RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Dr4sez/RM_2815050.MonDec92026482024 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: 1733804808 Database = /scratch/tmp/rModeler.Dr4sez/GCA_040954595.1_ASM4095459v1 - Sequences = 56 - Bases = 322493648 Storage Throughput = excellent ( 1458.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045618 bp ( 40025618 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:52 (hh:mm:ss) Elapsed Time Round Time: 00:11:13 (hh:mm:ss) Elapsed Time : 385 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6132 repeats masked totaling 1554465 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039170 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10032670 bp After Masking: 7341102 bp Masked: 26.83 % -- Input Database Coverage: 10039170 bp out of 322493648 bp ( 3.11 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:33 (hh:mm:ss) Elapsed Time, 2967 HSPs Collected Number of families returned by RECON: 700 Round Time: 00:03:27 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18794 repeats masked totaling 5096236 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046368 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30032868 bp After Masking: 21896588 bp Masked: 27.09 % -- Input Database Coverage: 40085538 bp out of 322493648 bp ( 12.43 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:11:05 (hh:mm:ss) Elapsed Time, 32325 HSPs Collected Number of families returned by RECON: 2990 Round Time: 00:13:25 (hh:mm:ss) Elapsed Time : 38 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60337 repeats masked totaling 14964216 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90065113 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90027134 bp After Masking: 65960828 bp Masked: 26.73 % -- Input Database Coverage: 130150651 bp out of 322493648 bp ( 40.36 % ) Sampling Time: 00:07:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:07:45 (hh:mm:ss) Elapsed Time, 228822 HSPs Collected Number of families returned by RECON: 11019 Round Time: 01:18:52 (hh:mm:ss) Elapsed Time : 275 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 150127 repeats masked totaling 38449142 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 192342638 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 192273617 bp After Masking: 133154753 bp Masked: 30.75 % -- Input Database Coverage: 322493289 bp out of 322493648 bp ( 100.00 % ) Sampling Time: 00:14:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 11637900 Comparison Time: 04:09:25 (hh:mm:ss) Elapsed Time, 526975 HSPs Collected Number of families returned by RECON: 25500 Round Time: 04:35:34 (hh:mm:ss) Elapsed Time : 517 families discovered. RepeatScout/RECON discovery complete: 1222 families found Classification Time: 00:51:15 (hh:mm:ss) Elapsed Time Program Time: 07:13:46 (hh:mm:ss) Elapsed Time