RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Y2kqbe/RM_6897.WedDec41216092024 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: 1733343368 Database = /scratch/tmp/rModeler.Y2kqbe/GCA_036010775.2_bColLiv1.mat.v2 - Sequences = 650 - Bases = 1181506259 - N50 = 121985148 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198565191-212747336 | [ 1 ] 184383047-198565191 | [ ] 170200903-184383047 | [ ] 156018758-170200902 | [ 1 ] 141836614-156018758 | [ ] 127654470-141836614 | [ ] 113472326-127654470 | [ 1 ] 99290181-113472325 | [ ] 85108037-99290181 | [ ] 70925893-85108037 | [ 1 ] 56743749-70925893 | [ 1 ] 42561604-56743748 | [ ] 28379460-42561604 | [ 4 ] 14197316-28379460 | [ 8 ] 15172-14197316 |************************************************** [ 633 ] Storage Throughput = fair ( 643.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023862 bp ( 40021153 non ambiguous ) - Num Contigs Represented = 118 - Sequence extraction : 00:01:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:18 (hh:mm:ss) Elapsed Time Round Time: 00:31:50 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2620 repeats masked totaling 909196 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016041 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10015441 bp After Masking: 8010962 bp Masked: 20.01 % -- Input Database Coverage: 10016041 bp out of 1181506259 bp ( 0.85 % ) Sampling Time: 00:15:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 3754 HSPs Collected Number of families returned by RECON: 190 Round Time: 00:21:21 (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 : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7986 repeats masked totaling 2667143 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007741 bp Num Contigs Represented = 96 Non ambiguous bp: Initial: 30005632 bp After Masking: 24287453 bp Masked: 19.06 % -- Input Database Coverage: 40023782 bp out of 1181506259 bp ( 3.39 % ) Sampling Time: 00:41:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:31:00 (hh:mm:ss) Elapsed Time, 4898 HSPs Collected Number of families returned by RECON: 1082 Round Time: 01:30:02 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:41:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25629 repeats masked totaling 8459251 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027305 bp Num Contigs Represented = 209 Non ambiguous bp: Initial: 90024514 bp After Masking: 73630489 bp Masked: 18.21 % -- Input Database Coverage: 130051087 bp out of 1181506259 bp ( 11.01 % ) Sampling Time: 01:46:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2598060 Comparison Time: 03:56:48 (hh:mm:ss) Elapsed Time, 69654 HSPs Collected Number of families returned by RECON: 7159 Round Time: 05:51:05 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 05:07:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86843 repeats masked totaling 28434183 bp(s). - TE Masking time 00:03:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046407 bp Num Contigs Represented = 386 Non ambiguous bp: Initial: 270038907 bp After Masking: 217382025 bp Masked: 19.50 % -- Input Database Coverage: 400097494 bp out of 1181506259 bp ( 33.86 % ) Sampling Time: 05:27:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23300551 Comparison Time: 32:26:31 (hh:mm:ss) Elapsed Time, 295669 HSPs Collected Number of families returned by RECON: 45835 Round Time: 38:56:59 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatScout/RECON discovery complete: 378 families found Classification Time: 00:27:48 (hh:mm:ss) Elapsed Time Program Time: 47:39:05 (hh:mm:ss) Elapsed Time