RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CXwFdf/RM_22439.SatJun291941362024 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: 1719715295 Database = /dev/shm/rModeler.CXwFdf/GCA_013621035.1_C_magur1.0 - Sequences = 3484 - Bases = 941297321 - N50 = 1323535 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 9226631-9885605 | [ 1 ] 8567658-9226631 | [ ] 7908685-8567658 | [ ] 7249712-7908685 | [ 1 ] 6590739-7249712 | [ 1 ] 5931766-6590739 | [ 1 ] 5272793-5931766 | [ 3 ] 4613820-5272793 | [ 9 ] 3954847-4613820 | [ 10 ] 3295874-3954847 | [ 14 ] 2636901-3295874 | [ 21 ] 1977928-2636901 | [ 41 ] 1318955-1977928 |* [ 82 ] 659982-1318955 |*** [ 207 ] 1009-659982 |************************************************** [ 3093 ] Storage Throughput = excellent ( 1031.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012274 bp ( 40001391 non ambiguous ) - Num Contigs Represented = 630 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:43 (hh:mm:ss) Elapsed Time Round Time: 00:26:25 (hh:mm:ss) Elapsed Time : 707 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14475 repeats masked totaling 2713413 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037105 bp Num Contigs Represented = 219 Non ambiguous bp: Initial: 10037090 bp After Masking: 6903001 bp Masked: 31.23 % -- Input Database Coverage: 10037105 bp out of 941297321 bp ( 1.07 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38226 Comparison Time: 00:06:25 (hh:mm:ss) Elapsed Time, 6491 HSPs Collected Number of families returned by RECON: 1392 Round Time: 00:07:52 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47323 repeats masked totaling 8634811 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017615 bp Num Contigs Represented = 529 Non ambiguous bp: Initial: 30006747 bp After Masking: 20159652 bp Masked: 32.82 % -- Input Database Coverage: 40054720 bp out of 941297321 bp ( 4.26 % ) Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 345696 Comparison Time: 00:35:03 (hh:mm:ss) Elapsed Time, 47763 HSPs Collected Number of families returned by RECON: 4954 Round Time: 00:40:22 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155636 repeats masked totaling 27936547 bp(s). - TE Masking time 00:02:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90063967 bp Num Contigs Represented = 1034 Non ambiguous bp: Initial: 90012307 bp After Masking: 58269195 bp Masked: 35.27 % -- Input Database Coverage: 130118687 bp out of 941297321 bp ( 13.82 % ) Sampling Time: 00:11:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2995128 Comparison Time: 04:02:53 (hh:mm:ss) Elapsed Time, 262222 HSPs Collected Number of families returned by RECON: 15617 Round Time: 04:26:40 (hh:mm:ss) Elapsed Time : 489 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 541621 repeats masked totaling 97466287 bp(s). - TE Masking time 00:15:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270141990 bp Num Contigs Represented = 1837 Non ambiguous bp: Initial: 270016603 bp After Masking: 161515828 bp Masked: 40.18 % -- Input Database Coverage: 400260677 bp out of 941297321 bp ( 42.52 % ) Sampling Time: 00:40:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27081120 Comparison Time: 30:35:11 (hh:mm:ss) Elapsed Time, 695463 HSPs Collected Number of families returned by RECON: 54243 Round Time: 32:50:43 (hh:mm:ss) Elapsed Time : 1033 families discovered. RepeatScout/RECON discovery complete: 2377 families found Classification Time: 01:52:28 (hh:mm:ss) Elapsed Time Program Time: 40:24:30 (hh:mm:ss) Elapsed Time