RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jD0E3V/RM_18087.SunJan141621302024 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: 1705278089 Database = /dev/shm/rModeler.jD0E3V/GCA_033349115.1_rMacSuw1.hap2 - Sequences = 199 - Bases = 1937254095 - N50 = 196068220 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 312952282-335304700 | [ 1 ] 290599864-312952281 | [ ] 268247447-290599864 | [ ] 245895029-268247446 | [ 1 ] 223542611-245895028 | [ ] 201190194-223542611 | [ ] 178837776-201190193 | [ 1 ] 156485358-178837775 | [ ] 134132941-156485358 | [ ] 111780523-134132940 |* [ 4 ] 89428105-111780522 | [ 2 ] 67075688-89428105 | [ 2 ] 44723270-67075687 | [ ] 22370852-44723269 |* [ 5 ] 18435-22370852 |************************************************** [ 183 ] Storage Throughput = excellent ( 1088.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012436 bp ( 40011236 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:03:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:07 (hh:mm:ss) Elapsed Time Round Time: 00:31:45 (hh:mm:ss) Elapsed Time : 559 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:49 (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... 14038 repeats masked totaling 2886435 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005905 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10005705 bp After Masking: 7038961 bp Masked: 29.65 % -- Input Database Coverage: 10005905 bp out of 1937254095 bp ( 0.52 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:11:44 (hh:mm:ss) Elapsed Time, 16651 HSPs Collected Number of families returned by RECON: 1677 Round Time: 00:14:34 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46357 repeats masked totaling 9426125 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006530 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30005530 bp After Masking: 20313262 bp Masked: 32.30 % -- Input Database Coverage: 40012435 bp out of 1937254095 bp ( 2.07 % ) Sampling Time: 00:04:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:37:59 (hh:mm:ss) Elapsed Time, 62538 HSPs Collected Number of families returned by RECON: 5045 Round Time: 00:45:29 (hh:mm:ss) Elapsed Time : 140 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157826 repeats masked totaling 32231678 bp(s). - TE Masking time 00:02:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015345 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 90012124 bp After Masking: 57085010 bp Masked: 36.58 % -- Input Database Coverage: 130027780 bp out of 1937254095 bp ( 6.71 % ) Sampling Time: 00:13:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 04:15:49 (hh:mm:ss) Elapsed Time, 256459 HSPs Collected Number of families returned by RECON: 14466 Round Time: 04:48:34 (hh:mm:ss) Elapsed Time : 460 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 542353 repeats masked totaling 110655837 bp(s). - TE Masking time 00:11:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026541 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 270015741 bp After Masking: 157549067 bp Masked: 41.65 % -- Input Database Coverage: 400054321 bp out of 1937254095 bp ( 20.65 % ) Sampling Time: 00:43:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 24:28:44 (hh:mm:ss) Elapsed Time, 704917 HSPs Collected Number of families returned by RECON: 45482 Round Time: 26:38:29 (hh:mm:ss) Elapsed Time : 1073 families discovered. RepeatScout/RECON discovery complete: 2271 families found Classification Time: 01:31:52 (hh:mm:ss) Elapsed Time Program Time: 34:30:43 (hh:mm:ss) Elapsed Time