RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fsfPLd/RM_28301.FriJan51006462024 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: 1704478005 Database = /dev/shm/rModeler.fsfPLd/GCA_026652325.1_ASM2665232v1 - Sequences = 134 - Bases = 10514040282 - N50 = 1527636511 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1789920899-1917772152 | [ 1 ] 1662069646-1789920899 | [ ] 1534218393-1662069646 | [ 1 ] 1406367140-1534218393 | [ 1 ] 1278515887-1406367140 | [ ] 1150664634-1278515887 | [ 2 ] 1022813381-1150664634 | [ 2 ] 894962128-1022813381 | [ ] 767110875-894962128 | [ 1 ] 639259622-767110875 | [ ] 511408369-639259622 | [ ] 383557116-511408369 | [ ] 255705863-383557116 | [ ] 127854610-255705863 | [ ] 3357-127854610 |************************************************** [ 126 ] Storage Throughput = excellent ( 1055.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000448 bp ( 40000448 non ambiguous ) - Num Contigs Represented = 10 - Sequence extraction : 00:28:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:56 (hh:mm:ss) Elapsed Time Round Time: 01:03:35 (hh:mm:ss) Elapsed Time : 564 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:07:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10999 repeats masked totaling 5201693 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000448 bp Num Contigs Represented = 10 Non ambiguous bp: Initial: 10000448 bp After Masking: 4190429 bp Masked: 58.10 % -- Input Database Coverage: 10000448 bp out of 10514040282 bp ( 0.10 % ) Sampling Time: 00:08:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:11:23 (hh:mm:ss) Elapsed Time, 16758 HSPs Collected Number of families returned by RECON: 1050 Round Time: 00:21:01 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:21:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33096 repeats masked totaling 16361760 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 29999920 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 29999920 bp After Masking: 11673985 bp Masked: 61.09 % -- Input Database Coverage: 40000368 bp out of 10514040282 bp ( 0.38 % ) Sampling Time: 00:24:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:54:20 (hh:mm:ss) Elapsed Time, 61026 HSPs Collected Number of families returned by RECON: 2959 Round Time: 01:21:33 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 01:03:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107345 repeats masked totaling 51315302 bp(s). - TE Masking time 00:03:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90002301 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 90001821 bp After Masking: 32681982 bp Masked: 63.69 % -- Input Database Coverage: 130002669 bp out of 10514040282 bp ( 1.24 % ) Sampling Time: 01:12:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:01:20 (hh:mm:ss) Elapsed Time, 246970 HSPs Collected Number of families returned by RECON: 8344 Round Time: 03:23:08 (hh:mm:ss) Elapsed Time : 321 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 03:10:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 365075 repeats masked totaling 172563524 bp(s). - TE Masking time 00:13:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032034 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270025874 bp After Masking: 79090553 bp Masked: 70.71 % -- Input Database Coverage: 400034703 bp out of 10514040282 bp ( 3.80 % ) Sampling Time: 03:41:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 10:44:02 (hh:mm:ss) Elapsed Time, 636852 HSPs Collected Number of families returned by RECON: 22461 Round Time: 14:59:44 (hh:mm:ss) Elapsed Time : 736 families discovered. RepeatScout/RECON discovery complete: 1730 families found Classification Time: 01:42:12 (hh:mm:ss) Elapsed Time Program Time: 22:51:13 (hh:mm:ss) Elapsed Time