RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.Ssuonx/RM_2534193.WedApr230518312025 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: 1745410711 Database = /data/tmp/rModeler.Ssuonx/GCA_048128805.1_fCenGer3.hap1.cur.20231027 - Sequences = 279 - Bases = 779177424 - N50 = 32697592 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 36371651-38969015 | [ 5 ] 33774287-36371650 | [ 4 ] 31176924-33774287 | [ 5 ] 28579560-31176923 | [ 4 ] 25982197-28579560 | [ 1 ] 23384833-25982196 | [ 5 ] 20787470-23384833 | [ ] 18190106-20787469 | [ ] 15592743-18190106 | [ ] 12995379-15592742 | [ ] 10398016-12995379 | [ ] 7800652-10398015 | [ ] 5203289-7800652 | [ ] 2605925-5203288 | [ ] 8562-2605925 |************************************************** [ 255 ] Storage Throughput = good ( 851.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013739 bp ( 40007739 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:11 (hh:mm:ss) Elapsed Time Round Time: 00:22:10 (hh:mm:ss) Elapsed Time : 647 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10879 repeats masked totaling 1387472 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004133 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10002533 bp After Masking: 7956830 bp Masked: 20.45 % -- Input Database Coverage: 10004133 bp out of 779177424 bp ( 1.28 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:56 (hh:mm:ss) Elapsed Time, 9429 HSPs Collected Number of families returned by RECON: 1949 Round Time: 00:09:51 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35142 repeats masked totaling 4662466 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009596 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30005196 bp After Masking: 22933520 bp Masked: 23.57 % -- Input Database Coverage: 40013729 bp out of 779177424 bp ( 5.14 % ) Sampling Time: 00:05:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:31:06 (hh:mm:ss) Elapsed Time, 66245 HSPs Collected Number of families returned by RECON: 6777 Round Time: 00:45:39 (hh:mm:ss) Elapsed Time : 150 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 120182 repeats masked totaling 16057432 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049773 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90032221 bp After Masking: 66299840 bp Masked: 26.36 % -- Input Database Coverage: 130063502 bp out of 779177424 bp ( 16.69 % ) Sampling Time: 00:15:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 03:24:07 (hh:mm:ss) Elapsed Time, 321880 HSPs Collected Number of families returned by RECON: 21716 Round Time: 04:28:22 (hh:mm:ss) Elapsed Time : 606 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 444324 repeats masked totaling 65226016 bp(s). - TE Masking time 00:11:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270056938 bp Num Contigs Represented = 141 Non ambiguous bp: Initial: 270007138 bp After Masking: 182405263 bp Masked: 32.44 % -- Input Database Coverage: 400120440 bp out of 779177424 bp ( 51.35 % ) Sampling Time: 00:53:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 23:09:42 (hh:mm:ss) Elapsed Time, 1103287 HSPs Collected Number of families returned by RECON: 71603 Round Time: 29:51:06 (hh:mm:ss) Elapsed Time : 1541 families discovered. RepeatScout/RECON discovery complete: 2972 families found Classification Time: 02:07:22 (hh:mm:ss) Elapsed Time Program Time: 37:44:30 (hh:mm:ss) Elapsed Time