RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UuZpl9/RM_3877336.ThuApr101846272025 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: 1744335986 Database = /dev/shm/rModeler.UuZpl9/GCF_043159975.1_mMacNem.hap1 - Sequences = 361 - Bases = 3116288670 - N50 = 159757195 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 217798394-233354531 | [ 1 ] 202242257-217798393 | [ 1 ] 186686121-202242257 | [ 2 ] 171129984-186686120 | [ 3 ] 155573848-171129984 | [ 1 ] 140017711-155573847 | [ 4 ] 124461574-140017710 | [ 1 ] 108905438-124461574 | [ 3 ] 93349301-108905437 | [ 1 ] 77793165-93349301 | [ 3 ] 62237028-77793164 | [ 1 ] 46680891-62237027 | [ ] 31124755-46680891 | [ ] 15568618-31124754 | [ 1 ] 12482-15568618 |************************************************** [ 339 ] Storage Throughput = excellent ( 1788.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001119 bp ( 40000519 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:31 (hh:mm:ss) Elapsed Time Round Time: 00:13:03 (hh:mm:ss) Elapsed Time : 296 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15296 repeats masked totaling 2874741 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012196 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10011996 bp After Masking: 6173093 bp Masked: 38.34 % -- Input Database Coverage: 10012196 bp out of 3116288670 bp ( 0.32 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 5985 HSPs Collected Number of families returned by RECON: 798 Round Time: 00:03:57 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47974 repeats masked totaling 9532131 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028843 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30028243 bp After Masking: 17564825 bp Masked: 41.51 % -- Input Database Coverage: 40041039 bp out of 3116288670 bp ( 1.28 % ) Sampling Time: 00:02:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:03 (hh:mm:ss) Elapsed Time, 23492 HSPs Collected Number of families returned by RECON: 2134 Round Time: 00:14:47 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155762 repeats masked totaling 31098532 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021960 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90020860 bp After Masking: 51397319 bp Masked: 42.91 % -- Input Database Coverage: 130062999 bp out of 3116288670 bp ( 4.17 % ) Sampling Time: 00:09:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:05:51 (hh:mm:ss) Elapsed Time, 170162 HSPs Collected Number of families returned by RECON: 7049 Round Time: 01:16:48 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 503859 repeats masked totaling 102025224 bp(s). - TE Masking time 00:02:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270011124 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 270007772 bp After Masking: 146015880 bp Masked: 45.92 % -- Input Database Coverage: 400074123 bp out of 3116288670 bp ( 12.84 % ) Sampling Time: 00:23:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 07:07:04 (hh:mm:ss) Elapsed Time, 688646 HSPs Collected Number of families returned by RECON: 28528 Round Time: 07:37:48 (hh:mm:ss) Elapsed Time : 413 families discovered. RepeatScout/RECON discovery complete: 976 families found Classification Time: 00:21:38 (hh:mm:ss) Elapsed Time Program Time: 09:48:01 (hh:mm:ss) Elapsed Time