ss) Elapsed Time : 252 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 219884 repeats masked totaling 33471606 bp(s). - TE Masking time 00:02:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036841 bp Num Contigs Represented = 243 Non ambiguous bp: Initial: 90034103 bp After Masking: 52617451 bp Masked: 41.56 % -- Input Database Coverage: 130088565 bp out of 1221847006 bp ( 10.65 % ) Sampling Time: 00:13:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2690040 Comparison Time: 02:41:49 (hh:mm:ss) Elapsed Time, 348723 HSPs Collected Number of families returned by RECON: 16990 Round Time: 03:12:58 (hh:mm:ss) Elapsed Time : 657 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 767076 repeats masked totaling 117663466 bp(s). - TE Masking time 00:12:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030765 bp Num Contigs Represented = 505 Non ambiguous bp: Initial: 270021616 bp After Masking: 140277365 bp Masked: 48.05 % -- Input Database Coverage: 400119330 bp out of 1221847006 bp ( 32.75 % ) Sampling Time: 00:45:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24022846 Comparison Time: 18:25:32 (hh:mm:ss) Elapsed Time, 747534 HSPs Collected Number of families returned by RECON: 47535 Round Time: 20:48:36 (hh:mm:ss) Elapsed Time : 1287 families discovered. RepeatScout/RECON discovery complete: 3040 families found Classification Time: 01:52:39 (hh:mm:ss) Elapsed Time Program Time: 26:59:42 (hh:mm:ss) Elapsed Time