RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.daIr3y/RM_6993.ThuJan50439072023 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: 1672922346 Database = /dev/shm/rModeler.daIr3y/GCA_903797595.2_bEriRub2.2 - Sequences = 1119 - Bases = 1086738418 - N50 = 68522085 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 138354551-148236322 | [ 1 ] 128472781-138354551 | [ ] 118591011-128472781 | [ ] 108709241-118591011 | [ 2 ] 98827471-108709241 | [ ] 88945701-98827471 | [ ] 79063931-88945701 | [ ] 69182161-79063931 | [ ] 59300391-69182161 | [ 3 ] 49418621-59300391 | [ ] 39536851-49418621 | [ ] 29655081-39536851 | [ 3 ] 19773311-29655081 | [ 4 ] 9891541-19773311 | [ 10 ] 9771-9891541 |************************************************* [ 1096 ] Storage Throughput = excellent ( 1045.16 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40048538 bp ( 40036152 non ambiguous ) - Num Contigs Represented = 145 - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:09 (hh:mm:ss) Elapsed Time Round Time: 00:27:31 (hh:mm:ss) Elapsed Time : 166 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 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3557 repeats masked totaling 969204 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013845 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 10010045 bp After Masking: 8810532 bp Masked: 11.98 % -- Input Database Coverage: 10013845 bp out of 1086738418 bp ( 0.92 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:07:28 (hh:mm:ss) Elapsed Time, 1091 HSPs Collected Number of families returned by RECON: 405 Round Time: 00:08:37 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10166 repeats masked totaling 2734331 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034692 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 30026106 bp After Masking: 26689532 bp Masked: 11.11 % -- Input Database Coverage: 40048537 bp out of 1086738418 bp ( 3.69 % ) Sampling Time: 00:02:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 00:42:56 (hh:mm:ss) Elapsed Time, 7395 HSPs Collected Number of families returned by RECON: 2013 Round Time: 00:46:14 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34016 repeats masked totaling 8619467 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035731 bp Num Contigs Represented = 245 Non ambiguous bp: Initial: 90012295 bp After Masking: 79270265 bp Masked: 11.93 % -- Input Database Coverage: 130084268 bp out of 1086738418 bp ( 11.97 % ) Sampling Time: 00:08:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2614041 Comparison Time: 05:09:21 (hh:mm:ss) Elapsed Time, 74333 HSPs Collected Number of families returned by RECON: 11935 Round Time: 05:28:43 (hh:mm:ss) Elapsed Time : 110 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107204 repeats masked totaling 29183958 bp(s). - TE Masking time 00:07:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270092831 bp Num Contigs Represented = 541 Non ambiguous bp: Initial: 270021693 bp After Masking: 233979831 bp Masked: 13.35 % -- Input Database Coverage: 400177099 bp out of 1086738418 bp ( 36.82 % ) Sampling Time: 00:31:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23705055 Comparison Time: 41:59:46 (hh:mm:ss) Elapsed Time, 291294 HSPs Collected Number of families returned by RECON: 78876 Round Time: 44:17:04 (hh:mm:ss) Elapsed Time : 350 families discovered. RepeatScout/RECON discovery complete: 637 families found Classification Time: 01:10:47 (hh:mm:ss) Elapsed Time Program Time: 52:18:56 (hh:mm:ss) Elapsed Time