the lastest version of repeatmodeler was error when running it, reveals "ERROR from search engine (3) "

[Jiangjiangzhang6]

RepeatModeler Round # 1

Searching for Repeats -- Sampling from the database...

• Gathering up to 40000000 bp
• Final Sample Size = 40003535 bp ( 40003535 non ambiguous )
• Num Contigs Represented = 10
• Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences...
• RepeatScout: Running build_lmer_table ( l = 14 )..
• RepeatScout: Running RepeatScout.. : 1444 raw families identified
• RepeatScout: Running filtering stage.. 1255 families remaining
• RepeatScout: 00:14:49 (hh:mm:ss) Elapsed Time : 0 found in 00:00:01 (hh:mm:ss) Elapsed Time
• Collecting repeat instances...Round Time: 00:15:24 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatModeler Round # 2

Searching for Repeats -- Sampling from the database...

• Gathering up to 10000000 bp
• Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... 804 Tandem Repeats Masked
• TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000454 bp Num Contigs Represented = 10 Non ambiguous bp: Initial: 10000454 bp After Masking: 9578375 bp Masked: 4.22 % -- Input Database Coverage: 10000454 bp out of 749771133 bp ( 1.33 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons...
  • Total Comparisons = 31125 WARNING: Retrying batch ( 1 ) [ 3 ]... WARNING: Retrying batch ( 1 ) [ 3 ]...

FATAL ERROR: RepeatModeler giving up. One or more

batches failed! Unfortunately this type of error cannot be recovered from. Please submit the following details to the feedback page at the repeatmasker website:

   http://www.repeatmasker.org

RepeatModeler Version: 2.0.4 Search Engine: rmblast [ 2.13.0+ ] Command Line: /public/home/zhangjiangjiang/software/RepeatModeler-2.0.4/RepeatModeler-database repeat_hap1 -threads 5 -LTRStruct Batch Number: 1 Disk Space: Filesystem 1K-blocks Used Available Use% Mounted on ParaStor300S_ParaStor300S 11128852512768 8931361878836 2197490633932 81% /public

System Memory: Further details about this problem may be found in the directory: /public/home/zhangjiangjiang/jjzhang/yan/genome/hemp/changsha/03.fusion/modif/repeat/RM_94657.MonMay12044552023

and the error information was ERROR from search engine (3)

ERROR from search engine (3)

ERROR from search engine (3)

ERROR from search engine (3)

ERROR from search engine (3)

[ywddwed]

Hi! I encountered the same error when running RepeatModeler. I want to know if you have solved this problem and how? Thanks!

[Jiangjiangzhang6]

I re-installed the software and the error was solution, and sometimes the conda environment would conflict with the software

	张江江

@. | ---- Replied Message ---- | From | @.> | | Date | 5/28/2023 21:37 | | To | @.> | | Cc | @.> , @.***> | | Subject | Re: [Dfam-consortium/RepeatModeler] the lastest version of repeatmodeler was error when running it, reveals "ERROR from search engine (3) " (Issue #205) |

Hi! I encountered the same error when running RepeatModeler. I want to know if you have solved this problem and how? Thanks!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[rmhubley]

Is this still a problem for you?

[Jiangjiangzhang6]

its ok, it had solved. thank you for your responsing

	张江江

@. | ---- Replied Message ---- | From | Robert @.> | | Date | 6/10/2023 03:51 | | To | @.> | | Cc | @.> , @.***> | | Subject | Re: [Dfam-consortium/RepeatModeler] the lastest version of repeatmodeler was error when running it, reveals "ERROR from search engine (3) " (Issue #205) |

Is this still a problem for you?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>