RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GWDTLO/RM_3993.WedNov291227232023 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: 1701289641 Database = /dev/shm/rModeler.GWDTLO/GCA_028858625.1_bColStr4.hap2 - Sequences = 243 - Bases = 1242527572 - N50 = 98266943 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195839760-209827101 | [ 1 ] 181852419-195839759 | [ ] 167865078-181852418 | [ ] 153877738-167865078 | [ ] 139890397-153877737 | [ ] 125903056-139890396 | [ ] 111915715-125903055 | [ 1 ] 97928375-111915715 | [ 2 ] 83941034-97928374 | [ 1 ] 69953693-83941033 | [ ] 55966352-69953692 | [ 1 ] 41979012-55966352 | [ 2 ] 27991671-41979011 |* [ 5 ] 14004330-27991670 |* [ 6 ] 16990-14004330 |************************************************* [ 224 ] Storage Throughput = excellent ( 1171.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40328599 bp ( 40033607 non ambiguous ) - Num Contigs Represented = 67 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:50 (hh:mm:ss) Elapsed Time Round Time: 00:30:49 (hh:mm:ss) Elapsed Time : 102 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 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3713 repeats masked totaling 1139999 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10082875 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10002862 bp After Masking: 8503436 bp Masked: 14.99 % -- Input Database Coverage: 10082875 bp out of 1242527572 bp ( 0.81 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:13 (hh:mm:ss) Elapsed Time, 374 HSPs Collected Number of families returned by RECON: 167 Round Time: 00:07:16 (hh:mm:ss) Elapsed Time : 0 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 00:01:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11373 repeats masked totaling 3245362 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30245644 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30030665 bp After Masking: 25399276 bp Masked: 15.42 % -- Input Database Coverage: 40328519 bp out of 1242527572 bp ( 3.25 % ) Sampling Time: 00:03:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:34:11 (hh:mm:ss) Elapsed Time, 4062 HSPs Collected Number of families returned by RECON: 1213 Round Time: 00:38:05 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33475 repeats masked totaling 9710640 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90440737 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90024440 bp After Masking: 74414809 bp Masked: 17.34 % -- Input Database Coverage: 130769256 bp out of 1242527572 bp ( 10.52 % ) Sampling Time: 00:11:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 04:01:59 (hh:mm:ss) Elapsed Time, 43331 HSPs Collected Number of families returned by RECON: 7602 Round Time: 04:17:16 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113772 repeats masked totaling 33831513 bp(s). - TE Masking time 00:04:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271078525 bp Num Contigs Represented = 135 Non ambiguous bp: Initial: 270001906 bp After Masking: 219287538 bp Masked: 18.78 % -- Input Database Coverage: 401847781 bp out of 1242527572 bp ( 32.34 % ) Sampling Time: 00:36:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 32:54:36 (hh:mm:ss) Elapsed Time, 200469 HSPs Collected Number of families returned by RECON: 52855 Round Time: 34:16:52 (hh:mm:ss) Elapsed Time : 225 families discovered. RepeatScout/RECON discovery complete: 417 families found Classification Time: 00:37:57 (hh:mm:ss) Elapsed Time Program Time: 40:28:15 (hh:mm:ss) Elapsed Time