RepeatModeler Version 2.0.4
===========================
Using output directory = /dev/shm/rModeler.BQRcP2/RM_25734.FriSep201806312024
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: 1726880791
Database = /dev/shm/rModeler.BQRcP2/GCA_002911725.1_ASM291172v1   - Sequences = 24809
  - Bases = 107772931
  - N50 = 6695
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  68020-72808 |                                                   [ 1 ]
  63233-68020 |                                                   [ 1 ]
  58446-63233 |                                                   [ 1 ]
  53659-58446 |                                                   [ 3 ]
  48872-53659 |                                                   [ 5 ]
  44084-48871 |                                                   [ 10 ]
  39297-44084 |                                                   [ 18 ]
  34510-39297 |                                                   [ 20 ]
  29723-34510 |                                                   [ 65 ]
  24936-29723 |                                                   [ 103 ]
  20148-24935 |                                                   [ 231 ]
  15361-20148 |*                                                  [ 442 ]
  10574-15361 |**                                                 [ 1111 ]
  5787-10574  |********                                           [ 3392 ]
  1000-5787   |************************************************** [ 19406 ]

  WARN: The N50 for this assembly is low ( <10,000 ).  The de novo methods
        employed by RepeatModeler are intended for use with long contiguous
        sequences and may not perform well with an over-abundance of short
        contigs in the database.
Storage Throughput = excellent ( 1129.54 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40149796 bp ( 40007016 non ambiguous )
   - Num Contigs Represented = 9273
   - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: 00:16:57 (hh:mm:ss) Elapsed Time
Round Time: 00:25:43 (hh:mm:ss) Elapsed Time : 575 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 00:00:10 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6415 repeats masked totaling 2793212 bp(s).
   - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10047222 bp
       Num Contigs Represented = 2382
       Non ambiguous bp:
             Initial: 10008100 bp
             After Masking: 7223363 bp
             Masked: 27.82 % 
 -- Input Database Coverage: 10047222 bp out of 107772931 bp ( 9.32 % )
Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 2835771
Comparison Time: 00:10:44 (hh:mm:ss) Elapsed Time, 4505 HSPs Collected
Number of families returned by RECON: 1586
Round Time: 00:11:17 (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 : 00:00:04 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       18482 repeats masked totaling 8227367 bp(s).
   - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 30104986 bp
       Num Contigs Represented = 6896
       Non ambiguous bp:
             Initial: 30001328 bp
             After Masking: 21797656 bp
             Masked: 27.34 % 
 -- Input Database Coverage: 40152208 bp out of 107772931 bp ( 37.26 % )
Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 23801550
Comparison Time: 00:41:08 (hh:mm:ss) Elapsed Time, 36517 HSPs Collected
Number of families returned by RECON: 5887
Round Time: 00:43:48 (hh:mm:ss) Elapsed Time : 28 families discovered.


RepeatModeler Round # 4
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 90000000 bp
   - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       42012 repeats masked totaling 18701092 bp(s).
   - TE Masking time 00:01:42 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 67620497 bp
       Num Contigs Represented = 15551
       Non ambiguous bp:
             Initial: 67388147 bp
             After Masking: 48729870 bp
             Masked: 27.69 % 
 -- Input Database Coverage: 107772705 bp out of 107772931 bp ( 100.00 % )
Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 121080141
Comparison Time: 02:15:03 (hh:mm:ss) Elapsed Time, 205295 HSPs Collected
Number of families returned by RECON: 12953
Round Time: 02:26:45 (hh:mm:ss) Elapsed Time : 246 families discovered.

RepeatScout/RECON discovery complete: 849 families found


Classification Time: 00:56:13 (hh:mm:ss) Elapsed Time


Program Time: 04:43:46 (hh:mm:ss) Elapsed Time