Comments (14)
Hello Josh,
Thanks for using LTR_retriever, and I am sorry you encounter an error.
The error message says the "paths" file is missing in the root directory of LTR_retriever. Please double check the file in the program directory in case you misplaced it. If the error persists, you may try to use a brand new LTR_retriever without any modifications, and see if the program has the same error.
Shujun
from ltr_retriever.
Hi Shujun,
Thanks for the quick response. I did as you suggested, but that didn't seem to solve the problem. I included a line of code beneath line 75 (bolded) in the LTR_retriever script:
$script_path="/Users/abcd/LTR_retriever-master"
And this solved the problem. I wonder if the issue was due to my using a macOS system...
Josh
from ltr_retriever.
Hi Josh,
Thanks for targeting the issue. I think it's very likely the problem of the macOSX system, on which LTR_retriever was not developed. I will fix this in the next version update. Do you encounter any other hiccups after hard-coding the $scrip_path?
Thanks,
Shujun
from ltr_retriever.
Hi Josh,
I researched this issue and found it exists in a couple of other scripts, so hard-coding the path in LTR_retriever won't fix this issue. Instead, I pushed a quick bugfix in the latest version of LTR_retriever just now. I was able to test it on a MacBook-pro that has the latest OS installed. I apologize for the difficulties you encountered. Please update your program and try it again. Please let me know if you have further problems running it on Mac, which I have not fully tested.
Thanks,
Shujun
from ltr_retriever.
Hi Shujun,
As far as I can tell, the program seems operational on my mac now. The quick update is much appreciated!
I only note one error message during the run, which appears after Module 1 is completed:
./bin/trf409.legacylinux64: ./bin/trf409.legacylinux64: cannot execute binary file
Regards,
Josh
from ltr_retriever.
Hi Josh,
Thank you for your feedback. This error message is produced due to the same bug, meaning the tandem repeat finder is not found in the incorrectly specified path and hence the unfavorable tandem repeats could exists in the output. Other related errors should also have occurred but with no checking mechanism for them. So please update your program and rerun it. You can just copy out the old paths file and move it to the new version folder, then installation is done. I am sorry for the troubles.
Regards,
Shujun
from ltr_retriever.
Hi Shujun,
I reran the program using the updated program (v1.7), but I still obtain the same error message for legacylinux64.
Best,
Josh
from ltr_retriever.
Ahh... the same bug, two more places fixed. Sorry for the fickle updates. Please pull the program again and rerun.
Best,
Shujun
from ltr_retriever.
Sorry for the hassle Shujun, but I got the same error again with my last run using the most recent version (still labeled as v1.7 when I ran the program).
Best,
Josh
from ltr_retriever.
Running in Mac seems to have more problems than I thought. I will get a Mac and fully test it. I am sorry to put you in a guinea pig position.
Best,
Shujun
from ltr_retriever.
Hi Josh,
The code should support Mac Os X well now. Please give it a shot and let me know if there are any hiccups. Thanks for testing it on your Mac, which has made the code better.
Best,
Shujun
from ltr_retriever.
Hi Shujun,
I just ran LTR_retriever v1.7.4 on my MacOS (High Sierra, 10.13.3), and it ran smoothly with no reported errors. Thank you once again for your quick responses, and for re-writing the code in a short amount of time!
Regards,
Josh
from ltr_retriever.
Actually, I did notice one thing, sorry Shujun.
A brief message appeared directly under the line for calling LTR_retriever (bolded):
perl LTR_retriever -genome ToxoDB35ME49Genome.fa -inharvest ToxoDB35.harvest.scn -nonTGCA ToxoDB35.harvest.nmtf.scn
Unrecognized escape \s passed through at LTR_retriever line 682.
Best,
Josh
from ltr_retriever.
Hi Josh,
Thank you for your feedback. That was just a minor warning, and would not affect any of your results. I will have it fixed in the next update. Hope you got what was expected. Thank you for using LTR_retriever!
Best,
Shujun
from ltr_retriever.
Related Issues (20)
- No tbl file HOT 2
- No candidate is found in the file(s) you specified. HOT 7
- Repeatmodeler 、RepeatMasker and LTR_retriever HOT 4
- Serious error ⇒ Dependency checking: Error: The RMblast engine is not installed in RepeatMasker! HOT 3
- Can one use EDTA genome.mod.pass.list and genome.mod.EDTA_TEanno.out output in LAI HOT 1
- No candidate is found in the file(s) you specified HOT 2
- Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129 HOT 10
- Are LTRs (insertion time of 0) the likely cause of somatic variation? HOT 2
- LTR_retriever warning HOT 1
- Total length annotated by RepeatMasker is longer than LTR_retriever HOT 3
- RE: Masking LTR HOT 2
- A question about LAI in autopolyploid HOT 2
- How to discover "sequencing gaps" in genome assemblies. HOT 3
- ask for help? panLTR HOT 1
- Running Ltr_retriever...Died at /app/RepeatModeler-2.0.4/LTRPipeline line 693. HOT 2
- No tbl file issue HOT 5
- LAI is not applicable on the current genome assembly HOT 3
- conda install errors HOT 1
- I can´t install LTR_retriever via conda HOT 4
- Invalid value for shared scalar HOT 10
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ltr_retriever.