RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AVxq0I/RM_28374.MonDec40626032023 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: 1701699961 Database = /dev/shm/rModeler.AVxq0I/GCA_030936135.1_bGavSte3.hap2 - Sequences = 1186 - Bases = 1321287916 - N50 = 63245685 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 124441046-133328454 | [ 1 ] 115553639-124441046 | [ ] 106666231-115553638 | [ 1 ] 97778824-106666231 | [ 1 ] 88891417-97778824 | [ 1 ] 80004009-88891416 | [ 1 ] 71116602-80004009 | [ ] 62229194-71116601 | [ 2 ] 53341787-62229194 | [ ] 44454380-53341787 | [ 2 ] 35566972-44454379 | [ 2 ] 26679565-35566972 | [ 1 ] 17792157-26679564 | [ 9 ] 8904750-17792157 | [ 8 ] 17343-8904750 |************************************************** [ 1157 ] Storage Throughput = excellent ( 1085.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037193 bp ( 40035148 non ambiguous ) - Num Contigs Represented = 112 - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:13 (hh:mm:ss) Elapsed Time Round Time: 00:27:56 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1539 repeats masked totaling 608486 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020530 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 10019930 bp After Masking: 8892642 bp Masked: 11.25 % -- Input Database Coverage: 10020530 bp out of 1321287916 bp ( 0.76 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:57 (hh:mm:ss) Elapsed Time, 610 HSPs Collected Number of families returned by RECON: 256 Round Time: 00:07:06 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4809 repeats masked totaling 1924478 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016583 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 30015138 bp After Masking: 26844580 bp Masked: 10.56 % -- Input Database Coverage: 40037113 bp out of 1321287916 bp ( 3.03 % ) Sampling Time: 00:03:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:34:40 (hh:mm:ss) Elapsed Time, 7506 HSPs Collected Number of families returned by RECON: 1424 Round Time: 00:38:18 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14668 repeats masked totaling 5203517 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038481 bp Num Contigs Represented = 192 Non ambiguous bp: Initial: 90034881 bp After Masking: 81169744 bp Masked: 9.85 % -- Input Database Coverage: 130075594 bp out of 1321287916 bp ( 9.84 % ) Sampling Time: 00:09:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2614041 Comparison Time: 04:40:07 (hh:mm:ss) Elapsed Time, 93674 HSPs Collected Number of families returned by RECON: 8440 Round Time: 04:59:44 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59072 repeats masked totaling 22367845 bp(s). - TE Masking time 00:05:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036069 bp Num Contigs Represented = 518 Non ambiguous bp: Initial: 270028869 bp After Masking: 233403593 bp Masked: 13.56 % -- Input Database Coverage: 400111663 bp out of 1321287916 bp ( 30.28 % ) Sampling Time: 00:37:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23698170 Comparison Time: 35:46:26 (hh:mm:ss) Elapsed Time, 578648 HSPs Collected Number of families returned by RECON: 48554 Round Time: 37:53:43 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatScout/RECON discovery complete: 398 families found Classification Time: 01:01:41 (hh:mm:ss) Elapsed Time Program Time: 45:08:28 (hh:mm:ss) Elapsed Time