RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.sC1zDg/RM_2901733.SatApr121229272025 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: 1744486166 Database = /data/tmp/rModeler.sC1zDg/GCA_047922985.1_bEudEle1_v1.hap1 - Sequences = 397 - Bases = 1109691113 - N50 = 113328688 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 177294498-189958320 | [ 1 ] 164630677-177294498 | [ ] 151966856-164630677 | [ ] 139303034-151966855 | [ 1 ] 126639213-139303034 | [ ] 113975392-126639213 | [ ] 101311570-113975391 | [ 1 ] 88647749-101311570 | [ ] 75983928-88647749 | [ ] 63320106-75983927 | [ 2 ] 50656285-63320106 | [ 1 ] 37992464-50656285 | [ 1 ] 25328642-37992463 | [ 3 ] 12664821-25328642 |* [ 9 ] 1000-12664821 |************************************************** [ 378 ] Storage Throughput = excellent ( 1175.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012421 bp ( 40009821 non ambiguous ) - Num Contigs Represented = 73 - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:45 (hh:mm:ss) Elapsed Time Round Time: 00:46:42 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1258 repeats masked totaling 523148 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038679 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10037979 bp After Masking: 9090702 bp Masked: 9.44 % -- Input Database Coverage: 10038679 bp out of 1109691113 bp ( 0.90 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:59 (hh:mm:ss) Elapsed Time, 5752 HSPs Collected Number of families returned by RECON: 228 Round Time: 00:09:03 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5095 repeats masked totaling 1926349 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013668 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30011768 bp After Masking: 26230997 bp Masked: 12.60 % -- Input Database Coverage: 40052347 bp out of 1109691113 bp ( 3.61 % ) Sampling Time: 00:05:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:33:52 (hh:mm:ss) Elapsed Time, 10329 HSPs Collected Number of families returned by RECON: 1234 Round Time: 00:41:46 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16316 repeats masked totaling 5561168 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015976 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 90011976 bp After Masking: 79516472 bp Masked: 11.66 % -- Input Database Coverage: 130068323 bp out of 1109691113 bp ( 11.72 % ) Sampling Time: 00:11:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 03:36:49 (hh:mm:ss) Elapsed Time, 47556 HSPs Collected Number of families returned by RECON: 7955 Round Time: 03:59:38 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63496 repeats masked totaling 21729271 bp(s). - TE Masking time 00:03:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027509 bp Num Contigs Represented = 190 Non ambiguous bp: Initial: 270016909 bp After Masking: 232892905 bp Masked: 13.75 % -- Input Database Coverage: 400095832 bp out of 1109691113 bp ( 36.05 % ) Sampling Time: 00:37:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23096206 Comparison Time: 27:21:14 (hh:mm:ss) Elapsed Time, 279768 HSPs Collected Number of families returned by RECON: 50711 Round Time: 29:18:51 (hh:mm:ss) Elapsed Time : 211 families discovered. RepeatScout/RECON discovery complete: 330 families found Classification Time: 00:45:21 (hh:mm:ss) Elapsed Time Program Time: 35:41:21 (hh:mm:ss) Elapsed Time