RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jf6hTf/RM_3907027.WedFeb260827052025 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: 1740587225 Database = /dev/shm/rModeler.jf6hTf/GCA_964166675.1_xgCepNemo3.hap2.1 - Sequences = 2975 - Bases = 3270717112 - N50 = 129717769 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 504831884-540891233 | [ 1 ] 468772535-504831883 | [ ] 432713186-468772534 | [ ] 396653837-432713185 | [ ] 360594488-396653836 | [ ] 324535139-360594487 | [ ] 288475790-324535138 | [ ] 252416442-288475790 | [ ] 216357093-252416441 | [ 1 ] 180297744-216357092 | [ ] 144238395-180297743 | [ 2 ] 108179046-144238394 | [ 10 ] 72119697-108179045 | [ 8 ] 36060348-72119696 | [ ] 1000-36060348 |************************************************** [ 2953 ] Storage Throughput = excellent ( 1726.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041719 bp ( 40028396 non ambiguous ) - Num Contigs Represented = 84 - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:25 (hh:mm:ss) Elapsed Time Round Time: 00:17:50 (hh:mm:ss) Elapsed Time : 733 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19729 repeats masked totaling 5493673 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036456 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10031585 bp After Masking: 2591624 bp Masked: 74.17 % -- Input Database Coverage: 10036456 bp out of 3270717112 bp ( 0.31 % ) Sampling Time: 00:02:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:45 (hh:mm:ss) Elapsed Time, 8054 HSPs Collected Number of families returned by RECON: 573 Round Time: 00:05:40 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61310 repeats masked totaling 17604307 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045261 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 30036809 bp After Masking: 7160134 bp Masked: 76.16 % -- Input Database Coverage: 40081717 bp out of 3270717112 bp ( 1.23 % ) Sampling Time: 00:06:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:09:52 (hh:mm:ss) Elapsed Time, 27243 HSPs Collected Number of families returned by RECON: 2112 Round Time: 00:35:50 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 186155 repeats masked totaling 53703247 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90074419 bp Num Contigs Represented = 196 Non ambiguous bp: Initial: 90032883 bp After Masking: 20728490 bp Masked: 76.98 % -- Input Database Coverage: 130156136 bp out of 3270717112 bp ( 3.98 % ) Sampling Time: 00:21:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2664586 Comparison Time: 00:42:35 (hh:mm:ss) Elapsed Time, 150385 HSPs Collected Number of families returned by RECON: 5762 Round Time: 01:06:09 (hh:mm:ss) Elapsed Time : 298 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:41:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 609297 repeats masked totaling 169178540 bp(s). - TE Masking time 00:04:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270125280 bp Num Contigs Represented = 442 Non ambiguous bp: Initial: 270001281 bp After Masking: 52684420 bp Masked: 80.49 % -- Input Database Coverage: 400281416 bp out of 3270717112 bp ( 12.24 % ) Sampling Time: 00:59:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23891328 Comparison Time: 03:39:37 (hh:mm:ss) Elapsed Time, 478396 HSPs Collected Number of families returned by RECON: 14933 Round Time: 04:44:38 (hh:mm:ss) Elapsed Time : 643 families discovered. RepeatScout/RECON discovery complete: 1739 families found Classification Time: 00:40:40 (hh:mm:ss) Elapsed Time Program Time: 07:30:47 (hh:mm:ss) Elapsed Time