RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HYp88F/RM_1110627.MonMar181844102024 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: 1710812650 Database = /dev/shm/rModeler.HYp88F/GCA_036172795.1_aPelIbe1.pri - Sequences = 99 - Bases = 2077659799 Storage Throughput = excellent ( 1265.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006530 bp ( 40005730 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:04:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:57 (hh:mm:ss) Elapsed Time Round Time: 00:33:02 (hh:mm:ss) Elapsed Time : 649 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15829 repeats masked totaling 2972671 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000724 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10000724 bp After Masking: 5012858 bp Masked: 49.88 % -- Input Database Coverage: 10000724 bp out of 2077659799 bp ( 0.48 % ) Sampling Time: 00:06:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 16707 HSPs Collected Number of families returned by RECON: 1303 Round Time: 00:11:38 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48940 repeats masked totaling 9178223 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005803 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30005003 bp After Masking: 14922235 bp Masked: 50.27 % -- Input Database Coverage: 40006527 bp out of 2077659799 bp ( 1.93 % ) Sampling Time: 00:22:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:24:05 (hh:mm:ss) Elapsed Time, 50381 HSPs Collected Number of families returned by RECON: 4088 Round Time: 00:47:28 (hh:mm:ss) Elapsed Time : 110 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 161984 repeats masked totaling 29488537 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032898 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90029698 bp After Masking: 43436919 bp Masked: 51.75 % -- Input Database Coverage: 130039425 bp out of 2077659799 bp ( 6.26 % ) Sampling Time: 01:00:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:21:23 (hh:mm:ss) Elapsed Time, 220975 HSPs Collected Number of families returned by RECON: 12098 Round Time: 03:28:15 (hh:mm:ss) Elapsed Time : 428 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:26:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:11:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 542164 repeats masked totaling 98236735 bp(s). - TE Masking time 00:08:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012606 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 270005206 bp After Masking: 119723740 bp Masked: 55.66 % -- Input Database Coverage: 400052031 bp out of 2077659799 bp ( 19.25 % ) Sampling Time: 02:46:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 16:18:44 (hh:mm:ss) Elapsed Time, 866718 HSPs Collected Number of families returned by RECON: 34800 Round Time: 19:50:11 (hh:mm:ss) Elapsed Time : 1164 families discovered. RepeatScout/RECON discovery complete: 2380 families found Classification Time: 01:34:38 (hh:mm:ss) Elapsed Time Program Time: 26:25:12 (hh:mm:ss) Elapsed Time