RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Ew6vOZ/RM_1015846.ThuFeb61843402025 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: 1738896218 Database = /dev/shm/rModeler.Ew6vOZ/GCF_042242105.1_fPemKlu1.hap1 - Sequences = 441 - Bases = 646252061 - N50 = 27811033 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34280133-36727992 | [ 1 ] 31832274-34280132 | [ ] 29384415-31832273 | [ 5 ] 26936556-29384414 | [ 5 ] 24488698-26936556 | [ 4 ] 22040839-24488697 | [ 6 ] 19592980-22040838 | [ 1 ] 17145121-19592979 | [ 1 ] 14697262-17145120 | [ 1 ] 12249404-14697262 | [ ] 9801545-12249403 | [ ] 7353686-9801544 | [ ] 4905827-7353685 | [ ] 2457968-4905826 | [ ] 10110-2457968 |************************************************** [ 417 ] Storage Throughput = excellent ( 1509.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025478 bp ( 40024278 non ambiguous ) - Num Contigs Represented = 68 - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:52 (hh:mm:ss) Elapsed Time Round Time: 00:09:36 (hh:mm:ss) Elapsed Time : 241 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4476 repeats masked totaling 622734 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025190 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10025190 bp After Masking: 8916952 bp Masked: 11.05 % -- Input Database Coverage: 10025190 bp out of 646252061 bp ( 1.55 % ) Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:47 (hh:mm:ss) Elapsed Time, 5477 HSPs Collected Number of families returned by RECON: 1384 Round Time: 00:03:20 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15678 repeats masked totaling 2341203 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040208 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 30039008 bp After Masking: 26209822 bp Masked: 12.75 % -- Input Database Coverage: 40065398 bp out of 646252061 bp ( 6.20 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:13:07 (hh:mm:ss) Elapsed Time, 54058 HSPs Collected Number of families returned by RECON: 5918 Round Time: 00:15:13 (hh:mm:ss) Elapsed Time : 106 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59620 repeats masked totaling 9111877 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010302 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 90007802 bp After Masking: 76594734 bp Masked: 14.90 % -- Input Database Coverage: 130075700 bp out of 646252061 bp ( 20.13 % ) Sampling Time: 00:04:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 01:23:29 (hh:mm:ss) Elapsed Time, 322255 HSPs Collected Number of families returned by RECON: 21228 Round Time: 01:33:06 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 227210 repeats masked totaling 36030293 bp(s). - TE Masking time 00:02:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270009320 bp Num Contigs Represented = 259 Non ambiguous bp: Initial: 270002420 bp After Masking: 221786077 bp Masked: 17.86 % -- Input Database Coverage: 400085020 bp out of 646252061 bp ( 61.91 % ) Sampling Time: 00:14:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23280076 Comparison Time: 10:16:49 (hh:mm:ss) Elapsed Time, 946340 HSPs Collected Number of families returned by RECON: 84740 Round Time: 11:24:36 (hh:mm:ss) Elapsed Time : 1047 families discovered. RepeatScout/RECON discovery complete: 1764 families found Classification Time: 00:37:49 (hh:mm:ss) Elapsed Time Program Time: 14:03:40 (hh:mm:ss) Elapsed Time