RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.j3N3PW/RM_3573392.SunApr130042112025 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: 1744530131 Database = /data/tmp/rModeler.j3N3PW/GCA_046562885.1_mPanOnc1_haplotype_1 - Sequences = 115 - Bases = 2303345105 - N50 = 158556951 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 225796785-241924008 | [ 1 ] 209669562-225796784 | [ 1 ] 193542340-209669562 | [ 1 ] 177415117-193542339 | [ ] 161287895-177415117 | [ 1 ] 145160672-161287894 |* [ 3 ] 129033450-145160672 |* [ 2 ] 112906227-129033449 | [ 1 ] 96779005-112906227 | [ ] 80651782-96779004 |** [ 4 ] 64524560-80651782 | [ 1 ] 48397337-64524559 |* [ 2 ] 32270115-48397337 | [ 1 ] 16142892-32270114 | [ ] 15670-16142892 |************************************************** [ 97 ] Storage Throughput = excellent ( 1653.28 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020705 bp ( 40020105 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:36 (hh:mm:ss) Elapsed Time Round Time: 00:16:35 (hh:mm:ss) Elapsed Time : 187 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 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11470 repeats masked totaling 2688038 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005052 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10005052 bp After Masking: 7233506 bp Masked: 27.70 % -- Input Database Coverage: 10005052 bp out of 2303345105 bp ( 0.43 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:42 (hh:mm:ss) Elapsed Time, 8513 HSPs Collected Number of families returned by RECON: 980 Round Time: 00:04:44 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38196 repeats masked totaling 7843816 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015573 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30014973 bp After Masking: 21868064 bp Masked: 27.14 % -- Input Database Coverage: 40020625 bp out of 2303345105 bp ( 1.74 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:19:13 (hh:mm:ss) Elapsed Time, 28620 HSPs Collected Number of families returned by RECON: 2562 Round Time: 00:22:09 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124672 repeats masked totaling 26810135 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019865 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90018065 bp After Masking: 62323983 bp Masked: 30.77 % -- Input Database Coverage: 130040490 bp out of 2303345105 bp ( 5.65 % ) Sampling Time: 00:06:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 01:47:29 (hh:mm:ss) Elapsed Time, 64094 HSPs Collected Number of families returned by RECON: 8148 Round Time: 01:58:40 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 414866 repeats masked totaling 87493637 bp(s). - TE Masking time 00:03:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019747 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 270016347 bp After Masking: 180076870 bp Masked: 33.31 % -- Input Database Coverage: 400060237 bp out of 2303345105 bp ( 17.37 % ) Sampling Time: 00:22:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 11:56:50 (hh:mm:ss) Elapsed Time, 182843 HSPs Collected Number of families returned by RECON: 36185 Round Time: 12:30:02 (hh:mm:ss) Elapsed Time : 320 families discovered. RepeatScout/RECON discovery complete: 742 families found Classification Time: 00:18:13 (hh:mm:ss) Elapsed Time Program Time: 15:30:23 (hh:mm:ss) Elapsed Time