RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GZBEn9/RM_5575.SatApr121424082025 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: 1744493046 Database = /dev/shm/rModeler.GZBEn9/GCA_047830755.1_bZonAlb1.hap1 - Sequences = 180 - Bases = 1278938765 - N50 = 74180225 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146136328-156573735 | [ 1 ] 135698922-146136328 | [ ] 125261516-135698922 | [ ] 114824110-125261516 | [ 2 ] 104386704-114824110 | [ ] 93949298-104386704 | [ ] 83511892-93949298 | [ 1 ] 73074485-83511891 | [ 2 ] 62637079-73074485 | [ 1 ] 52199673-62637079 | [ ] 41762267-52199673 | [ 3 ] 31324861-41762267 | [ 2 ] 20887455-31324861 | [ 3 ] 10450049-20887455 |*** [ 10 ] 12643-10450049 |************************************************** [ 155 ] Storage Throughput = excellent ( 1604.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017558 bp ( 40015358 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:59 (hh:mm:ss) Elapsed Time Round Time: 00:13:35 (hh:mm:ss) Elapsed Time : 235 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3695 repeats masked totaling 1301790 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029204 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10029004 bp After Masking: 7994376 bp Masked: 20.29 % -- Input Database Coverage: 10029204 bp out of 1278938765 bp ( 0.78 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 6992 HSPs Collected Number of families returned by RECON: 409 Round Time: 00:04:09 (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 : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10398 repeats masked totaling 3742012 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028278 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30026278 bp After Masking: 23905489 bp Masked: 20.38 % -- Input Database Coverage: 40057482 bp out of 1278938765 bp ( 3.13 % ) Sampling Time: 00:03:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:56 (hh:mm:ss) Elapsed Time, 8482 HSPs Collected Number of families returned by RECON: 1635 Round Time: 00:16:39 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34152 repeats masked totaling 12535572 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017007 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 90013607 bp After Masking: 71159565 bp Masked: 20.95 % -- Input Database Coverage: 130074489 bp out of 1278938765 bp ( 10.17 % ) Sampling Time: 00:07:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 01:20:23 (hh:mm:ss) Elapsed Time, 97555 HSPs Collected Number of families returned by RECON: 9790 Round Time: 01:34:53 (hh:mm:ss) Elapsed Time : 136 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114718 repeats masked totaling 43794809 bp(s). - TE Masking time 00:02:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270008377 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 270001077 bp After Masking: 207269353 bp Masked: 23.23 % -- Input Database Coverage: 400082866 bp out of 1278938765 bp ( 31.28 % ) Sampling Time: 00:22:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 09:49:55 (hh:mm:ss) Elapsed Time, 365923 HSPs Collected Number of families returned by RECON: 63066 Round Time: 10:38:09 (hh:mm:ss) Elapsed Time : 347 families discovered. RepeatScout/RECON discovery complete: 736 families found Classification Time: 00:28:48 (hh:mm:ss) Elapsed Time Program Time: 13:16:13 (hh:mm:ss) Elapsed Time