RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.cVvNdc/RM_2242616.TueSep90106462025
Search Engine = rmblast 2.14.1+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1757405205
Database = /dev/shm/rModeler.cVvNdc/GCA_003690985.1_ASM369098v1 
  - Sequences = 10236
  - Bases = 39405040
  - N50 = 148052
  - Contig Histogram:
  Size(bp)                                                        Count
  -----------------------------------------------------------------------
  527690-565368 |                                                   [ 3 ]
  490012-527689 |                                                   [  ]
  452334-490011 |                                                   [ 1 ]
  414656-452333 |                                                   [ 1 ]
  376978-414655 |                                                   [ 6 ]
  339300-376977 |                                                   [  ]
  301622-339299 |                                                   [ 2 ]
  263945-301622 |                                                   [ 11 ]
  226267-263944 |                                                   [ 10 ]
  188589-226266 |                                                   [ 17 ]
  150911-188588 |                                                   [ 27 ]
  113233-150910 |                                                   [ 38 ]
  75555-113232  |                                                   [ 45 ]
  37877-75554   |                                                   [ 83 ]
  200-37877     |************************************************** [ 9992 ]

Storage Throughput = excellent ( 1656.87 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 39404956 bp ( 39345395 non ambiguous )
   - Num Contigs Represented = 10236
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 342 raw families identified
   - RepeatScout: Running filtering stage.. 324 families remaining
   - RepeatScout: 00:00:57 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 311 families... 00:00:38 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 44 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:01:41 (hh:mm:ss) Elapsed Time : 267 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 00:00:06 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       3732 repeats masked totaling 854195 bp(s).
   - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10050804 bp
       Num Contigs Represented = 2632
       Non ambiguous bp:
             Initial: 10037449 bp
             After Masking: 9109794 bp
             Masked: 9.24 % 
 -- Input Database Coverage: 10050804 bp out of 39405040 bp ( 25.51 % )
Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 3716901
Comparison Time: 00:11:48 (hh:mm:ss) Elapsed Time, 3401 HSPs Collected
Number of families returned by RECON: 770
Round Time: 00:12:08 (hh:mm:ss) Elapsed Time : 4 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       12327 repeats masked totaling 2681936 bp(s).
   - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 29354072 bp
       Num Contigs Represented = 7744
       Non ambiguous bp:
             Initial: 29307866 bp
             After Masking: 26402981 bp
             Masked: 9.91 % 
 -- Input Database Coverage: 39404876 bp out of 39405040 bp ( 100.00 % )
Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 33747220
Comparison Time: 00:38:38 (hh:mm:ss) Elapsed Time, 19090 HSPs Collected
Number of families returned by RECON: 3398
Round Time: 00:39:27 (hh:mm:ss) Elapsed Time : 26 families discovered.

RepeatScout/RECON discovery complete: 297 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.cVvNdc/RM_2242616.TueSep90106462025
# Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib
#   - 18011 proteins
# Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib
#   - 26292 consensus sequences
  - Looking for simple/tandem and low complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

Classification Time: 00:00:20 (hh:mm:ss) Elapsed Time


Program Time: 00:53:36 (hh:mm:ss) Elapsed Time