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ZWang-Lab / tRFtarget

tRFtarget (http://trftarget.net/) is a comprehensive platform consolidating both computationally predicted and experimentally validated binding interactions between transfer RNA-derived fragments (tRFs) and target transcripts across multiple organisms.
http://trftarget.net/
MIT License
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Fragments not found in database #17

Closed tphinney30 closed 1 month ago

tphinney30 commented 1 month ago

I am trying to determine the targets of the differently expressed tRFs in my dataset. Of the 70 fragments I have, only seven were found in your database, so I was unable to find the targets for the remaining fragments. I am wondering if there was a workaround so I can find the remaining targets. Thanks.

az7jh2 commented 1 month ago

Thank you for your interest in tRFtarget.

For tRF targets not indexed in tRFtarget, we offer a web service for users to upload their own sequences and identify targets. Please refer to http://trftarget.net/online_targets to submit your request to the web service.

If you encounter any issues while using the web service, please let me know.

Additionally, I noticed you opened two other GitHub issues with the same content. I will close the others so we can communicate in this issue.

az7jh2 commented 1 month ago

All sequences uploaded by users will be kept confidential and automatically deleted after 14 days. You can also download a Docker image of our pipeline to run it on your local computer. For local execution, please refer to our GitHub repository, tRFtarget-pipeline.

tphinney30 commented 1 month ago

Thank you for your timely response and your advice. I have downloaded the pipeline and in an attempt to run it, my docker container continuously exits soon after. I am greeted with "Exited (1)" status. There are no error logs when I search so I am unsure of how to try and diagnose the problem. Thanks in advance.

az7jh2 commented 1 month ago

Could you please post your command to run the pipeline and the log file here? I will review them to identify the issue.

tphinney30 commented 1 month ago

I am thankful for the help. I do not believe the container is running at all because there is nothing produced for logs. I am not sure where I am going wrong. query file is one I made in text edit that follows FASTA format but is a .txt file, and my target sequence is downloaded from (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.39) and is a .fa file. My commands are as follows docker pull az7jh2/trftarget:0.3.2 docker run -it --rm az7jh2/trftarget:0.3.2 tRFtarget -v docker run -it --rm -v /Users/tphinney30/Desktop/tRFtarget:/data az7jh2/trftarget:0.3.2 tRFtarget -q DE-TRF.fa.txt -t GRCh38.p13 -n 1 --e_rnahybrid -15 --e_intarna 0 -b 1 -s 6 everything works great up until executing the final line. Thanks again.

az7jh2 commented 1 month ago

I also tested the setup on my local computer.

For installation of the latest tRFtarget-pipeline v0.3.2, the commands are exactly the same as yours

docker pull az7jh2/trftarget:0.3.2
docker run -it --rm az7jh2/trftarget:0.3.2 tRFtarget -v

installation

Since I do not have the Differential tRF sequences from your project, I used five arbitrary human tRF sequences in our databases for testing, and renamed the file with a .txt extension. You can find this file here: test_tRF.fasta.txt.

For the target sequences, I was unsure which file you used, so I selected GCF_000001405.39_GRCh38.p13_rna.fna.gz for testing. After downloading, I uncompressed it to a fasta file, as the pipeline currently does not support compressed files as input.

I put these two files in a folder named testfolder, which will be mounted as the data folder in the Docker image during pipeline running.

files

And my running command was similar with yours:

docker run -it --rm -v /root/testfolder:/data az7jh2/trftarget:0.3.2 tRFtarget -q test_tRF.fasta.txt -t GCF_000001405.39_GRCh38.p13_rna.fna -n 8 --e_rnahybrid -15 --e_intarna 0 -b 1 -s 6

except I increased the number of CPU cores to 8 to enable parallel computing.

The pipeline executed correctly.

run

Could you try this example on your computer using the same input tRF and target sequences to verify if the Docker image works first? Then we can move on to your real dataset to address the issue.

tphinney30 commented 1 month ago

Hello, I tried the example with the test inputs; I ended up with the same results: the image was not running. Is this because I am attempting to run on my Mac, not a Linux OS? However, I could solve this with the command "--platform," but I am unsure. My outputs match yours except for the final line of running tRFtarget. When I attempt to execute the command, the image does not run. Sorry to be a hassle, but I'm unsure what is happening. Thanks for your help.

az7jh2 commented 1 month ago

Hi.

The tRFtarget-pipeline image currently supports Linux operating systems such as Ubuntu and macOS with Intel CPUs (not Apple Silicon series such as M1, M2, M3, etc.). You can find the supported OS in the image manifest as linux/amd64 (see the OS/ARCH in this page).

I uploaded two files, including tRF and target sequences for testing (you can find them here), and the whole pipeline ran successfully on Ubuntu and macOS 13 with Intel CPUs (see the GitHub workflow here).

Can you post the type of CPU of your Mac and the version of macOS here? The pipeline may run into issues on Macs with Apple Silicon CPUs. If so, I am afraid you might need to find another computer, use a virtual machine, or try our online service.

Additionally, can you please also post a screenshot of the command line interface after typing and running the tRFtarget command?

tphinney30 commented 1 month ago

I am using an M1. the image appears to be running flawlessly in a virtual machine. Thank you so much for your help!

az7jh2 commented 1 month ago

I am glad to help and happy that you have run the Docker image successfully.

If you have any other questions, please feel free to reach out. If you don't mind, I will go ahead and close this GitHub issue.