RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Q6WEFy/RM_2067.FriDec60525022024 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: 1733491501 Database = /scratch/tmp/rModeler.Q6WEFy/GCA_037039175.1_mMicPen1.hap2 - Sequences = 143 - Bases = 2156400253 - N50 = 125724489 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 207288090-222093578 | [ 1 ] 192482602-207288089 | [ ] 177677114-192482601 | [ ] 162871627-177677114 | [ ] 148066139-162871626 | [ 1 ] 133260651-148066138 |* [ 3 ] 118455163-133260650 | [ 2 ] 103649676-118455163 |* [ 4 ] 88844188-103649675 | [ 1 ] 74038700-88844187 |* [ 3 ] 59233212-74038699 | [ ] 44427725-59233212 | [ 2 ] 29622237-44427724 |** [ 5 ] 14816749-29622236 | [ ] 11262-14816749 |************************************************** [ 121 ] Storage Throughput = fair ( 602.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002954 bp ( 40002754 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:02:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:41 (hh:mm:ss) Elapsed Time Round Time: 00:34:35 (hh:mm:ss) Elapsed Time : 281 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14318 repeats masked totaling 2577823 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001700 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10001700 bp After Masking: 7092973 bp Masked: 29.08 % -- Input Database Coverage: 10001700 bp out of 2156400253 bp ( 0.46 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 6881 HSPs Collected Number of families returned by RECON: 792 Round Time: 00:07:48 (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 : 00:01:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42953 repeats masked totaling 7846720 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001252 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30001052 bp After Masking: 21084591 bp Masked: 29.72 % -- Input Database Coverage: 40002952 bp out of 2156400253 bp ( 1.86 % ) Sampling Time: 00:05:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:27:19 (hh:mm:ss) Elapsed Time, 20297 HSPs Collected Number of families returned by RECON: 2384 Round Time: 00:34:17 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 141531 repeats masked totaling 25594901 bp(s). - TE Masking time 00:01:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004852 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90004652 bp After Masking: 61477970 bp Masked: 31.69 % -- Input Database Coverage: 130007804 bp out of 2156400253 bp ( 6.03 % ) Sampling Time: 00:15:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:10:29 (hh:mm:ss) Elapsed Time, 95909 HSPs Collected Number of families returned by RECON: 8724 Round Time: 03:33:59 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 457889 repeats masked totaling 85159419 bp(s). - TE Masking time 00:06:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031894 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 270029494 bp After Masking: 175881411 bp Masked: 34.87 % -- Input Database Coverage: 400039698 bp out of 2156400253 bp ( 18.55 % ) Sampling Time: 00:46:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 24:45:25 (hh:mm:ss) Elapsed Time, 274547 HSPs Collected Number of families returned by RECON: 36022 Round Time: 26:31:12 (hh:mm:ss) Elapsed Time : 385 families discovered. RepeatScout/RECON discovery complete: 887 families found Classification Time: 00:39:53 (hh:mm:ss) Elapsed Time Program Time: 32:01:44 (hh:mm:ss) Elapsed Time