RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FPYaW1/RM_3769112.SunJul141339042024 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: 1720989543 Database = /dev/shm/rModeler.FPYaW1/GCF_026213295.1_NIFS_Gcha_1.0 - Sequences = 168 - Bases = 629936721 - N50 = 27968553 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34308804-36758684 | [ 2 ] 31858924-34308804 | [ 2 ] 29409044-31858924 | [ ] 26959164-29409044 |** [ 7 ] 24509284-26959164 |* [ 3 ] 22059404-24509284 |* [ 4 ] 19609524-22059404 |* [ 3 ] 17159644-19609524 | [ 2 ] 14709764-17159644 | [ ] 12259884-14709764 | [ ] 9810004-12259884 | [ ] 7360124-9810004 | [ ] 4910244-7360124 | [ ] 2460364-4910244 | [ ] 10484-2460364 |************************************************** [ 145 ] Storage Throughput = excellent ( 1323.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030477 bp ( 40012672 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:23 (hh:mm:ss) Elapsed Time Round Time: 00:25:45 (hh:mm:ss) Elapsed Time : 616 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7487 repeats masked totaling 1625768 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028166 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10024261 bp After Masking: 7397007 bp Masked: 26.21 % -- Input Database Coverage: 10028166 bp out of 629936721 bp ( 1.59 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:42 (hh:mm:ss) Elapsed Time, 5004 HSPs Collected Number of families returned by RECON: 1241 Round Time: 00:09:03 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22389 repeats masked totaling 4795224 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042228 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30028328 bp After Masking: 21990787 bp Masked: 26.77 % -- Input Database Coverage: 40070394 bp out of 629936721 bp ( 6.36 % ) Sampling Time: 00:06:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:32:09 (hh:mm:ss) Elapsed Time, 49383 HSPs Collected Number of families returned by RECON: 4426 Round Time: 00:40:16 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73086 repeats masked totaling 15751920 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90059538 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 90021523 bp After Masking: 64792604 bp Masked: 28.03 % -- Input Database Coverage: 130129932 bp out of 629936721 bp ( 20.66 % ) Sampling Time: 00:19:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 03:08:54 (hh:mm:ss) Elapsed Time, 315522 HSPs Collected Number of families returned by RECON: 14935 Round Time: 03:46:19 (hh:mm:ss) Elapsed Time : 494 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 285281 repeats masked totaling 63987657 bp(s). - TE Masking time 00:12:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270160111 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 270037345 bp After Masking: 178131000 bp Masked: 34.03 % -- Input Database Coverage: 400290043 bp out of 629936721 bp ( 63.54 % ) Sampling Time: 01:04:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 21:41:00 (hh:mm:ss) Elapsed Time, 859411 HSPs Collected Number of families returned by RECON: 49561 Round Time: 24:03:31 (hh:mm:ss) Elapsed Time : 1171 families discovered. RepeatScout/RECON discovery complete: 2346 families found Classification Time: 02:10:48 (hh:mm:ss) Elapsed Time Program Time: 31:15:42 (hh:mm:ss) Elapsed Time