RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.70YIkc/RM_1361427.WedNov291624382023 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: 1701303877 Database = /dev/shm/rModeler.70YIkc/GCF_030020395.1_mManPen7.hap1 - Sequences = 661 - Bases = 2840164579 - N50 = 158319429 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 221313704-237121291 | [ 3 ] 205506118-221313704 | [ ] 189698531-205506117 | [ 1 ] 173890945-189698531 | [ 1 ] 158083358-173890944 | [ 2 ] 142275772-158083358 | [ 1 ] 126468185-142275771 | [ 3 ] 110660599-126468185 | [ 1 ] 94853012-110660598 | [ 2 ] 79045426-94853012 | [ 3 ] 63237839-79045425 | [ 1 ] 47430253-63237839 | [ ] 31622666-47430252 | [ 2 ] 15815080-31622666 | [ 1 ] 7494-15815080 |************************************************** [ 640 ] Storage Throughput = excellent ( 1257.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40089664 bp ( 40009064 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:03:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:40 (hh:mm:ss) Elapsed Time Round Time: 00:34:28 (hh:mm:ss) Elapsed Time : 169 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:55 (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... 5765 repeats masked totaling 2978998 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10077680 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10037680 bp After Masking: 6974587 bp Masked: 30.52 % -- Input Database Coverage: 10077680 bp out of 2840164579 bp ( 0.35 % ) Sampling Time: 00:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:07:15 (hh:mm:ss) Elapsed Time, 5333 HSPs Collected Number of families returned by RECON: 796 Round Time: 00:22:04 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20504 repeats masked totaling 10172950 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30051981 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30011381 bp After Masking: 19635743 bp Masked: 34.57 % -- Input Database Coverage: 40129661 bp out of 2840164579 bp ( 1.41 % ) Sampling Time: 00:06:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 01:04:22 (hh:mm:ss) Elapsed Time, 228075 HSPs Collected Number of families returned by RECON: 2115 Round Time: 01:12:54 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69855 repeats masked totaling 32042625 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90131414 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 90039765 bp After Masking: 57493353 bp Masked: 36.15 % -- Input Database Coverage: 130261075 bp out of 2840164579 bp ( 4.59 % ) Sampling Time: 00:15:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 04:02:59 (hh:mm:ss) Elapsed Time, 770564 HSPs Collected Number of families returned by RECON: 7970 Round Time: 05:32:40 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 250589 repeats masked totaling 107007779 bp(s). - TE Masking time 00:06:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270541524 bp Num Contigs Represented = 211 Non ambiguous bp: Initial: 270004017 bp After Masking: 161389653 bp Masked: 40.23 % -- Input Database Coverage: 400802599 bp out of 2840164579 bp ( 14.11 % ) Sampling Time: 00:50:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23089410 Comparison Time: 24:42:45 (hh:mm:ss) Elapsed Time, 9138011 HSPs Collected Number of families returned by RECON: 30290 Round Time: 25:54:57 (hh:mm:ss) Elapsed Time : 292 families discovered. RepeatScout/RECON discovery complete: 710 families found Classification Time: 00:39:12 (hh:mm:ss) Elapsed Time Program Time: 34:16:15 (hh:mm:ss) Elapsed Time