RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gvkScV/RM_442440.FriDec12206012023 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: 1701497160 Database = /dev/shm/rModeler.gvkScV/GCF_027887145.1_bAmmCau1.pri - Sequences = 282 - Bases = 1241209685 - N50 = 78532051 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146676973-157152855 | [ 1 ] 136201092-146676973 | [ ] 125725211-136201092 | [ ] 115249330-125725211 | [ 2 ] 104773449-115249330 | [ ] 94297568-104773449 | [ ] 83821687-94297568 | [ 1 ] 73345806-83821687 | [ 2 ] 62869925-73345806 | [ 1 ] 52394044-62869925 | [ ] 41918163-52394044 | [ 2 ] 31442282-41918163 | [ 1 ] 20966401-31442282 | [ 4 ] 10490520-20966401 |* [ 9 ] 14639-10490520 |************************************************** [ 259 ] Storage Throughput = excellent ( 1362.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013462 bp ( 40004941 non ambiguous ) - Num Contigs Represented = 76 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:23 (hh:mm:ss) Elapsed Time Round Time: 00:26:15 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2891 repeats masked totaling 713941 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027445 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10024141 bp After Masking: 8267771 bp Masked: 17.52 % -- Input Database Coverage: 10027445 bp out of 1241209685 bp ( 0.81 % ) Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:19 (hh:mm:ss) Elapsed Time, 1037 HSPs Collected Number of families returned by RECON: 281 Round Time: 00:08:15 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8866 repeats masked totaling 2440897 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025964 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30020747 bp After Masking: 24448699 bp Masked: 18.56 % -- Input Database Coverage: 40053409 bp out of 1241209685 bp ( 3.23 % ) Sampling Time: 00:03:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:30:58 (hh:mm:ss) Elapsed Time, 6577 HSPs Collected Number of families returned by RECON: 1642 Round Time: 00:35:19 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26681 repeats masked totaling 7286915 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90249946 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 90023616 bp After Masking: 72042536 bp Masked: 19.97 % -- Input Database Coverage: 130303355 bp out of 1241209685 bp ( 10.50 % ) Sampling Time: 00:14:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:19:20 (hh:mm:ss) Elapsed Time, 93976 HSPs Collected Number of families returned by RECON: 9731 Round Time: 03:38:54 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 94193 repeats masked totaling 28630270 bp(s). - TE Masking time 00:05:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270800064 bp Num Contigs Represented = 203 Non ambiguous bp: Initial: 270031107 bp After Masking: 209324850 bp Masked: 22.48 % -- Input Database Coverage: 401103419 bp out of 1241209685 bp ( 32.32 % ) Sampling Time: 00:43:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23164221 Comparison Time: 26:34:51 (hh:mm:ss) Elapsed Time, 435876 HSPs Collected Number of families returned by RECON: 63881 Round Time: 28:15:35 (hh:mm:ss) Elapsed Time : 294 families discovered. RepeatScout/RECON discovery complete: 564 families found Classification Time: 00:54:07 (hh:mm:ss) Elapsed Time Program Time: 33:58:25 (hh:mm:ss) Elapsed Time