RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.DL1qsm/RM_137822.ThuSep120554242024
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: 1726145663
Database = /dev/shm/rModeler.DL1qsm/GCA_001650055.1_ASM165005v1   - Sequences = 234
  - Bases = 6630005
  - N50 = 173800
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  558120-597968 |                                                   [ 1 ]
  518272-558119 |                                                   [  ]
  478424-518271 |                                                   [  ]
  438576-478423 |                                                   [ 2 ]
  398728-438575 |                                                   [  ]
  358880-398727 |                                                   [  ]
  319032-358879 |                                                   [ 1 ]
  279185-319032 |                                                   [ 1 ]
  239337-279184 |                                                   [ 1 ]
  199489-239336 |                                                   [ 2 ]
  159641-199488 |*                                                  [ 4 ]
  119793-159640 |                                                   [ 3 ]
  79945-119792  |*                                                  [ 7 ]
  40097-79944   |****                                               [ 16 ]
  250-40097     |************************************************** [ 196 ]

Storage Throughput = excellent ( 1465.97 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 6629891 bp ( 6629891 non ambiguous )
   - Num Contigs Represented = 234
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:01:50 (hh:mm:ss) Elapsed Time
Round Time: 00:01:58 (hh:mm:ss) Elapsed Time : 1 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       33 repeats masked totaling 1951 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 6629891 bp
       Num Contigs Represented = 234
       Non ambiguous bp:
             Initial: 6629891 bp
             After Masking: 6606266 bp
             Masked: 0.36 % 
 -- Input Database Coverage: 6629891 bp out of 6630005 bp ( 100.00 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 63546
Comparison Time: 00:03:51 (hh:mm:ss) Elapsed Time, 1384 HSPs Collected
Number of families returned by RECON: 310
Round Time: 00:04:14 (hh:mm:ss) Elapsed Time : 2 families discovered.

RepeatScout/RECON discovery complete: 3 families found


Classification Time: 00:00:07 (hh:mm:ss) Elapsed Time


Program Time: 00:06:19 (hh:mm:ss) Elapsed Time