RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QcLjwp/RM_2528798.WedApr160328342025 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: 1744799314 Database = /dev/shm/rModeler.QcLjwp/GCA_011762505.3_mArvNil1.pat.X - Sequences = 1596 - Bases = 2496777707 - N50 = 86386494 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 155975538-167116563 | [ 1 ] 144834513-155975537 | [ 1 ] 133693489-144834513 | [ 2 ] 122552464-133693488 | [ 1 ] 111411440-122552464 | [ ] 100270415-111411439 | [ 2 ] 89129390-100270414 | [ 1 ] 77988366-89129390 | [ 6 ] 66847341-77988365 | [ 3 ] 55706317-66847341 | [ 1 ] 44565292-55706316 | [ 7 ] 33424267-44565291 | [ 2 ] 22283243-33424267 | [ 4 ] 11142218-22283242 | [ 1 ] 1194-11142218 |************************************************** [ 1564 ] Storage Throughput = excellent ( 1748.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40192924 bp ( 40020995 non ambiguous ) - Num Contigs Represented = 95 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:10 (hh:mm:ss) Elapsed Time Round Time: 00:11:46 (hh:mm:ss) Elapsed Time : 338 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12325 repeats masked totaling 2367470 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10077419 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10013419 bp After Masking: 7284062 bp Masked: 27.26 % -- Input Database Coverage: 10077419 bp out of 2496777707 bp ( 0.40 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:03:11 (hh:mm:ss) Elapsed Time, 12376 HSPs Collected Number of families returned by RECON: 894 Round Time: 00:04:16 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40764 repeats masked totaling 8005676 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30115425 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30007496 bp After Masking: 20700053 bp Masked: 31.02 % -- Input Database Coverage: 40192844 bp out of 2496777707 bp ( 1.61 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:14:49 (hh:mm:ss) Elapsed Time, 24505 HSPs Collected Number of families returned by RECON: 2496 Round Time: 00:18:00 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 133119 repeats masked totaling 26208480 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90955780 bp Num Contigs Represented = 163 Non ambiguous bp: Initial: 90011897 bp After Masking: 59959703 bp Masked: 33.39 % -- Input Database Coverage: 131148624 bp out of 2496777707 bp ( 5.25 % ) Sampling Time: 00:12:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2646150 Comparison Time: 01:29:03 (hh:mm:ss) Elapsed Time, 91590 HSPs Collected Number of families returned by RECON: 8781 Round Time: 01:44:48 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 431545 repeats masked totaling 83787067 bp(s). - TE Masking time 00:02:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272306554 bp Num Contigs Represented = 318 Non ambiguous bp: Initial: 270005168 bp After Masking: 174869245 bp Masked: 35.23 % -- Input Database Coverage: 403455178 bp out of 2496777707 bp ( 16.16 % ) Sampling Time: 00:30:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23629375 Comparison Time: 10:55:21 (hh:mm:ss) Elapsed Time, 253369 HSPs Collected Number of families returned by RECON: 38662 Round Time: 11:36:43 (hh:mm:ss) Elapsed Time : 395 families discovered. RepeatScout/RECON discovery complete: 999 families found Classification Time: 00:19:19 (hh:mm:ss) Elapsed Time Program Time: 14:14:52 (hh:mm:ss) Elapsed Time