RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.7vyfPa/RM_3671508.FriNov151432312024 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: 1731709951 Database = /scratch/tmp/rModeler.7vyfPa/GCA_036850765.1_mSacBil1_pri_phased_curated - Sequences = 257 - Bases = 2612326447 - N50 = 317915018 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 381195639-408423836 | [ 2 ] 353967442-381195638 | [ ] 326739245-353967441 | [ ] 299511049-326739245 | [ 2 ] 272282852-299511048 | [ ] 245054655-272282851 | [ 1 ] 217826458-245054654 | [ ] 190598262-217826458 | [ 1 ] 163370065-190598261 | [ ] 136141868-163370064 | [ 1 ] 108913671-136141867 | [ 1 ] 81685475-108913671 | [ 3 ] 54457278-81685474 | [ 2 ] 27229081-54457277 | [ ] 885-27229081 |************************************************** [ 244 ] Storage Throughput = excellent ( 1529.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40789064 bp ( 40036385 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:02:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:05:59 (hh:mm:ss) Elapsed Time Round Time: 00:19:33 (hh:mm:ss) Elapsed Time : 300 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12381 repeats masked totaling 3712147 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10161541 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10001541 bp After Masking: 6168931 bp Masked: 38.32 % -- Input Database Coverage: 10161541 bp out of 2612326447 bp ( 0.39 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:07 (hh:mm:ss) Elapsed Time, 4788 HSPs Collected Number of families returned by RECON: 764 Round Time: 00:04:21 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39704 repeats masked totaling 11691480 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30627443 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30034764 bp After Masking: 18009832 bp Masked: 40.04 % -- Input Database Coverage: 40788984 bp out of 2612326447 bp ( 1.56 % ) Sampling Time: 00:03:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:13:19 (hh:mm:ss) Elapsed Time, 16570 HSPs Collected Number of families returned by RECON: 1843 Round Time: 00:16:50 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121732 repeats masked totaling 35762916 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91199177 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 90005787 bp After Masking: 53021698 bp Masked: 41.09 % -- Input Database Coverage: 131988161 bp out of 2612326447 bp ( 5.05 % ) Sampling Time: 00:09:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2611755 Comparison Time: 01:12:58 (hh:mm:ss) Elapsed Time, 81881 HSPs Collected Number of families returned by RECON: 6884 Round Time: 01:25:03 (hh:mm:ss) Elapsed Time : 190 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 401731 repeats masked totaling 113927597 bp(s). - TE Masking time 00:02:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273140015 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270031347 bp After Masking: 152629989 bp Masked: 43.48 % -- Input Database Coverage: 405128176 bp out of 2612326447 bp ( 15.51 % ) Sampling Time: 00:28:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23396220 Comparison Time: 08:01:42 (hh:mm:ss) Elapsed Time, 184838 HSPs Collected Number of families returned by RECON: 28280 Round Time: 08:37:36 (hh:mm:ss) Elapsed Time : 355 families discovered. RepeatScout/RECON discovery complete: 908 families found Classification Time: 00:18:36 (hh:mm:ss) Elapsed Time Program Time: 11:01:59 (hh:mm:ss) Elapsed Time