RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.iRlCdb/RM_11076.MonMay81019072023 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: 1683566345 Database = /dev/shm/rModeler.iRlCdb/GCA_027408225.1_bGalGal5.pri - Sequences = 252 - Bases = 1109044877 - N50 = 111844616 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 186089466-199380628 | [ 1 ] 172798304-186089465 | [ ] 159507142-172798303 | [ ] 146215980-159507141 | [ 1 ] 132924818-146215979 | [ ] 119633656-132924817 | [ ] 106342494-119633655 | [ 1 ] 93051333-106342494 | [ ] 79760171-93051332 | [ 2 ] 66469009-79760170 | [ ] 53177847-66469008 | [ 1 ] 39886685-53177846 | [ ] 26595523-39886684 | [ 3 ] 13304361-26595522 |* [ 8 ] 13200-13304361 |************************************************** [ 235 ] Storage Throughput = excellent ( 1203.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40099679 bp ( 40031281 non ambiguous ) - Num Contigs Represented = 65 - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:42 (hh:mm:ss) Elapsed Time Round Time: 00:41:59 (hh:mm:ss) Elapsed Time : 138 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4258 repeats masked totaling 1188986 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10052957 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10007352 bp After Masking: 8076903 bp Masked: 19.29 % -- Input Database Coverage: 10052957 bp out of 1109044877 bp ( 0.91 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:11:22 (hh:mm:ss) Elapsed Time, 395 HSPs Collected Number of families returned by RECON: 188 Round Time: 00:14:48 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12288 repeats masked totaling 3192979 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046642 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30023849 bp After Masking: 24731913 bp Masked: 17.63 % -- Input Database Coverage: 40099599 bp out of 1109044877 bp ( 3.62 % ) Sampling Time: 00:09:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:51:54 (hh:mm:ss) Elapsed Time, 10001 HSPs Collected Number of families returned by RECON: 1216 Round Time: 01:03:28 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36323 repeats masked totaling 9062265 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90141942 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 90025785 bp After Masking: 75146007 bp Masked: 16.53 % -- Input Database Coverage: 130241541 bp out of 1109044877 bp ( 11.74 % ) Sampling Time: 00:20:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 05:08:33 (hh:mm:ss) Elapsed Time, 32630 HSPs Collected Number of families returned by RECON: 8288 Round Time: 05:32:12 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:44:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 117397 repeats masked totaling 30138573 bp(s). - TE Masking time 00:04:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270442915 bp Num Contigs Represented = 131 Non ambiguous bp: Initial: 270029867 bp After Masking: 224066787 bp Masked: 17.02 % -- Input Database Coverage: 400684456 bp out of 1109044877 bp ( 36.13 % ) Sampling Time: 01:02:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 41:12:35 (hh:mm:ss) Elapsed Time, 201369 HSPs Collected Number of families returned by RECON: 54562 Round Time: 43:55:43 (hh:mm:ss) Elapsed Time : 209 families discovered. RepeatScout/RECON discovery complete: 421 families found Classification Time: 01:36:10 (hh:mm:ss) Elapsed Time Program Time: 53:04:20 (hh:mm:ss) Elapsed Time