RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DOxZPr/RM_29556.SatDec311117502022 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: 1672514269 Database = /dev/shm/rModeler.DOxZPr/GCF_904848185.1_fAcaLat1.1 - Sequences = 66 - Bases = 685144197 Storage Throughput = excellent ( 1111.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022898 bp ( 40021298 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:37 (hh:mm:ss) Elapsed Time Round Time: 00:32:04 (hh:mm:ss) Elapsed Time : 305 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5764 repeats masked totaling 648937 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001486 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000986 bp After Masking: 9176948 bp Masked: 8.24 % -- Input Database Coverage: 10001486 bp out of 685144197 bp ( 1.46 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:50 (hh:mm:ss) Elapsed Time, 10488 HSPs Collected Number of families returned by RECON: 1854 Round Time: 00:07:53 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19989 repeats masked totaling 2405485 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021410 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30020310 bp After Masking: 27019774 bp Masked: 10.00 % -- Input Database Coverage: 40022896 bp out of 685144197 bp ( 5.84 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:38:38 (hh:mm:ss) Elapsed Time, 67636 HSPs Collected Number of families returned by RECON: 6831 Round Time: 00:43:34 (hh:mm:ss) Elapsed Time : 145 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 78824 repeats masked totaling 10581554 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040834 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 90038634 bp After Masking: 77559460 bp Masked: 13.86 % -- Input Database Coverage: 130063730 bp out of 685144197 bp ( 18.98 % ) Sampling Time: 00:07:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 04:34:49 (hh:mm:ss) Elapsed Time, 268770 HSPs Collected Number of families returned by RECON: 22752 Round Time: 05:01:12 (hh:mm:ss) Elapsed Time : 468 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 312888 repeats masked totaling 45526779 bp(s). - TE Masking time 00:09:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270009877 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 270004477 bp After Masking: 219236813 bp Masked: 18.80 % -- Input Database Coverage: 400073607 bp out of 685144197 bp ( 58.39 % ) Sampling Time: 00:25:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 35:32:54 (hh:mm:ss) Elapsed Time, 896107 HSPs Collected Number of families returned by RECON: 84955 Round Time: 39:01:23 (hh:mm:ss) Elapsed Time : 1184 families discovered. RepeatScout/RECON discovery complete: 2129 families found Classification Time: 01:36:51 (hh:mm:ss) Elapsed Time Program Time: 47:02:57 (hh:mm:ss) Elapsed Time