RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.MGvdDy/RM_3516727.ThuNov142044522024 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: 1731645891 Database = /scratch/tmp/rModeler.MGvdDy/GCA_964106895.1_bNumArq3.hap1.1 - Sequences = 1819 - Bases = 1348876333 - N50 = 70415703 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 132515718-141981056 | [ 2 ] 123050381-132515718 | [ ] 113585044-123050381 | [ ] 104119707-113585044 | [ ] 94654370-104119707 | [ ] 85189033-94654370 | [ 1 ] 75723696-85189033 | [ 2 ] 66258359-75723696 | [ 2 ] 56793022-66258359 | [ 4 ] 47327685-56793022 | [ ] 37862348-47327685 | [ 2 ] 28397011-37862348 | [ 1 ] 18931674-28397011 | [ 2 ] 9466337-18931674 | [ 5 ] 1000-9466337 |************************************************** [ 1798 ] Storage Throughput = excellent ( 1518.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017792 bp ( 40011392 non ambiguous ) - Num Contigs Represented = 158 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:10 (hh:mm:ss) Elapsed Time Round Time: 00:16:35 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2604 repeats masked totaling 1017155 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030602 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 10028802 bp After Masking: 8583022 bp Masked: 14.42 % -- Input Database Coverage: 10030602 bp out of 1348876333 bp ( 0.74 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:21:14 (hh:mm:ss) Elapsed Time, 52916 HSPs Collected Number of families returned by RECON: 203 Round Time: 00:21:51 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7761 repeats masked totaling 2991894 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027104 bp Num Contigs Represented = 132 Non ambiguous bp: Initial: 30022504 bp After Masking: 25966214 bp Masked: 13.51 % -- Input Database Coverage: 40057706 bp out of 1348876333 bp ( 2.97 % ) Sampling Time: 00:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 02:33:24 (hh:mm:ss) Elapsed Time, 1215702 HSPs Collected Number of families returned by RECON: 1392 Round Time: 02:35:59 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24266 repeats masked totaling 8282988 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028286 bp Num Contigs Represented = 298 Non ambiguous bp: Initial: 90018686 bp After Masking: 78312399 bp Masked: 13.00 % -- Input Database Coverage: 130085992 bp out of 1348876333 bp ( 9.64 % ) Sampling Time: 00:04:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2662278 Comparison Time: 11:18:23 (hh:mm:ss) Elapsed Time, 14714626 HSPs Collected Number of families returned by RECON: 7313 Round Time: 11:27:16 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86786 repeats masked totaling 30455813 bp(s). - TE Masking time 00:01:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270060854 bp Num Contigs Represented = 666 Non ambiguous bp: Initial: 270032438 bp After Masking: 230203922 bp Masked: 14.75 % -- Input Database Coverage: 400146846 bp out of 1348876333 bp ( 29.67 % ) Sampling Time: 00:14:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24036711 Comparison Time: 65:47:48 (hh:mm:ss) Elapsed Time, 139831147 HSPs Collected Number of families returned by RECON: 46650 Round Time: 67:44:32 (hh:mm:ss) Elapsed Time : 255 families discovered. RepeatScout/RECON discovery complete: 438 families found Classification Time: 00:17:42 (hh:mm:ss) Elapsed Time Program Time: 82:43:55 (hh:mm:ss) Elapsed Time