RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.rBJwBJ/RM_3315910.SatNov161742352024 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: 1731807754 Database = /scratch/tmp/rModeler.rBJwBJ/GCA_037038515.1_mMicPen1.hap1 - Sequences = 181 - Bases = 2369135991 - N50 = 128925859 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 208143698-223010037 | [ 1 ] 193277359-208143698 | [ ] 178411020-193277359 | [ ] 163544681-178411020 | [ ] 148678342-163544681 | [ 1 ] 133812003-148678342 |* [ 4 ] 118945664-133812003 | [ 2 ] 104079325-118945664 |* [ 4 ] 89212986-104079325 | [ 1 ] 74346647-89212986 | [ 2 ] 59480308-74346647 | [ 1 ] 44613969-59480308 | [ 2 ] 29747630-44613969 |* [ 6 ] 14881291-29747630 | [ ] 14952-14881291 |************************************************** [ 157 ] Storage Throughput = excellent ( 1480.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001864 bp ( 40001464 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:47 (hh:mm:ss) Elapsed Time Round Time: 00:11:07 (hh:mm:ss) Elapsed Time : 282 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (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... 15157 repeats masked totaling 2974133 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034334 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10034334 bp After Masking: 6819387 bp Masked: 32.04 % -- Input Database Coverage: 10034334 bp out of 2369135991 bp ( 0.42 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 6751 HSPs Collected Number of families returned by RECON: 681 Round Time: 00:03:46 (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 : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47889 repeats masked totaling 9179957 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007374 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30006974 bp After Masking: 19673767 bp Masked: 34.44 % -- Input Database Coverage: 40041708 bp out of 2369135991 bp ( 1.69 % ) Sampling Time: 00:02:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:19 (hh:mm:ss) Elapsed Time, 20462 HSPs Collected Number of families returned by RECON: 2088 Round Time: 00:15:04 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149422 repeats masked totaling 29210637 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028301 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90027301 bp After Masking: 57920230 bp Masked: 35.66 % -- Input Database Coverage: 130070009 bp out of 2369135991 bp ( 5.49 % ) Sampling Time: 00:07:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:08:12 (hh:mm:ss) Elapsed Time, 92706 HSPs Collected Number of families returned by RECON: 7682 Round Time: 01:17:08 (hh:mm:ss) Elapsed Time : 167 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 474880 repeats masked totaling 92859559 bp(s). - TE Masking time 00:02:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021195 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 270020095 bp After Masking: 168523563 bp Masked: 37.59 % -- Input Database Coverage: 400091204 bp out of 2369135991 bp ( 16.89 % ) Sampling Time: 00:22:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 08:12:42 (hh:mm:ss) Elapsed Time, 303090 HSPs Collected Number of families returned by RECON: 33610 Round Time: 08:45:52 (hh:mm:ss) Elapsed Time : 392 families discovered. RepeatScout/RECON discovery complete: 909 families found Classification Time: 00:19:10 (hh:mm:ss) Elapsed Time Program Time: 10:52:07 (hh:mm:ss) Elapsed Time