RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.stSoH3/RM_3896.TueJan31527492023 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: 1672788468 Database = /dev/shm/rModeler.stSoH3/GCF_900634775.1_fGouWil2.1 - Sequences = 441 - Bases = 937150793 - N50 = 40234402 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 67622631-72451976 | [ 1 ] 62793286-67622630 | [ ] 57963941-62793285 | [ ] 53134596-57963940 | [ ] 48305251-53134595 | [ ] 43475906-48305250 | [ 4 ] 38646561-43475905 | [ 6 ] 33817217-38646561 | [ 5 ] 28987872-33817216 | [ 2 ] 24158527-28987871 | [ 4 ] 19329182-24158526 | [ ] 14499837-19329181 | [ ] 9670492-14499836 | [ 1 ] 4841147-9670491 | [ ] 11803-4841147 |************************************************** [ 418 ] Storage Throughput = excellent ( 1041.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40741921 bp ( 40024725 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:10 (hh:mm:ss) Elapsed Time Round Time: 00:33:31 (hh:mm:ss) Elapsed Time : 1239 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21450 repeats masked totaling 3589636 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10227915 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10037461 bp After Masking: 5964732 bp Masked: 40.58 % -- Input Database Coverage: 10227915 bp out of 937150793 bp ( 1.09 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:07:32 (hh:mm:ss) Elapsed Time, 24433 HSPs Collected Number of families returned by RECON: 1713 Round Time: 00:12:48 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67462 repeats masked totaling 11211317 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30553926 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30027184 bp After Masking: 17718307 bp Masked: 40.99 % -- Input Database Coverage: 40781841 bp out of 937150793 bp ( 4.35 % ) Sampling Time: 00:04:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:34:57 (hh:mm:ss) Elapsed Time, 64793 HSPs Collected Number of families returned by RECON: 5199 Round Time: 00:41:53 (hh:mm:ss) Elapsed Time : 147 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 215181 repeats masked totaling 35121587 bp(s). - TE Masking time 00:04:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91495535 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 90013859 bp After Masking: 51504041 bp Masked: 42.78 % -- Input Database Coverage: 132277376 bp out of 937150793 bp ( 14.11 % ) Sampling Time: 00:14:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2659971 Comparison Time: 03:36:35 (hh:mm:ss) Elapsed Time, 335123 HSPs Collected Number of families returned by RECON: 13981 Round Time: 04:17:15 (hh:mm:ss) Elapsed Time : 638 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 721755 repeats masked totaling 121880709 bp(s). - TE Masking time 00:23:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273939579 bp Num Contigs Represented = 234 Non ambiguous bp: Initial: 270030632 bp After Masking: 138357364 bp Masked: 48.76 % -- Input Database Coverage: 406216955 bp out of 937150793 bp ( 43.35 % ) Sampling Time: 00:51:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23780856 Comparison Time: 25:30:01 (hh:mm:ss) Elapsed Time, 842270 HSPs Collected Number of families returned by RECON: 41602 Round Time: 27:47:34 (hh:mm:ss) Elapsed Time : 1421 families discovered. RepeatScout/RECON discovery complete: 3465 families found Classification Time: 02:31:53 (hh:mm:ss) Elapsed Time Program Time: 36:04:54 (hh:mm:ss) Elapsed Time