RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FV2U3j/RM_1556289.WedMar62149542024 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: 1709790592 Database = /dev/shm/rModeler.FV2U3j/GCA_035609135.1_aEleCoq1.hap2 - Sequences = 827 - Bases = 3362534901 - N50 = 308506731 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 494196176-529495234 | [ 1 ] 458897119-494196176 | [ ] 423598062-458897119 | [ ] 388299005-423598062 | [ ] 352999948-388299005 | [ ] 317700891-352999948 | [ 1 ] 282401834-317700891 | [ 3 ] 247102777-282401834 | [ 1 ] 211803720-247102777 | [ 2 ] 176504663-211803720 | [ 1 ] 141205606-176504663 | [ 1 ] 105906549-141205606 | [ 3 ] 70607492-105906549 | [ ] 35308435-70607492 | [ ] 9378-35308435 |************************************************** [ 814 ] Storage Throughput = excellent ( 1082.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033920 bp ( 40032520 non ambiguous ) - Num Contigs Represented = 67 - Sequence extraction : 00:05:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:34 (hh:mm:ss) Elapsed Time Round Time: 00:36:00 (hh:mm:ss) Elapsed Time : 980 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21396 repeats masked totaling 4533677 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008876 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10008676 bp After Masking: 4055619 bp Masked: 59.48 % -- Input Database Coverage: 10008876 bp out of 3362534901 bp ( 0.30 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:22 (hh:mm:ss) Elapsed Time, 11845 HSPs Collected Number of families returned by RECON: 1606 Round Time: 00:10:22 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:05:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68946 repeats masked totaling 14305894 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024964 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30023764 bp After Masking: 12225704 bp Masked: 59.28 % -- Input Database Coverage: 40033840 bp out of 3362534901 bp ( 1.19 % ) Sampling Time: 00:11:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:22:15 (hh:mm:ss) Elapsed Time, 90187 HSPs Collected Number of families returned by RECON: 4857 Round Time: 00:35:49 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 224269 repeats masked totaling 46737217 bp(s). - TE Masking time 00:02:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023075 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 90018075 bp After Masking: 32900536 bp Masked: 63.45 % -- Input Database Coverage: 130056915 bp out of 3362534901 bp ( 3.87 % ) Sampling Time: 00:34:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 01:50:10 (hh:mm:ss) Elapsed Time, 318075 HSPs Collected Number of families returned by RECON: 12058 Round Time: 02:34:49 (hh:mm:ss) Elapsed Time : 549 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:40:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 738868 repeats masked totaling 154663412 bp(s). - TE Masking time 00:09:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026447 bp Num Contigs Represented = 243 Non ambiguous bp: Initial: 270015647 bp After Masking: 83350416 bp Masked: 69.13 % -- Input Database Coverage: 400083362 bp out of 3362534901 bp ( 11.90 % ) Sampling Time: 01:43:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 10:44:37 (hh:mm:ss) Elapsed Time, 792055 HSPs Collected Number of families returned by RECON: 29157 Round Time: 13:04:53 (hh:mm:ss) Elapsed Time : 1280 families discovered. RepeatScout/RECON discovery complete: 3015 families found Classification Time: 01:29:04 (hh:mm:ss) Elapsed Time Program Time: 18:30:57 (hh:mm:ss) Elapsed Time