RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dzVHFe/RM_658503.TueMay162301442023 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: 1684303303 Database = /dev/shm/rModeler.dzVHFe/GCF_028500815.1_bRisTri1.patW.cur.20221130 - Sequences = 716 - Bases = 1353621101 - N50 = 94792718 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204964893-219604264 | [ 1 ] 190325522-204964892 | [ ] 175686152-190325522 | [ ] 161046781-175686151 | [ 1 ] 146407410-161046780 | [ ] 131768040-146407410 | [ ] 117128669-131768039 | [ 1 ] 102489298-117128668 | [ ] 87849928-102489298 | [ 2 ] 73210557-87849927 | [ 2 ] 58571186-73210556 | [ ] 43931816-58571186 | [ 3 ] 29292445-43931815 | [ 1 ] 14653074-29292444 | [ 6 ] 13704-14653074 |************************************************** [ 699 ] Storage Throughput = good ( 989.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031012 bp ( 40026185 non ambiguous ) - Num Contigs Represented = 106 - Sequence extraction : 00:02:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:07 (hh:mm:ss) Elapsed Time Round Time: 00:26:17 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2042 repeats masked totaling 723608 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001748 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10001535 bp After Masking: 8416118 bp Masked: 15.85 % -- Input Database Coverage: 10001748 bp out of 1353621101 bp ( 0.74 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:36 (hh:mm:ss) Elapsed Time, 789 HSPs Collected Number of families returned by RECON: 211 Round Time: 00:08:11 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6170 repeats masked totaling 2270950 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029252 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 30024638 bp After Masking: 25532376 bp Masked: 14.96 % -- Input Database Coverage: 40031000 bp out of 1353621101 bp ( 2.96 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:35:05 (hh:mm:ss) Elapsed Time, 33221 HSPs Collected Number of families returned by RECON: 1276 Round Time: 00:39:50 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20647 repeats masked totaling 7467825 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90088676 bp Num Contigs Represented = 194 Non ambiguous bp: Initial: 90001675 bp After Masking: 75769817 bp Masked: 15.81 % -- Input Database Coverage: 130119676 bp out of 1353621101 bp ( 9.61 % ) Sampling Time: 00:11:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2604903 Comparison Time: 03:44:16 (hh:mm:ss) Elapsed Time, 86261 HSPs Collected Number of families returned by RECON: 7063 Round Time: 04:07:15 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69536 repeats masked totaling 24196052 bp(s). - TE Masking time 00:03:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270196244 bp Num Contigs Represented = 342 Non ambiguous bp: Initial: 270030599 bp After Masking: 226856083 bp Masked: 15.99 % -- Input Database Coverage: 400315920 bp out of 1353621101 bp ( 29.57 % ) Sampling Time: 00:37:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23205078 Comparison Time: 28:14:30 (hh:mm:ss) Elapsed Time, 3094252 HSPs Collected Number of families returned by RECON: 45255 Round Time: 29:24:07 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatScout/RECON discovery complete: 379 families found Classification Time: 00:32:38 (hh:mm:ss) Elapsed Time Program Time: 35:18:18 (hh:mm:ss) Elapsed Time