RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.66ij6p/RM_2973926.TueNov280946382023 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: 1701193598 Database = /dev/shm/rModeler.66ij6p/GCF_030490865.1_bPoeAtr1.hap1 - Sequences = 307 - Bases = 1251133642 - N50 = 146584261 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 169461081-181565373 | [ 1 ] 157356789-169461080 | [ ] 145252498-157356789 | [ 2 ] 133148206-145252497 | [ ] 121043915-133148206 | [ ] 108939623-121043914 | [ 1 ] 96835332-108939623 | [ 1 ] 84731040-96835331 | [ ] 72626749-84731040 | [ 1 ] 60522457-72626748 | [ ] 48418166-60522457 | [ ] 36313874-48418165 | [ 2 ] 24209583-36313874 | [ 3 ] 12105291-24209582 |* [ 7 ] 1000-12105291 |************************************************** [ 289 ] Storage Throughput = excellent ( 1078.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028096 bp ( 40010017 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:01:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:37 (hh:mm:ss) Elapsed Time Round Time: 00:21:34 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3629 repeats masked totaling 1007582 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030129 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10029929 bp After Masking: 8681847 bp Masked: 13.44 % -- Input Database Coverage: 10030129 bp out of 1251133642 bp ( 0.80 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:08:12 (hh:mm:ss) Elapsed Time, 4267 HSPs Collected Number of families returned by RECON: 303 Round Time: 00:10:13 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10762 repeats masked totaling 3179205 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037887 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30020008 bp After Masking: 25985681 bp Masked: 13.44 % -- Input Database Coverage: 40068016 bp out of 1251133642 bp ( 3.20 % ) Sampling Time: 00:04:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:38:55 (hh:mm:ss) Elapsed Time, 123016 HSPs Collected Number of families returned by RECON: 1480 Round Time: 00:43:44 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32274 repeats masked totaling 8994642 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90059631 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90026764 bp After Masking: 78122382 bp Masked: 13.22 % -- Input Database Coverage: 130127647 bp out of 1251133642 bp ( 10.40 % ) Sampling Time: 00:13:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 04:00:52 (hh:mm:ss) Elapsed Time, 554112 HSPs Collected Number of families returned by RECON: 9367 Round Time: 04:19:24 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107093 repeats masked totaling 30950944 bp(s). - TE Masking time 00:06:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270217432 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 270016727 bp After Masking: 231205300 bp Masked: 14.37 % -- Input Database Coverage: 400345079 bp out of 1251133642 bp ( 32.00 % ) Sampling Time: 00:38:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 30:26:32 (hh:mm:ss) Elapsed Time, 4375942 HSPs Collected Number of families returned by RECON: 61232 Round Time: 31:46:01 (hh:mm:ss) Elapsed Time : 306 families discovered. RepeatScout/RECON discovery complete: 597 families found Classification Time: 01:23:14 (hh:mm:ss) Elapsed Time Program Time: 38:44:10 (hh:mm:ss) Elapsed Time