RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7150Xv/RM_30328.SunJan141619512024 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: 1705277989 Database = /dev/shm/rModeler.7150Xv/GCA_033958435.1_ASM3395843v1 - Sequences = 134 - Bases = 2180317067 - N50 = 139425650 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 357587831-383128740 | [ 1 ] 332046923-357587831 | [ ] 306506014-332046922 | [ ] 280965106-306506014 | [ 1 ] 255424197-280965105 | [ ] 229883289-255424197 | [ ] 204342380-229883288 | [ 1 ] 178801472-204342380 | [ ] 153260563-178801471 | [ ] 127719655-153260563 | [ 2 ] 102178746-127719654 | [ 1 ] 76637838-102178746 | [ ] 51096929-76637837 |* [ 4 ] 25556021-51096929 |**** [ 11 ] 15113-25556021 |************************************************** [ 113 ] Storage Throughput = excellent ( 1143.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002133 bp ( 40001733 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:02:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:53 (hh:mm:ss) Elapsed Time Round Time: 00:34:49 (hh:mm:ss) Elapsed Time : 474 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12981 repeats masked totaling 3553010 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000551 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10000351 bp After Masking: 6404443 bp Masked: 35.96 % -- Input Database Coverage: 10000551 bp out of 2180317067 bp ( 0.46 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:11:44 (hh:mm:ss) Elapsed Time, 15340 HSPs Collected Number of families returned by RECON: 1348 Round Time: 00:14:15 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39950 repeats masked totaling 10594904 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001502 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30001302 bp After Masking: 19093390 bp Masked: 36.36 % -- Input Database Coverage: 40002053 bp out of 2180317067 bp ( 1.83 % ) Sampling Time: 00:03:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:37:09 (hh:mm:ss) Elapsed Time, 67617 HSPs Collected Number of families returned by RECON: 3894 Round Time: 00:47:37 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138351 repeats masked totaling 35746620 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033638 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90033638 bp After Masking: 53532408 bp Masked: 40.54 % -- Input Database Coverage: 130035691 bp out of 2180317067 bp ( 5.96 % ) Sampling Time: 00:11:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 04:00:08 (hh:mm:ss) Elapsed Time, 193835 HSPs Collected Number of families returned by RECON: 11290 Round Time: 04:23:02 (hh:mm:ss) Elapsed Time : 344 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 475264 repeats masked totaling 117635706 bp(s). - TE Masking time 00:10:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039130 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 270039130 bp After Masking: 150057970 bp Masked: 44.43 % -- Input Database Coverage: 400074821 bp out of 2180317067 bp ( 18.35 % ) Sampling Time: 00:37:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 22:49:12 (hh:mm:ss) Elapsed Time, 447502 HSPs Collected Number of families returned by RECON: 36707 Round Time: 24:26:23 (hh:mm:ss) Elapsed Time : 838 families discovered. RepeatScout/RECON discovery complete: 1802 families found Classification Time: 01:10:53 (hh:mm:ss) Elapsed Time Program Time: 31:36:59 (hh:mm:ss) Elapsed Time