RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.aWD1YI/RM_925629.SunMar160242572025 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: 1742118148 Database = /dev/shm/rModeler.aWD1YI/GCA_022644695.1_ASM2264469v1 - Sequences = 14 - Bases = 2017999361 Storage Throughput = excellent ( 1892.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041793 bp ( 40039093 non ambiguous ) - Num Contigs Represented = 14 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:04:37 (hh:mm:ss) Elapsed Time Round Time: 01:59:32 (hh:mm:ss) Elapsed Time : 1161 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12932 repeats masked totaling 5322714 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040342 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10039342 bp After Masking: 4657542 bp Masked: 53.61 % -- Input Database Coverage: 10040342 bp out of 2017999361 bp ( 0.50 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 01:55:12 (hh:mm:ss) Elapsed Time, 5203 HSPs Collected Number of families returned by RECON: 1238 Round Time: 02:00:59 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39423 repeats masked totaling 16066169 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041451 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 30039751 bp After Masking: 13713575 bp Masked: 54.35 % -- Input Database Coverage: 40081793 bp out of 2017999361 bp ( 1.99 % ) Sampling Time: 00:03:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 05:45:36 (hh:mm:ss) Elapsed Time, 43650 HSPs Collected Number of families returned by RECON: 4270 Round Time: 05:58:12 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121292 repeats masked totaling 49995708 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043875 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 90038075 bp After Masking: 39230739 bp Masked: 56.43 % -- Input Database Coverage: 130125668 bp out of 2017999361 bp ( 6.45 % ) Sampling Time: 00:07:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 17:17:26 (hh:mm:ss) Elapsed Time, 360046 HSPs Collected Number of families returned by RECON: 13495 Round Time: 18:20:50 (hh:mm:ss) Elapsed Time : 450 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 399976 repeats masked totaling 166231334 bp(s). - TE Masking time 00:07:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270043726 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 270021726 bp After Masking: 101793044 bp Masked: 62.30 % -- Input Database Coverage: 400169394 bp out of 2017999361 bp ( 19.83 % ) Sampling Time: 00:22:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 53:25:34 (hh:mm:ss) Elapsed Time, 1579874 HSPs Collected Number of families returned by RECON: 41462 Round Time: 56:07:43 (hh:mm:ss) Elapsed Time : 1005 families discovered. RepeatScout/RECON discovery complete: 2683 families found Classification Time: 01:05:35 (hh:mm:ss) Elapsed Time Program Time: 85:32:51 (hh:mm:ss) Elapsed Time