RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pIP3x6/RM_1855744.TueApr220816272025 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: 1745334985 Database = /dev/shm/rModeler.pIP3x6/GCA_965153285.1_rPodTil1.hap1.1 - Sequences = 258 - Bases = 1462327121 - N50 = 97787859 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 126078946-135084514 | [ 1 ] 117073378-126078945 | [ 2 ] 108067811-117073378 | [ ] 99062243-108067810 | [ 2 ] 90056676-99062243 | [ 1 ] 81051108-90056675 | [ 2 ] 72045540-81051107 | [ 2 ] 63039973-72045540 | [ 1 ] 54034405-63039972 | [ 2 ] 45028838-54034405 | [ 2 ] 36023270-45028837 | [ 3 ] 27017702-36023269 | [ ] 18012135-27017702 | [ 1 ] 9006567-18012134 | [ 1 ] 1000-9006567 |************************************************** [ 238 ] Storage Throughput = excellent ( 1779.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020517 bp ( 40013717 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:37 (hh:mm:ss) Elapsed Time Round Time: 00:09:59 (hh:mm:ss) Elapsed Time : 548 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19099 repeats masked totaling 3224993 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031588 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10029388 bp After Masking: 6562392 bp Masked: 34.57 % -- Input Database Coverage: 10031588 bp out of 1462327121 bp ( 0.69 % ) Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:45 (hh:mm:ss) Elapsed Time, 10074 HSPs Collected Number of families returned by RECON: 1316 Round Time: 00:03:21 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57835 repeats masked totaling 9837968 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028928 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30024328 bp After Masking: 19425591 bp Masked: 35.30 % -- Input Database Coverage: 40060516 bp out of 1462327121 bp ( 2.74 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:11:47 (hh:mm:ss) Elapsed Time, 43143 HSPs Collected Number of families returned by RECON: 4379 Round Time: 00:13:38 (hh:mm:ss) Elapsed Time : 112 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 181670 repeats masked totaling 30625497 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036273 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 90025073 bp After Masking: 56722069 bp Masked: 36.99 % -- Input Database Coverage: 130096789 bp out of 1462327121 bp ( 8.90 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 01:08:21 (hh:mm:ss) Elapsed Time, 195334 HSPs Collected Number of families returned by RECON: 14270 Round Time: 01:16:37 (hh:mm:ss) Elapsed Time : 435 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 608612 repeats masked totaling 102576525 bp(s). - TE Masking time 00:02:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270047474 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 270011841 bp After Masking: 158765229 bp Masked: 41.20 % -- Input Database Coverage: 400144263 bp out of 1462327121 bp ( 27.36 % ) Sampling Time: 00:13:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 07:44:35 (hh:mm:ss) Elapsed Time, 503318 HSPs Collected Number of families returned by RECON: 49699 Round Time: 08:26:01 (hh:mm:ss) Elapsed Time : 1054 families discovered. RepeatScout/RECON discovery complete: 2181 families found Classification Time: 00:32:03 (hh:mm:ss) Elapsed Time Program Time: 10:41:39 (hh:mm:ss) Elapsed Time