RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FT3Ihl/RM_3172182.FriApr111107272025 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: 1744394847 Database = /dev/shm/rModeler.FT3Ihl/GCA_049354655.1_calJac240_alt - Sequences = 22 - Bases = 2760247778 Storage Throughput = excellent ( 1786.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002817 bp ( 40002817 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:11 (hh:mm:ss) Elapsed Time Round Time: 00:12:43 (hh:mm:ss) Elapsed Time : 263 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15535 repeats masked totaling 3101225 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000595 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10000595 bp After Masking: 6395983 bp Masked: 36.04 % -- Input Database Coverage: 10000595 bp out of 2760247778 bp ( 0.36 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 5087 HSPs Collected Number of families returned by RECON: 769 Round Time: 00:03:35 (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 : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48554 repeats masked totaling 9789947 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002142 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30002142 bp After Masking: 18564896 bp Masked: 38.12 % -- Input Database Coverage: 40002737 bp out of 2760247778 bp ( 1.45 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:11:15 (hh:mm:ss) Elapsed Time, 27414 HSPs Collected Number of families returned by RECON: 2564 Round Time: 00:13:38 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151439 repeats masked totaling 31250473 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90126221 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 90028776 bp After Masking: 55256333 bp Masked: 38.62 % -- Input Database Coverage: 130128958 bp out of 2760247778 bp ( 4.71 % ) Sampling Time: 00:04:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 01:06:31 (hh:mm:ss) Elapsed Time, 116828 HSPs Collected Number of families returned by RECON: 8656 Round Time: 01:13:02 (hh:mm:ss) Elapsed Time : 190 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 477154 repeats masked totaling 101539520 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270025316 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 270025316 bp After Masking: 156996319 bp Masked: 41.86 % -- Input Database Coverage: 400154274 bp out of 2760247778 bp ( 14.50 % ) Sampling Time: 00:15:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 07:42:10 (hh:mm:ss) Elapsed Time, 237820 HSPs Collected Number of families returned by RECON: 32583 Round Time: 08:19:09 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatScout/RECON discovery complete: 949 families found Classification Time: 00:18:38 (hh:mm:ss) Elapsed Time Program Time: 10:20:45 (hh:mm:ss) Elapsed Time