Running Ltr_retriever...Died at /software/RepeatModeler-2.0.4/LTRPipeline line 693. #201
Comments
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Hi. Ran into the same issue. Any resolution yet? I checked really quick and the soft link directing to the tmp directory is broken. The reason is that such file is not available in the path specified. |
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I was trying to run repeatmodeler with four fungal genomes. I got the same error for all four genomes. Has anyone figured out the solution to this issue yet? |
Were you able to get it running without the error? If yes, can you please share how you fixed it? |
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Throwing my hat into the ring also with this error. All other steps completed successfully using the conda install of repeatmodeler. I paste below the programs and versions in my conda environment. Happy to provide any more info for this (log files, etc etc) if that is useful. |
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@ehs220 @ShirelyI been working on identyfying the problem and I think I have it. It seems that if you go to the directory for the LTR with the RM_xxxx run file the symlink for the My path with the broken seq.fa What I have done so far is What I am now running is in the same directory the command within the
This is creating files succesfully this time, so it looks like it is working. @rmhubley I think the problem is within the LTRPipeline is the following lines (line 602 and 603). The symlink is failing. My perl is beyond atrocious so I have 0 idea how to fix this. Happy to provide any additional information if needed, and I can update if fixing the symlink actually works. Ben |
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@benyoung93 - thanks for the suggestion. I am not able to reproduce this problem, so it's hard to know if this is the problem or why it would be so. If someone can reproduce this problem (especially with a small input file -- say a 10MB portion of an assembly), then we could try to identify the issue. Another option is to try changing that line in the code from: to: and see if copying rather than linking fixes it for them. |
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Hi, I just came across the same issue. I had never had this problem before, even with the latest version. I had to reinstall a new copy of the repeat modeler, and that's when the ltr pipeline failed. I tried it with a small sample of my genome and had the same error. Here is the genome sample if that would help. |
Tried this, did not worked. If that helps, the pipeline was working fine and suddenly stopped working |
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HI all Sorry, I have been in the lab doing lab work. I can try and reproduce this problem in the next few weeks if you are still interested in finding a bug fix. Ben |
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Hello everyone |
@minhasbushra Finally, did the error has been solved? if solved, could give me some advice about it? thanks |
Describe the issue
Running Ltr_retriever...Died at /software/RepeatModeler-2.0.4/LTRPipeline line 693.
A concise description of the bug, including any error messages.
Reproduction steps
BuildDatabase -name G G.fasta
RepeatModeler -database G -threads 16 -LTRStruct >repeatmodeler.log 2>&1
Log output
LTR Structural Analysis
Running LtrHarvest... : 00:05:55 (hh:mm:ss) Elapsed Time
Running Ltr_retriever...Died at /data/data1/zx/software/RepeatModeler-2.0.4/LTRPipeline line 693.
LTRPipeline Time: 00:06:04 (hh:mm:ss) Elapsed Time
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?
manual installation from repeatmasker.org
Which version of RepeatModeler do you have? The output of
RepeatModelerwithout any options will be a help page with the version of the program displayed at the top.RepeatModeler 2.0.4
Which version of RepeatMasker is this RepeatModeler installation using? Have you installed RepBase RepeatMasker Edition for RepeatMasker, or the full Dfam database?
RepeatMasker 4.1.4, RepBase RepeatMasker Edition for RepeatMasker installed
Operating system and version. The output of
uname -aandlsb_release -acan be used to find this.Additional context
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