RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4QILkp/RM_3674298.SatNov252138562023 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: 1700977135 Database = /dev/shm/rModeler.4QILkp/GCF_949987535.1_mBalAcu1.1 - Sequences = 1374 - Bases = 2772885358 - N50 = 117579512 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 185419678-198663870 | [ 2 ] 172175487-185419678 | [ 1 ] 158931296-172175487 | [ ] 145687104-158931295 | [ 1 ] 132442913-145687104 | [ 2 ] 119198722-132442913 | [ 1 ] 105954530-119198721 | [ 5 ] 92710339-105954530 | [ 3 ] 79466148-92710339 | [ 4 ] 66221956-79466147 | [ 1 ] 52977765-66221956 | [ 1 ] 39733574-52977765 | [ 1 ] 26489382-39733573 | [ ] 13245191-26489382 | [ ] 1000-13245191 |************************************************** [ 1352 ] Storage Throughput = excellent ( 1212.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031185 bp ( 40028585 non ambiguous ) - Num Contigs Represented = 132 - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:24 (hh:mm:ss) Elapsed Time Round Time: 00:30:11 (hh:mm:ss) Elapsed Time : 207 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (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... 9493 repeats masked totaling 3224943 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017673 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 10017273 bp After Masking: 6403113 bp Masked: 36.08 % -- Input Database Coverage: 10017673 bp out of 2772885358 bp ( 0.36 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:14 (hh:mm:ss) Elapsed Time, 101162 HSPs Collected Number of families returned by RECON: 834 Round Time: 00:09:12 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31451 repeats masked totaling 9947985 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013510 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 30011310 bp After Masking: 18905298 bp Masked: 37.01 % -- Input Database Coverage: 40031183 bp out of 2772885358 bp ( 1.44 % ) Sampling Time: 00:04:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:28:02 (hh:mm:ss) Elapsed Time, 42527 HSPs Collected Number of families returned by RECON: 2476 Round Time: 00:33:56 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102462 repeats masked totaling 32405739 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016879 bp Num Contigs Represented = 246 Non ambiguous bp: Initial: 90006679 bp After Masking: 52924237 bp Masked: 41.20 % -- Input Database Coverage: 130048062 bp out of 2772885358 bp ( 4.69 % ) Sampling Time: 00:13:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 02:36:39 (hh:mm:ss) Elapsed Time, 167412 HSPs Collected Number of families returned by RECON: 7514 Round Time: 02:55:55 (hh:mm:ss) Elapsed Time : 169 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 348450 repeats masked totaling 108158253 bp(s). - TE Masking time 00:04:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027196 bp Num Contigs Represented = 532 Non ambiguous bp: Initial: 270003155 bp After Masking: 149195017 bp Masked: 44.74 % -- Input Database Coverage: 400075258 bp out of 2772885358 bp ( 14.43 % ) Sampling Time: 00:42:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23252790 Comparison Time: 20:01:40 (hh:mm:ss) Elapsed Time, 436125 HSPs Collected Number of families returned by RECON: 28527 Round Time: 21:03:25 (hh:mm:ss) Elapsed Time : 334 families discovered. RepeatScout/RECON discovery complete: 793 families found Classification Time: 00:33:20 (hh:mm:ss) Elapsed Time Program Time: 25:45:59 (hh:mm:ss) Elapsed Time