RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Ugtfpy/RM_2030688.SatJul271136482024 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: 1722105407 Database = /dev/shm/rModeler.Ugtfpy/GCF_021347895.1_KAUST_Apoly_ChrSc - Sequences = 81 - Bases = 956771783 Storage Throughput = excellent ( 1178.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012939 bp ( 40010064 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:16 (hh:mm:ss) Elapsed Time Round Time: 00:21:17 (hh:mm:ss) Elapsed Time : 570 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9842 repeats masked totaling 2095089 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022529 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10021704 bp After Masking: 7593623 bp Masked: 24.23 % -- Input Database Coverage: 10022529 bp out of 956771783 bp ( 1.05 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:00 (hh:mm:ss) Elapsed Time, 7650 HSPs Collected Number of families returned by RECON: 1539 Round Time: 00:08:39 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30215 repeats masked totaling 6393470 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030478 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30028428 bp After Masking: 22652064 bp Masked: 24.56 % -- Input Database Coverage: 40053007 bp out of 956771783 bp ( 4.19 % ) Sampling Time: 00:03:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:31:49 (hh:mm:ss) Elapsed Time, 61293 HSPs Collected Number of families returned by RECON: 5260 Round Time: 00:37:35 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105170 repeats masked totaling 22044274 bp(s). - TE Masking time 00:01:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016094 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 90008620 bp After Masking: 64860461 bp Masked: 27.94 % -- Input Database Coverage: 130069101 bp out of 956771783 bp ( 13.59 % ) Sampling Time: 00:10:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:17:00 (hh:mm:ss) Elapsed Time, 323815 HSPs Collected Number of families returned by RECON: 15860 Round Time: 03:41:06 (hh:mm:ss) Elapsed Time : 537 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 384716 repeats masked totaling 83374644 bp(s). - TE Masking time 00:10:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270052067 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 270031163 bp After Masking: 177323129 bp Masked: 34.33 % -- Input Database Coverage: 400121168 bp out of 956771783 bp ( 41.82 % ) Sampling Time: 00:35:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 20:18:42 (hh:mm:ss) Elapsed Time, 730867 HSPs Collected Number of families returned by RECON: 53649 Round Time: 21:55:56 (hh:mm:ss) Elapsed Time : 1128 families discovered. RepeatScout/RECON discovery complete: 2362 families found Classification Time: 01:50:05 (hh:mm:ss) Elapsed Time Program Time: 28:34:39 (hh:mm:ss) Elapsed Time