RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fm2ZHw/RM_80128.TueJan31613082023 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: 1672791188 Database = /dev/shm/rModeler.fm2ZHw/GCF_013347855.1_fAngAng1.pri - Sequences = 54 - Bases = 979045926 Storage Throughput = excellent ( 1497.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40244993 bp ( 40037752 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:43 (hh:mm:ss) Elapsed Time Round Time: 00:15:12 (hh:mm:ss) Elapsed Time : 363 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 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6163 repeats masked totaling 1093408 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10081157 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10039857 bp After Masking: 8239990 bp Masked: 17.93 % -- Input Database Coverage: 10081157 bp out of 979045926 bp ( 1.03 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:06 (hh:mm:ss) Elapsed Time, 4443 HSPs Collected Number of families returned by RECON: 1085 Round Time: 00:07:43 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19080 repeats masked totaling 3396913 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30203836 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30037895 bp After Masking: 24598909 bp Masked: 18.11 % -- Input Database Coverage: 40284993 bp out of 979045926 bp ( 4.11 % ) Sampling Time: 00:03:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:32:06 (hh:mm:ss) Elapsed Time, 38017 HSPs Collected Number of families returned by RECON: 4453 Round Time: 00:36:33 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67689 repeats masked totaling 11706477 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90208738 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90032301 bp After Masking: 72351102 bp Masked: 19.64 % -- Input Database Coverage: 130493731 bp out of 979045926 bp ( 13.33 % ) Sampling Time: 00:11:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 02:34:51 (hh:mm:ss) Elapsed Time, 211055 HSPs Collected Number of families returned by RECON: 16121 Round Time: 02:52:46 (hh:mm:ss) Elapsed Time : 421 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 259184 repeats masked totaling 48109170 bp(s). - TE Masking time 00:03:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271220886 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 270009064 bp After Masking: 204163958 bp Masked: 24.39 % -- Input Database Coverage: 401714617 bp out of 979045926 bp ( 41.03 % ) Sampling Time: 00:32:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 17:20:01 (hh:mm:ss) Elapsed Time, 742774 HSPs Collected Number of families returned by RECON: 61769 Round Time: 18:56:09 (hh:mm:ss) Elapsed Time : 1099 families discovered. RepeatScout/RECON discovery complete: 1986 families found Classification Time: 01:05:23 (hh:mm:ss) Elapsed Time Program Time: 23:53:46 (hh:mm:ss) Elapsed Time