RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.V1q5Xe/RM_9235.SunNov171336242024 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: 1731879382 Database = /scratch/tmp/rModeler.V1q5Xe/GCA_043159975.1_mMacNem.hap1 - Sequences = 362 - Bases = 3116305216 - 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 |************************************************** [ 340 ] Storage Throughput = fair ( 575.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006300 bp ( 40005700 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:03:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:25 (hh:mm:ss) Elapsed Time Round Time: 00:32:45 (hh:mm:ss) Elapsed Time : 268 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13691 repeats masked totaling 2890366 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003334 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10003134 bp After Masking: 6384624 bp Masked: 36.17 % -- Input Database Coverage: 10003334 bp out of 3116305216 bp ( 0.32 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:15 (hh:mm:ss) Elapsed Time, 9960 HSPs Collected Number of families returned by RECON: 815 Round Time: 00:08:23 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44063 repeats masked totaling 9007664 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002886 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30002486 bp After Masking: 18465787 bp Masked: 38.45 % -- Input Database Coverage: 40006220 bp out of 3116305216 bp ( 1.28 % ) Sampling Time: 00:04:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:30:19 (hh:mm:ss) Elapsed Time, 73860 HSPs Collected Number of families returned by RECON: 2683 Round Time: 00:36:38 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142752 repeats masked totaling 30377340 bp(s). - TE Masking time 00:01:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024776 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90023876 bp After Masking: 52282142 bp Masked: 41.92 % -- Input Database Coverage: 130030996 bp out of 3116305216 bp ( 4.17 % ) Sampling Time: 00:15:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:01:27 (hh:mm:ss) Elapsed Time, 171163 HSPs Collected Number of families returned by RECON: 7529 Round Time: 03:22:09 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 466313 repeats masked totaling 99665232 bp(s). - TE Masking time 00:07:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270042102 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 270037102 bp After Masking: 149663622 bp Masked: 44.58 % -- Input Database Coverage: 400073098 bp out of 3116305216 bp ( 12.84 % ) Sampling Time: 00:46:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 22:52:50 (hh:mm:ss) Elapsed Time, 959702 HSPs Collected Number of families returned by RECON: 29812 Round Time: 24:24:13 (hh:mm:ss) Elapsed Time : 411 families discovered. RepeatScout/RECON discovery complete: 935 families found Classification Time: 00:48:45 (hh:mm:ss) Elapsed Time Program Time: 29:52:53 (hh:mm:ss) Elapsed Time