RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.9ReVaF/RM_2773063.SunApr131835522025 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: 1744594551 Database = /data/tmp/rModeler.9ReVaF/GCA_045362495.1_fLetNeb1.hap1 - Sequences = 226 - Bases = 1133212262 - N50 = 48448782 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 51560455-55243022 | [ 3 ] 47877889-51560455 |** [ 9 ] 44195323-47877889 |* [ 5 ] 40512757-44195323 | [ 4 ] 36830191-40512757 | [ 1 ] 33147625-36830191 | [ 2 ] 29465059-33147625 | [ ] 25782493-29465059 | [ ] 22099927-25782493 | [ ] 18417361-22099927 | [ ] 14734795-18417361 | [ ] 11052229-14734795 | [ ] 7369663-11052229 | [ ] 3687097-7369663 | [ ] 4531-3687097 |************************************************** [ 202 ] Storage Throughput = excellent ( 1494.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013138 bp ( 40012138 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:20 (hh:mm:ss) Elapsed Time Round Time: 00:13:06 (hh:mm:ss) Elapsed Time : 691 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12714 repeats masked totaling 1831841 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009084 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10008684 bp After Masking: 7877344 bp Masked: 21.29 % -- Input Database Coverage: 10009084 bp out of 1133212262 bp ( 0.88 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:04 (hh:mm:ss) Elapsed Time, 19742 HSPs Collected Number of families returned by RECON: 2415 Round Time: 00:05:12 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (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... 44213 repeats masked totaling 6684365 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004049 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30003449 bp After Masking: 22551696 bp Masked: 24.84 % -- Input Database Coverage: 40013133 bp out of 1133212262 bp ( 3.53 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:18:44 (hh:mm:ss) Elapsed Time, 103829 HSPs Collected Number of families returned by RECON: 7530 Round Time: 00:22:56 (hh:mm:ss) Elapsed Time : 223 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 162603 repeats masked totaling 24881427 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027273 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 90024273 bp After Masking: 62762831 bp Masked: 30.28 % -- Input Database Coverage: 130040406 bp out of 1133212262 bp ( 11.48 % ) Sampling Time: 00:06:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:55:41 (hh:mm:ss) Elapsed Time, 387944 HSPs Collected Number of families returned by RECON: 20001 Round Time: 02:10:39 (hh:mm:ss) Elapsed Time : 612 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 570490 repeats masked totaling 90023277 bp(s). - TE Masking time 00:07:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030658 bp Num Contigs Represented = 96 Non ambiguous bp: Initial: 270023658 bp After Masking: 171132810 bp Masked: 36.62 % -- Input Database Coverage: 400071064 bp out of 1133212262 bp ( 35.30 % ) Sampling Time: 00:25:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 12:28:05 (hh:mm:ss) Elapsed Time, 1231385 HSPs Collected Number of families returned by RECON: 60288 Round Time: 13:54:50 (hh:mm:ss) Elapsed Time : 1604 families discovered. RepeatScout/RECON discovery complete: 3176 families found Classification Time: 01:20:52 (hh:mm:ss) Elapsed Time Program Time: 18:07:35 (hh:mm:ss) Elapsed Time