RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nKOE6k/RM_2352429.SatApr121516462025 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: 1744496205 Database = /dev/shm/rModeler.nKOE6k/GCA_047511655.1_mCasCan1.hap1 - Sequences = 502 - Bases = 2828089101 - N50 = 163075497 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195582309-209551656 | [ 3 ] 181612962-195582308 | [ 2 ] 167643615-181612961 | [ 1 ] 153674268-167643614 | [ 3 ] 139704921-153674267 | [ 3 ] 125735574-139704920 | [ 2 ] 111766227-125735573 | [ 1 ] 97796880-111766226 | [ 1 ] 83827533-97796879 | [ 1 ] 69858186-83827532 | [ 1 ] 55888839-69858185 | [ ] 41919492-55888838 | [ 2 ] 27950145-41919491 | [ ] 13980798-27950144 | [ ] 11452-13980798 |************************************************** [ 482 ] Storage Throughput = excellent ( 1664.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031740 bp ( 40030940 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:28 (hh:mm:ss) Elapsed Time Round Time: 00:16:47 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11366 repeats masked totaling 2591316 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005810 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10005610 bp After Masking: 7317279 bp Masked: 26.87 % -- Input Database Coverage: 10005810 bp out of 2828089101 bp ( 0.35 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:37 (hh:mm:ss) Elapsed Time, 60514 HSPs Collected Number of families returned by RECON: 774 Round Time: 00:05:24 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36674 repeats masked totaling 8470471 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025850 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30025250 bp After Masking: 21036195 bp Masked: 29.94 % -- Input Database Coverage: 40031660 bp out of 2828089101 bp ( 1.42 % ) Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:21:06 (hh:mm:ss) Elapsed Time, 481724 HSPs Collected Number of families returned by RECON: 2399 Round Time: 00:23:23 (hh:mm:ss) Elapsed Time : 46 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 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 117392 repeats masked totaling 27168180 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008551 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90006951 bp After Masking: 61361313 bp Masked: 31.83 % -- Input Database Coverage: 130040211 bp out of 2828089101 bp ( 4.60 % ) Sampling Time: 00:05:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:51:12 (hh:mm:ss) Elapsed Time, 3076697 HSPs Collected Number of families returned by RECON: 8291 Round Time: 02:04:53 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:41 (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... 393065 repeats masked totaling 89694505 bp(s). - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036001 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 270032801 bp After Masking: 176127766 bp Masked: 34.78 % -- Input Database Coverage: 400076212 bp out of 2828089101 bp ( 14.15 % ) Sampling Time: 00:18:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 16:13:06 (hh:mm:ss) Elapsed Time, 41760660 HSPs Collected Number of families returned by RECON: 34354 Round Time: 17:22:47 (hh:mm:ss) Elapsed Time : 412 families discovered. RepeatScout/RECON discovery complete: 864 families found Classification Time: 00:24:20 (hh:mm:ss) Elapsed Time Program Time: 20:37:34 (hh:mm:ss) Elapsed Time