RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RwT3PX/RM_3368170.SunJul201614132025 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: 1753053252 Database = /dev/shm/rModeler.RwT3PX/GCA_965194765.1_mBalPhy2.hap2.1 - Sequences = 2448 - Bases = 2850212336 - N50 = 108081554 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 174258792-186705778 | [ 3 ] 161811807-174258792 | [ ] 149364822-161811807 | [ 1 ] 136917837-149364822 | [ 1 ] 124470852-136917837 | [ ] 112023866-124470851 | [ 4 ] 99576881-112023866 | [ 2 ] 87129896-99576881 | [ 5 ] 74682911-87129896 | [ 2 ] 62235926-74682911 | [ ] 49788940-62235925 | [ 2 ] 37341955-49788940 | [ ] 24894970-37341955 | [ 1 ] 12447985-24894970 | [ ] 1000-12447985 |************************************************** [ 2427 ] Storage Throughput = excellent ( 1175.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033112 bp ( 40030112 non ambiguous ) - Num Contigs Represented = 189 - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:36 (hh:mm:ss) Elapsed Time Round Time: 00:39:35 (hh:mm:ss) Elapsed Time : 211 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8808 repeats masked totaling 3101623 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035013 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 10034613 bp After Masking: 6246325 bp Masked: 37.75 % -- Input Database Coverage: 10035013 bp out of 2850212336 bp ( 0.35 % ) Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:21 (hh:mm:ss) Elapsed Time, 8892 HSPs Collected Number of families returned by RECON: 696 Round Time: 00:06:40 (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 : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30162 repeats masked totaling 10374321 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038019 bp Num Contigs Represented = 146 Non ambiguous bp: Initial: 30035419 bp After Masking: 17901784 bp Masked: 40.40 % -- Input Database Coverage: 40073032 bp out of 2850212336 bp ( 1.41 % ) Sampling Time: 00:04:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:22:43 (hh:mm:ss) Elapsed Time, 32889 HSPs Collected Number of families returned by RECON: 2348 Round Time: 00:28:30 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101961 repeats masked totaling 34111824 bp(s). - TE Masking time 00:01:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022330 bp Num Contigs Represented = 383 Non ambiguous bp: Initial: 90014722 bp After Masking: 50810120 bp Masked: 43.55 % -- Input Database Coverage: 130095362 bp out of 2850212336 bp ( 4.56 % ) Sampling Time: 00:14:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 02:32:34 (hh:mm:ss) Elapsed Time, 117818 HSPs Collected Number of families returned by RECON: 7495 Round Time: 02:53:47 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 340101 repeats masked totaling 108989606 bp(s). - TE Masking time 00:06:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026736 bp Num Contigs Represented = 871 Non ambiguous bp: Initial: 270001136 bp After Masking: 144700099 bp Masked: 46.41 % -- Input Database Coverage: 400122098 bp out of 2850212336 bp ( 14.04 % ) Sampling Time: 00:45:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23643126 Comparison Time: 19:49:14 (hh:mm:ss) Elapsed Time, 587136 HSPs Collected Number of families returned by RECON: 28639 Round Time: 20:55:10 (hh:mm:ss) Elapsed Time : 307 families discovered. RepeatScout/RECON discovery complete: 759 families found Classification Time: 00:43:40 (hh:mm:ss) Elapsed Time Program Time: 25:47:22 (hh:mm:ss) Elapsed Time