RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.owL06c/RM_936.FriJan120429542024 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: 1705062592 Database = /dev/shm/rModeler.owL06c/GCA_026229955.1_mPerMan1.0.p - Sequences = 1838 - Bases = 2847741276 - N50 = 46861540 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 120666331-129284778 | [ 2 ] 112047885-120666331 | [ ] 103429438-112047884 | [ 2 ] 94810992-103429438 | [ ] 86192546-94810992 | [ ] 77574099-86192545 | [ 2 ] 68955653-77574099 | [ 2 ] 60337206-68955652 | [ 3 ] 51718760-60337206 | [ 3 ] 43100314-51718760 | [ 7 ] 34481867-43100313 | [ 4 ] 25863421-34481867 | [ 4 ] 17244974-25863420 | [ 14 ] 8626528-17244974 | [ 28 ] 8082-8626528 |************************************************* [ 1767 ] Storage Throughput = excellent ( 1172.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017098 bp ( 40016598 non ambiguous ) - Num Contigs Represented = 193 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:01 (hh:mm:ss) Elapsed Time Round Time: 00:31:17 (hh:mm:ss) Elapsed Time : 372 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16176 repeats masked totaling 2899128 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016466 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 10016466 bp After Masking: 6139115 bp Masked: 38.71 % -- Input Database Coverage: 10016466 bp out of 2847741276 bp ( 0.35 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:06 (hh:mm:ss) Elapsed Time, 3317 HSPs Collected Number of families returned by RECON: 581 Round Time: 00:06:24 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50145 repeats masked totaling 9165306 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000552 bp Num Contigs Represented = 167 Non ambiguous bp: Initial: 30000052 bp After Masking: 18286281 bp Masked: 39.05 % -- Input Database Coverage: 40017018 bp out of 2847741276 bp ( 1.41 % ) Sampling Time: 00:05:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:26:03 (hh:mm:ss) Elapsed Time, 18188 HSPs Collected Number of families returned by RECON: 2140 Round Time: 00:32:00 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 154223 repeats masked totaling 28444187 bp(s). - TE Masking time 00:02:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034746 bp Num Contigs Represented = 302 Non ambiguous bp: Initial: 90033546 bp After Masking: 54242821 bp Masked: 39.75 % -- Input Database Coverage: 130051764 bp out of 2847741276 bp ( 4.57 % ) Sampling Time: 00:12:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 03:06:13 (hh:mm:ss) Elapsed Time, 100839 HSPs Collected Number of families returned by RECON: 7207 Round Time: 03:26:25 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 509715 repeats masked totaling 96235882 bp(s). - TE Masking time 00:09:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270011172 bp Num Contigs Represented = 472 Non ambiguous bp: Initial: 270008672 bp After Masking: 152112286 bp Masked: 43.66 % -- Input Database Coverage: 400062936 bp out of 2847741276 bp ( 14.05 % ) Sampling Time: 00:34:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23314206 Comparison Time: 24:41:48 (hh:mm:ss) Elapsed Time, 266342 HSPs Collected Number of families returned by RECON: 27784 Round Time: 25:51:26 (hh:mm:ss) Elapsed Time : 413 families discovered. RepeatScout/RECON discovery complete: 1021 families found Classification Time: 01:02:47 (hh:mm:ss) Elapsed Time Program Time: 31:30:19 (hh:mm:ss) Elapsed Time