RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ckhi8M/RM_34271.SatJan140516532023 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: 1673702212 Database = /dev/shm/rModeler.ckhi8M/GCF_903995435.1_mAcoRus1.1 - Sequences = 623 - Bases = 2301522284 - N50 = 67302882 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 116759295-125099172 | [ 2 ] 108419418-116759295 | [ ] 100079541-108419418 | [ 1 ] 91739664-100079541 | [ ] 83399787-91739664 | [ 3 ] 75059910-83399787 | [ 3 ] 66720033-75059910 | [ 4 ] 58380156-66720033 |* [ 12 ] 50040279-58380156 | [ 2 ] 41700402-50040279 | [ 5 ] 33360525-41700402 | [ 1 ] 25020648-33360525 | [ ] 16680771-25020648 | [ ] 8340894-16680771 | [ ] 1017-8340894 |************************************************** [ 590 ] Storage Throughput = excellent ( 1343.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40061901 bp ( 40002259 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:25 (hh:mm:ss) Elapsed Time Round Time: 00:29:02 (hh:mm:ss) Elapsed Time : 225 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13201 repeats masked totaling 2480460 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021688 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10010960 bp After Masking: 7264462 bp Masked: 27.43 % -- Input Database Coverage: 10021688 bp out of 2301522284 bp ( 0.44 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:59 (hh:mm:ss) Elapsed Time, 6953 HSPs Collected Number of families returned by RECON: 833 Round Time: 00:07:50 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42616 repeats masked totaling 7497197 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30080209 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30031295 bp After Masking: 21799605 bp Masked: 27.41 % -- Input Database Coverage: 40101897 bp out of 2301522284 bp ( 1.74 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:29:29 (hh:mm:ss) Elapsed Time, 22984 HSPs Collected Number of families returned by RECON: 2694 Round Time: 00:33:43 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143243 repeats masked totaling 25725126 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90422682 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 90028103 bp After Masking: 62138573 bp Masked: 30.98 % -- Input Database Coverage: 130524579 bp out of 2301522284 bp ( 5.67 % ) Sampling Time: 00:09:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 03:03:02 (hh:mm:ss) Elapsed Time, 90886 HSPs Collected Number of families returned by RECON: 9009 Round Time: 03:16:47 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 477251 repeats masked totaling 83676065 bp(s). - TE Masking time 00:04:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270829455 bp Num Contigs Represented = 149 Non ambiguous bp: Initial: 270022945 bp After Masking: 179406005 bp Masked: 33.56 % -- Input Database Coverage: 401354034 bp out of 2301522284 bp ( 17.44 % ) Sampling Time: 00:30:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 22:28:51 (hh:mm:ss) Elapsed Time, 288627 HSPs Collected Number of families returned by RECON: 41214 Round Time: 23:38:13 (hh:mm:ss) Elapsed Time : 400 families discovered. RepeatScout/RECON discovery complete: 840 families found Classification Time: 00:31:17 (hh:mm:ss) Elapsed Time Program Time: 28:36:52 (hh:mm:ss) Elapsed Time