RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ccgGqQ/RM_122796.SatJan70435422023 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: 1673094942 Database = /dev/shm/rModeler.ccgGqQ/GCF_004027225.2_bStrHab1.2.pri - Sequences = 89 - Bases = 1148597545 Storage Throughput = excellent ( 1688.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40609197 bp ( 40017778 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:15 (hh:mm:ss) Elapsed Time Round Time: 00:18:40 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2170 repeats masked totaling 781153 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10166026 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10001806 bp After Masking: 9145796 bp Masked: 8.56 % -- Input Database Coverage: 10166026 bp out of 1148597545 bp ( 0.89 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 440 HSPs Collected Number of families returned by RECON: 206 Round Time: 00:06:59 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6173 repeats masked totaling 2323831 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30443091 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30015892 bp After Masking: 27566421 bp Masked: 8.16 % -- Input Database Coverage: 40609117 bp out of 1148597545 bp ( 3.54 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:25:51 (hh:mm:ss) Elapsed Time, 4012 HSPs Collected Number of families returned by RECON: 1438 Round Time: 00:28:07 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19892 repeats masked totaling 7002079 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90770895 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90033714 bp After Masking: 82605518 bp Masked: 8.25 % -- Input Database Coverage: 131380012 bp out of 1148597545 bp ( 11.44 % ) Sampling Time: 00:05:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 02:35:07 (hh:mm:ss) Elapsed Time, 31999 HSPs Collected Number of families returned by RECON: 9133 Round Time: 02:41:57 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71214 repeats masked totaling 24047408 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272906080 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 270030109 bp After Masking: 244421802 bp Masked: 9.48 % -- Input Database Coverage: 404286092 bp out of 1148597545 bp ( 35.20 % ) Sampling Time: 00:16:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23334696 Comparison Time: 18:31:23 (hh:mm:ss) Elapsed Time, 151868 HSPs Collected Number of families returned by RECON: 61857 Round Time: 19:15:29 (hh:mm:ss) Elapsed Time : 166 families discovered. RepeatScout/RECON discovery complete: 267 families found Classification Time: 00:13:05 (hh:mm:ss) Elapsed Time Program Time: 23:04:17 (hh:mm:ss) Elapsed Time