RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tPEn2I/RM_2413536.TueJul91105392024 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: 1720548338 Database = /dev/shm/rModeler.tPEn2I/GCF_030265055.1_RoL_Dexc_1.0 - Sequences = 57 - Bases = 519378276 Storage Throughput = excellent ( 1092.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014256 bp ( 40014216 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:37 (hh:mm:ss) Elapsed Time Round Time: 00:20:44 (hh:mm:ss) Elapsed Time : 620 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18297 repeats masked totaling 2545343 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010196 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10010196 bp After Masking: 6437268 bp Masked: 35.69 % -- Input Database Coverage: 10010196 bp out of 519378276 bp ( 1.93 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:29 (hh:mm:ss) Elapsed Time, 10520 HSPs Collected Number of families returned by RECON: 1613 Round Time: 00:07:36 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57472 repeats masked totaling 7731403 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004043 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30004003 bp After Masking: 19620036 bp Masked: 34.61 % -- Input Database Coverage: 40014239 bp out of 519378276 bp ( 7.70 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:26:05 (hh:mm:ss) Elapsed Time, 66588 HSPs Collected Number of families returned by RECON: 5668 Round Time: 00:31:24 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 191906 repeats masked totaling 25918059 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030148 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90030108 bp After Masking: 55335308 bp Masked: 38.54 % -- Input Database Coverage: 130044387 bp out of 519378276 bp ( 25.04 % ) Sampling Time: 00:15:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:41:04 (hh:mm:ss) Elapsed Time, 239081 HSPs Collected Number of families returned by RECON: 16833 Round Time: 03:05:16 (hh:mm:ss) Elapsed Time : 469 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 652768 repeats masked totaling 87744618 bp(s). - TE Masking time 00:08:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270008368 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 270008248 bp After Masking: 156970919 bp Masked: 41.86 % -- Input Database Coverage: 400052755 bp out of 519378276 bp ( 77.03 % ) Sampling Time: 00:43:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 18:36:21 (hh:mm:ss) Elapsed Time, 585643 HSPs Collected Number of families returned by RECON: 58633 Round Time: 20:39:05 (hh:mm:ss) Elapsed Time : 955 families discovered. RepeatScout/RECON discovery complete: 2256 families found Classification Time: 01:06:34 (hh:mm:ss) Elapsed Time Program Time: 25:50:39 (hh:mm:ss) Elapsed Time