RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.k4OHS6/RM_19576.WedNov291922302023 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: 1701314547 Database = /dev/shm/rModeler.k4OHS6/GCA_029633845.1_fLamInc1.hap1 - Sequences = 1059 - Bases = 1477069270 - N50 = 63093359 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 129165171-138390503 | [ 2 ] 119939840-129165171 | [ ] 110714509-119939840 | [ 1 ] 101489178-110714509 | [ ] 92263847-101489178 | [ ] 83038515-92263846 | [ ] 73813184-83038515 | [ 1 ] 64587853-73813184 | [ 3 ] 55362522-64587853 | [ 4 ] 46137191-55362522 | [ 3 ] 36911859-46137190 | [ 5 ] 27686528-36911859 | [ 1 ] 18461197-27686528 | [ 1 ] 9235866-18461197 | [ ] 10535-9235866 |************************************************* [ 1038 ] Storage Throughput = excellent ( 1186.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045857 bp ( 40026938 non ambiguous ) - Num Contigs Represented = 102 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:45 (hh:mm:ss) Elapsed Time Round Time: 00:39:31 (hh:mm:ss) Elapsed Time : 587 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10512 repeats masked totaling 3120560 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005384 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10000784 bp After Masking: 5234745 bp Masked: 47.66 % -- Input Database Coverage: 10005384 bp out of 1477069270 bp ( 0.68 % ) Sampling Time: 00:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 5899 HSPs Collected Number of families returned by RECON: 1361 Round Time: 00:09:31 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32373 repeats masked totaling 10132091 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040393 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 30026074 bp After Masking: 15305409 bp Masked: 49.03 % -- Input Database Coverage: 40045777 bp out of 1477069270 bp ( 2.71 % ) Sampling Time: 00:13:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:25:56 (hh:mm:ss) Elapsed Time, 44228 HSPs Collected Number of families returned by RECON: 4288 Round Time: 00:41:05 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102440 repeats masked totaling 32125805 bp(s). - TE Masking time 00:02:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90074835 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 90039155 bp After Masking: 45157179 bp Masked: 49.85 % -- Input Database Coverage: 130120612 bp out of 1477069270 bp ( 8.81 % ) Sampling Time: 00:41:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 02:24:10 (hh:mm:ss) Elapsed Time, 286661 HSPs Collected Number of families returned by RECON: 12099 Round Time: 03:18:41 (hh:mm:ss) Elapsed Time : 586 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:22:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 384996 repeats masked totaling 119037143 bp(s). - TE Masking time 00:14:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270135886 bp Num Contigs Represented = 356 Non ambiguous bp: Initial: 270026650 bp After Masking: 115637975 bp Masked: 57.18 % -- Input Database Coverage: 400256498 bp out of 1477069270 bp ( 27.10 % ) Sampling Time: 01:47:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23362030 Comparison Time: 16:09:08 (hh:mm:ss) Elapsed Time, 829616 HSPs Collected Number of families returned by RECON: 33158 Round Time: 19:01:40 (hh:mm:ss) Elapsed Time : 1486 families discovered. RepeatScout/RECON discovery complete: 2743 families found Classification Time: 02:48:29 (hh:mm:ss) Elapsed Time Program Time: 26:38:57 (hh:mm:ss) Elapsed Time