RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nd78Vo/RM_19948.FriFeb71220082025 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: 1738959583 Database = /dev/shm/rModeler.nd78Vo/GCA_046129655.1_bCyaCrs1.hap1 - Sequences = 316 - Bases = 1227176437 - N50 = 77204880 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 148262112-158851056 | [ 1 ] 137673168-148262111 | [ ] 127084224-137673167 | [ ] 116495280-127084223 | [ 2 ] 105906336-116495279 | [ ] 95317392-105906335 | [ ] 84728448-95317391 | [ ] 74139505-84728448 | [ 3 ] 63550561-74139504 | [ 1 ] 52961617-63550560 | [ ] 42372673-52961616 | [ 1 ] 31783729-42372672 | [ 3 ] 21194785-31783728 | [ 4 ] 10605841-21194784 |* [ 8 ] 16898-10605841 |************************************************** [ 293 ] Storage Throughput = excellent ( 1911.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008756 bp ( 40006556 non ambiguous ) - Num Contigs Represented = 70 - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:02 (hh:mm:ss) Elapsed Time Round Time: 00:41:11 (hh:mm:ss) Elapsed Time : 152 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 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3130 repeats masked totaling 1275420 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002493 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10002293 bp After Masking: 8556801 bp Masked: 14.45 % -- Input Database Coverage: 10002493 bp out of 1227176437 bp ( 0.82 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 01:54:50 (hh:mm:ss) Elapsed Time, 839 HSPs Collected Number of families returned by RECON: 276 Round Time: 02:00:23 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10899 repeats masked totaling 4030123 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006183 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30004183 bp After Masking: 25370078 bp Masked: 15.44 % -- Input Database Coverage: 40008676 bp out of 1227176437 bp ( 3.26 % ) Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 05:48:34 (hh:mm:ss) Elapsed Time, 7444 HSPs Collected Number of families returned by RECON: 1360 Round Time: 05:55:01 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36983 repeats masked totaling 13798881 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020492 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 90014092 bp After Masking: 74158320 bp Masked: 17.61 % -- Input Database Coverage: 130029168 bp out of 1227176437 bp ( 10.60 % ) Sampling Time: 00:07:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 18:05:12 (hh:mm:ss) Elapsed Time, 60860 HSPs Collected Number of families returned by RECON: 8578 Round Time: 18:29:14 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116676 repeats masked totaling 44845808 bp(s). - TE Masking time 00:02:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018127 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 270000927 bp After Masking: 219175355 bp Masked: 18.82 % -- Input Database Coverage: 400047295 bp out of 1227176437 bp ( 32.60 % ) Sampling Time: 00:22:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 41:31:39 (hh:mm:ss) Elapsed Time, 400077 HSPs Collected Number of families returned by RECON: 58195 Round Time: 42:25:39 (hh:mm:ss) Elapsed Time : 296 families discovered. RepeatScout/RECON discovery complete: 561 families found Classification Time: 00:27:12 (hh:mm:ss) Elapsed Time Program Time: 69:58:40 (hh:mm:ss) Elapsed Time