RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.oy5hPx/RM_7478.WedDec61314292023 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: 1701897267 Database = /dev/shm/rModeler.oy5hPx/GCA_949357685.1_fGobGob1.1 - Sequences = 231 - Bases = 1460679231 - N50 = 58329458 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 81509766-87331821 | [ 1 ] 75687711-81509765 | [ 1 ] 69865656-75687710 | [ 1 ] 64043602-69865656 | [ 2 ] 58221547-64043601 |* [ 5 ] 52399492-58221546 |* [ 7 ] 46577437-52399491 |* [ 5 ] 40755383-46577437 | [ 3 ] 34933328-40755382 | [ ] 29111273-34933327 | [ ] 23289218-29111272 | [ ] 17467164-23289218 | [ ] 11645109-17467163 | [ ] 5823054-11645108 | [ ] 1000-5823054 |************************************************** [ 206 ] Storage Throughput = excellent ( 1132.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043908 bp ( 40037594 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:22 (hh:mm:ss) Elapsed Time Round Time: 00:45:15 (hh:mm:ss) Elapsed Time : 1374 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19235 repeats masked totaling 4359986 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020053 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10018139 bp After Masking: 4669328 bp Masked: 53.39 % -- Input Database Coverage: 10020053 bp out of 1460679231 bp ( 0.69 % ) Sampling Time: 00:02:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:23 (hh:mm:ss) Elapsed Time, 7963 HSPs Collected Number of families returned by RECON: 1495 Round Time: 00:08:37 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58271 repeats masked totaling 13557808 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023842 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30019442 bp After Masking: 13768953 bp Masked: 54.13 % -- Input Database Coverage: 40043895 bp out of 1460679231 bp ( 2.74 % ) Sampling Time: 00:08:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:24:56 (hh:mm:ss) Elapsed Time, 67592 HSPs Collected Number of families returned by RECON: 4653 Round Time: 00:35:54 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 178317 repeats masked totaling 40598417 bp(s). - TE Masking time 00:04:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025899 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90010938 bp After Masking: 40919861 bp Masked: 54.54 % -- Input Database Coverage: 130069794 bp out of 1460679231 bp ( 8.90 % ) Sampling Time: 00:27:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 02:40:28 (hh:mm:ss) Elapsed Time, 421027 HSPs Collected Number of families returned by RECON: 12677 Round Time: 03:25:13 (hh:mm:ss) Elapsed Time : 693 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:59:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 619577 repeats masked totaling 140286174 bp(s). - TE Masking time 00:22:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270063704 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 270022307 bp After Masking: 104430282 bp Masked: 61.33 % -- Input Database Coverage: 400133498 bp out of 1460679231 bp ( 27.39 % ) Sampling Time: 01:31:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 16:38:28 (hh:mm:ss) Elapsed Time, 1515123 HSPs Collected Number of families returned by RECON: 31664 Round Time: 19:20:51 (hh:mm:ss) Elapsed Time : 1414 families discovered. RepeatScout/RECON discovery complete: 3606 families found Classification Time: 02:43:04 (hh:mm:ss) Elapsed Time Program Time: 26:58:54 (hh:mm:ss) Elapsed Time