RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5M6KL6/RM_18937.MonJan20830072023 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: 1672677006 Database = /dev/shm/rModeler.5M6KL6/GCF_902150065.1_fMyrMur1.1 - Sequences = 87 - Bases = 835254674 Storage Throughput = excellent ( 1023.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041687 bp ( 40038894 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:07 (hh:mm:ss) Elapsed Time Round Time: 00:26:24 (hh:mm:ss) Elapsed Time : 493 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6928 repeats masked totaling 1128571 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002200 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10002187 bp After Masking: 8565617 bp Masked: 14.36 % -- Input Database Coverage: 10002200 bp out of 835254674 bp ( 1.20 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:08:04 (hh:mm:ss) Elapsed Time, 11767 HSPs Collected Number of families returned by RECON: 2248 Round Time: 00:09:30 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23250 repeats masked totaling 3781989 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039407 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30036627 bp After Masking: 25290965 bp Masked: 15.80 % -- Input Database Coverage: 40041607 bp out of 835254674 bp ( 4.79 % ) Sampling Time: 00:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:47:36 (hh:mm:ss) Elapsed Time, 87057 HSPs Collected Number of families returned by RECON: 8234 Round Time: 00:54:12 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89475 repeats masked totaling 14862960 bp(s). - TE Masking time 00:02:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90086952 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90001918 bp After Masking: 72499873 bp Masked: 19.45 % -- Input Database Coverage: 130128559 bp out of 835254674 bp ( 15.58 % ) Sampling Time: 00:09:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 05:47:31 (hh:mm:ss) Elapsed Time, 387547 HSPs Collected Number of families returned by RECON: 26251 Round Time: 06:24:43 (hh:mm:ss) Elapsed Time : 652 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 356630 repeats masked totaling 61937162 bp(s). - TE Masking time 00:18:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270879811 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 270007271 bp After Masking: 199712485 bp Masked: 26.03 % -- Input Database Coverage: 401008370 bp out of 835254674 bp ( 48.01 % ) Sampling Time: 00:38:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 43:53:07 (hh:mm:ss) Elapsed Time, 1207229 HSPs Collected Number of families returned by RECON: 85300 Round Time: 48:22:08 (hh:mm:ss) Elapsed Time : 1704 families discovered. RepeatScout/RECON discovery complete: 3057 families found Classification Time: 02:19:03 (hh:mm:ss) Elapsed Time Program Time: 58:36:00 (hh:mm:ss) Elapsed Time