FastaDB::compact - Error could not locate file /home/xly/work8/403/repeat/RM_3970586.SunAug270923512023/round-4/sampleDB-4.fa!

[YDD99]

Describe the issue

RepeatModeler Round #4 Searching for Repeats -- Sampling from the database. . .- Gathering up to 91731253 bp FastaDB::compact - Error could not locate file /home/xly/work8/403/repeat/RM_3970586.SunAug270923512023/round-4/sampleDB-4.fa! at /opt/RepeatNodeler/RepeatModeler line 920.

Reproduction steps

1. Steps to reproduce the behavior, including the command lines given to the program

singularity exec ~/soft/tetools_latest.sif BuildDatabase -name 1701 ~/work8/403/Finalfasta/wYB1701.final.fasta Building database 1701: Reading /home/xly/work8/403/Finalfasta/WYB1701.final.fasta. . .Number of sequences (bp) added to database: 64144 ( 41744380 bp )

singularity exec ~/soft/tetools_ latest.sif RepeatModeler -database 1701 -threads 25RepeatModeler Version 2.0.4 aaEaaaa==== Using output directory = /home/xly/work8/403/repeat/RM_3970586.SunAug270923512023Search Engine = rmblast 2.14.0+ Threads = 25 Dependencies:TRF 4.09，RECON 1.08，RepeatScout 1.0.6,RepeatNasker 4.1.5LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1693099426 Database =/home/xly/work8/403/repeat/1701 .......

• and links to publicly available genome assemblies and other data files (if available).

Log output

Please paste or attach any and all log output, which includes useful information including data file statistics and version numbers. An easy way to capture this is to redirect the log output to a file e.g RepeatModeler -database mydb >& output.log. The log output should include the "random seed" value at the start of the run. This number will be necessary in order to reproduce the run exactly.

Environment (please include as much of the following information as you can find out):

• How did you install RepeatModeler? e.g. manual installation from repeatmasker.org, bioconda, the Dfam TE Tools container, or as part of another bioinformatics tool?

singularity exec~/soft/tetools_latest.sif RepeatModeler -database 1701 -threads 25

• Which version of RepeatModeler do you have? The output of RepeatModeler without any options will be a help page with the version of the program displayed at the top.

• Which version of RepeatMasker is this RepeatModeler installation using? Have you installed RepBase RepeatMasker Edition for RepeatMasker, or the full Dfam database?

• Operating system and version. The output of uname -a and lsb_release -a can be used to find this.

Additional context

• Add any other context you have about the problem here. Some possible examples:
  • If an older version of RepeatModeler worked before
  • If the problem only happens with specific data files

[rmhubley]

Do you have plenty of disk space where this run was operating (/home/xly/work8/403/repeat/)?

[rmhubley]

I assume this problem has gone away, or are you still having problems getting a run to complete under Singularity?

[Smeds]

Any updates on this issue? I just ran into the same error.