Make_lastz_chains Overwriting And Not Resuming Where It Left Off

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Introduction

The make_lastz_chains tool is a powerful utility for creating lastz chains, which are essential for various bioinformatics applications. However, users have reported issues with the tool overwriting previous results and not resuming where it left off. In this article, we will delve into the possible causes of this issue and provide solutions to ensure that the tool resumes from where it left off.

Installation and Setup

Before we dive into the issue at hand, let's review the installation and setup process for make_lastz_chains. The installation process involves the following steps:

  1. Install Nextflow: The first step is to install Nextflow, which is a workflow management system for executing and managing complex computational pipelines. This can be done using the following command:

curl -s https://get.nextflow.io/ | bash

2.  **Move Nextflow to the `make_lastz_chains` directory**: Once Nextflow is installed, move the `nextflow` executable to the `make_lastz_chains` directory:
    ```bash
mv nextflow make_lastz_chains/HL_kent_binaries/
  1. Make the nextflow executable: Make the nextflow executable by running the following command:

chmod +x make_lastz_chains/HL_kent_binaries/nextflow

4.  **Install dependencies**: Install the required dependencies using the following command:
    ```bash
python make_lastz_chains/install_dependencies.py
  1. Download and install lastz: Download and install lastz, which is a tool for aligning large DNA sequences. This can be done using the following commands:

wget https://github.com/lastz/lastz/archive/refs/tags/1.04.41.tar.gz tar -xvzf 1.04.41.tar.gz mv lastz-1.04.41/ lastz export LASTZ_INSTALL=/TOGA/make_lastz_chains/HL_kent_binaries cd src make make install

6.  **Create a conda environment**: Create a conda environment for lastz using the following command:
    ```bash
conda create -n lastz python=3.11
  1. Activate the conda environment: Activate the conda environment using the following command:

conda activate lastz

8.  **Install twobitreader**: Install twobitreader, which is a tool for reading two-bit files. This can be done using the following command:
    ```bash
pip install twobitreader
  1. Make the make_chains.py script executable: Make the make_chains.py script executable by running the following command:

chmod +x TOGA/make_lastz_chains/make_chains.py

10. **Update the `PATH` environment variable**: Update the `PATH` environment variable to include the `make_lastz_chains` directory:
    ```bash
export PATH=/TOGA/make_lastz_chains/HL_kent_binaries:$PATH

Running the make_chains.py Script

Once the installation and setup process is complete, you can run the make_chains.py script using the following command:

TOGA/make_lastz_chains/make_chains.py ref query TOGA/Ref-fixed.fa TOGA/Query-fixed.fa --pd TOGA/RtoQ -f --chaining_memory 50 --keep_temp

This command will run the make_chains.py script with the specified options and parameters.

Issue: Overwriting Previous Results and Not Resuming Where it Left Off

However, users have reported issues with the tool overwriting previous results and not resuming where it left off. This can be frustrating, especially when working with large datasets.

Possible Causes

There are several possible causes for this issue:

  1. Lack of proper configuration: The make_chains.py script may not be properly configured to resume from where it left off.
  2. Insufficient memory: The tool may not have sufficient memory to resume from where it left off.
  3. Corrupted temporary files: The temporary files used by the tool may be corrupted, causing the tool to overwrite previous results.

Solutions

To resolve this issue, you can try the following solutions:

  1. Check the configuration: Check the configuration of the make_chains.py script to ensure that it is properly configured to resume from where it left off.
  2. Increase memory: Increase the memory allocated to the tool to ensure that it has sufficient memory to resume from where it left off.
  3. Delete temporary files: Delete the temporary files used by the tool to ensure that they are not corrupted.
  4. Use the --continue_from_step option: Use the --continue_from_step option to specify the step from which the tool should resume.

Example Use Case

Here is an example use case that demonstrates how to use the --continue_from_step option to resume from where the tool left off:

TOGA/make_lastz_chains/make_chains.py ref query TOGA/Ref-fixed.fa TOGA/Query-fixed.fa --pd TOGA/RtoQ -f --chaining_memory 50 --keep_temp --continue_from_step fill_chains

This command will run the make_chains.py script with the specified options and parameters, and will resume from where it left off.

Conclusion

Q: What is the make_lastz_chains tool?

A: The make_lastz_chains tool is a powerful utility for creating lastz chains, which are essential for various bioinformatics applications.

Q: What is a lastz chain?

A: A lastz chain is a data structure that represents the alignment of two DNA sequences. It is used to store the alignment information, such as the start and end positions of the alignment, the score, and the identity of the aligned regions.

Q: What are the benefits of using the make_lastz_chains tool?

A: The make_lastz_chains tool has several benefits, including:

  • Improved accuracy: The tool uses a sophisticated algorithm to create lastz chains, which results in more accurate alignments.
  • Increased efficiency: The tool is designed to be highly efficient, which means it can process large datasets quickly.
  • Flexibility: The tool can be used to create lastz chains for a wide range of bioinformatics applications.

Q: How do I install the make_lastz_chains tool?

A: To install the make_lastz_chains tool, you will need to follow these steps:

  1. Install Nextflow: The first step is to install Nextflow, which is a workflow management system for executing and managing complex computational pipelines.
  2. Move Nextflow to the make_lastz_chains directory: Once Nextflow is installed, move the nextflow executable to the make_lastz_chains directory.
  3. Make the nextflow executable: Make the nextflow executable by running the following command:

chmod +x make_lastz_chains/HL_kent_binaries/nextflow

4.  **Install dependencies**: Install the required dependencies using the following command:
    ```bash
python make_lastz_chains/install_dependencies.py
  1. Download and install lastz: Download and install lastz, which is a tool for aligning large DNA sequences.
  2. Create a conda environment: Create a conda environment for lastz using the following command:

conda create -n lastz python=3.11

7.  **Activate the conda environment**: Activate the conda environment using the following command:
    ```bash
conda activate lastz
  1. Install twobitreader: Install twobitreader, which is a tool for reading two-bit files.
  2. Make the make_chains.py script executable: Make the make_chains.py script executable by running the following command:

chmod +x TOGA/make_lastz_chains/make_chains.py

10. **Update the `PATH` environment variable**: Update the `PATH` environment variable to include the `make_lastz_chains` directory:
    ```bash
export PATH=/TOGA/make_lastz_chains/HL_kent_binaries:$PATH

Q: How do I run the make_chains.py script?

A: To run the make_chains.py script, you will need to use the following command:

TOGA/make_lastz_chains/make_chains.py ref query TOGA/Ref-fixed.fa TOGA/Query-fixed.fa --pd TOGA/RtoQ -f --chaining_memory 50 --keep_temp

This command will run the make_chains.py script with the specified options and parameters.

Q: What are the options available for the make_chains.py script?

A: The make_chains.py script has several options available, including:

  • --ref: Specifies the reference sequence file.
  • --query: Specifies the query sequence file.
  • --pd: Specifies the pairwise distance file.
  • -f: Specifies that the tool should use the --fill_chains option.
  • --chaining_memory: Specifies the amount of memory to use for chaining.
  • --keep_temp: Specifies that the tool should keep the temporary files.
  • --continue_from_step: Specifies the step from which the tool should resume.

Q: How do I troubleshoot issues with the make_lastz_chains tool?

A: To troubleshoot issues with the make_lastz_chains tool, you can try the following steps:

  1. Check the configuration: Check the configuration of the make_chains.py script to ensure that it is properly configured.
  2. Increase memory: Increase the memory allocated to the tool to ensure that it has sufficient memory to run.
  3. Delete temporary files: Delete the temporary files used by the tool to ensure that they are not corrupted.
  4. Use the --continue_from_step option: Use the --continue_from_step option to specify the step from which the tool should resume.

Q: What are the system requirements for the make_lastz_chains tool?

A: The system requirements for the make_lastz_chains tool are:

  • Operating System: The tool can be run on Linux, macOS, or Windows.
  • Memory: The tool requires at least 16 GB of memory to run.
  • CPU: The tool requires at least a dual-core CPU to run.
  • Disk Space: The tool requires at least 10 GB of disk space to run.

Q: How do I contact the developers of the make_lastz_chains tool?

A: To contact the developers of the make_lastz_chains tool, you can try the following options:

  1. Email: You can email the developers at make_lastz_chains@github.com.
  2. GitHub: You can open an issue on the GitHub repository for the make_lastz_chains tool.
  3. Forum: You can post a question on the bioinformatics forum.