RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NDAl9D/RM_25965.TueDec261519572023 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: 1703632796 Database = /dev/shm/rModeler.NDAl9D/GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri - Sequences = 443 - Bases = 3271621005 - N50 = 144887152 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 211302992-226395330 | [ 1 ] 196210655-211302992 | [ 2 ] 181118317-196210654 | [ 2 ] 166025980-181118317 | [ 1 ] 150933642-166025979 | [ 1 ] 135841305-150933642 | [ 5 ] 120748967-135841304 | [ 2 ] 105656630-120748967 | [ 3 ] 90564292-105656629 | [ 2 ] 75471955-90564292 | [ 2 ] 60379617-75471954 | [ 2 ] 45287280-60379617 | [ 1 ] 30194942-45287279 | [ 1 ] 15102605-30194942 | [ 1 ] 10268-15102605 |************************************************** [ 417 ] Storage Throughput = excellent ( 1162.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40078539 bp ( 40038539 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:09 (hh:mm:ss) Elapsed Time Round Time: 00:31:28 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11972 repeats masked totaling 2870071 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025830 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10025830 bp After Masking: 6007695 bp Masked: 40.08 % -- Input Database Coverage: 10025830 bp out of 3271621005 bp ( 0.31 % ) Sampling Time: 00:05:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:10 (hh:mm:ss) Elapsed Time, 5558 HSPs Collected Number of families returned by RECON: 830 Round Time: 00:10:51 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39895 repeats masked totaling 9408562 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30052629 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30012629 bp After Masking: 17365040 bp Masked: 42.14 % -- Input Database Coverage: 40078459 bp out of 3271621005 bp ( 1.23 % ) Sampling Time: 00:14:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:25:35 (hh:mm:ss) Elapsed Time, 26093 HSPs Collected Number of families returned by RECON: 2251 Round Time: 00:40:35 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 129046 repeats masked totaling 30531713 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90136796 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90016796 bp After Masking: 49773141 bp Masked: 44.71 % -- Input Database Coverage: 130215255 bp out of 3271621005 bp ( 3.98 % ) Sampling Time: 00:44:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 02:51:03 (hh:mm:ss) Elapsed Time, 109137 HSPs Collected Number of families returned by RECON: 6993 Round Time: 03:50:03 (hh:mm:ss) Elapsed Time : 197 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:50:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 419653 repeats masked totaling 98751231 bp(s). - TE Masking time 00:08:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270149552 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 270011006 bp After Masking: 140396545 bp Masked: 48.00 % -- Input Database Coverage: 400364807 bp out of 3271621005 bp ( 12.24 % ) Sampling Time: 02:11:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 20:26:13 (hh:mm:ss) Elapsed Time, 365847 HSPs Collected Number of families returned by RECON: 27478 Round Time: 23:00:28 (hh:mm:ss) Elapsed Time : 377 families discovered. RepeatScout/RECON discovery complete: 900 families found Classification Time: 00:41:38 (hh:mm:ss) Elapsed Time Program Time: 28:55:03 (hh:mm:ss) Elapsed Time