Stuck On Rule Untip

Mar 13, 2025 by ADMIN 20 views

Introduction

Assembling genomes using Verkko can be a complex and time-consuming process. When encountering issues, it's essential to identify the root cause and explore possible solutions. In this article, we'll delve into a specific problem where a Verkko assembly has been stuck on the "rule untip" step for an extended period. We'll examine the differences between Verkko 2.1 and 2.2.1, explore potential causes, and discuss possible workarounds.

Background

The user has been running a Verkko 2.2.1 assembly for five days, with the "rule untip" step being the bottleneck. In contrast, the same input data assembled using Verkko 2.1 completes this step in under 20 minutes. The user has tried restarting the run, but the issue persists. This raises questions about the changes between the two versions and potential workarounds to speed up the assembly process.

Command and Input Data

The command used to run Verkko for both versions is:

verkko -d ${asm} --no-nano --local-cpus 64 --hic1 ${hic_r1} --hic2 ${hic_r2} --hifi ${hifi}

The genome being assembled is a mostly diploid human genome, approximately 3.1G in size, with an approximate coverage of 30x for both HiFi and Hi-C data.

Output and Error Messages

The output and error messages from the Verkko 2.2.1 run are as follows:

Launching release v2.2.1
Using snakemake 7.32.4.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 64
Rules claiming more threads will be scaled down.
Provided resources: mem_gb=629

rule untip:
    input: 2-processGraph/unitig-unrolled-hifi-resolved.gfa, 1-buildGraph/hifi_nodecov.csv, emptyfile
    output: 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.gfa, 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.hifi-coverage.csv, 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.ont-coverage.csv
    log: 5-untip/untip.err
    jobid: 4
    reason: Missing output files: 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.gfa, 5-untip/unitig-unrolled-unitig-unrolled-popped-unitig-normal-connected-tip.hifi-coverage.csv
    resources: tmpdir=/tmp, job_id=1, n_cpus=1, mem_gb=64, time_h=24

Potential Causes and Workarounds

Version Differences: The user has updated from Verkko 2.1 to 2.2.1, which may have introduced changes that affect the "rule untip" step. It's essential to investigate the differences between the two versions and identify potential causes.
Input Data: The user has uncompressed the HiFi input data as a solution to issue 320. This may have affected the assembly process, leading to the current issue.
Python Version: Verkko 2.2.1 requires Python 3.10, but the user is running Python 3.9.19. This may cause conflicts with the environment, leading to the issue.
Resource Allocation: The user has allocated 64 cores and 629 GB of memory, which may not be sufficient for the assembly process.

Possible Solutions

Downgrade to Verkko 2.1: If the issue is specific to Verkko 2.2.1, downgrading to Verkko 2.1 may resolve the issue.
Update Python Version: Updating the Python version to 3.10 may resolve the issue, but this may require updating the environment.
Increase Resource Allocation: Increasing the resource allocation, such as adding more cores or memory, may help speed up the assembly process.
Optimize the Assembly Process: Optimizing the assembly process, such as using a different algorithm or parameter settings, may help resolve the issue.

Conclusion

Introduction

Q&A

Q: What is the "rule untip" step in Verkko assembly?

A: The "rule untip" step is a critical step in the Verkko assembly process, where the algorithm attempts to resolve the topology of the assembly graph.

Q: Why is the "rule untip" step taking so long to complete?

A: There are several potential causes for the "rule untip" step to take a long time to complete, including differences between Verkko 2.1 and 2.2.1, input data issues, Python version conflicts, and resource allocation limitations.

Q: What are the differences between Verkko 2.1 and 2.2.1?

A: Verkko 2.2.1 has several changes compared to Verkko 2.1, including updated algorithms, new parameters, and improved performance. However, these changes may also introduce new issues, such as the "rule untip" step taking a long time to complete.

Q: How can I troubleshoot the "rule untip" step?

A: To troubleshoot the "rule untip" step, you can try the following:

Check the Verkko 2.2.1 documentation for any changes or updates that may affect the assembly process.
Investigate the input data and ensure that it is correct and complete.
Check the Python version and ensure that it is compatible with Verkko 2.2.1.
Increase the resource allocation, such as adding more cores or memory, to see if it improves the assembly process.

Q: Can I use the 5-untip folder from the run with Verkko 2.1?

A: Yes, you can try using the 5-untip folder from the run with Verkko 2.1 to see if it resolves the issue. However, this may not be a permanent solution and may require further troubleshooting.

Q: What are the system requirements for Verkko 2.2.1?

A: The system requirements for Verkko 2.2.1 include Python 3.10, which may not be compatible with some systems. You may need to update your Python version or use a different version of Verkko.

Q: How can I optimize the assembly process?

A: To optimize the assembly process, you can try the following:

Use a different algorithm or parameter settings.
Increase the resource allocation, such as adding more cores or memory.
Use a different input data or assembly graph.
Try different versions of Verkko or other assembly tools.

Conclusion

The "rule untip" step in Verkko assembly can be a complex and time-consuming process. By understanding the differences between Verkko 2.1 and 2.2.1, exploring potential causes, and discussing possible workarounds, we can identify the root cause of the issue and find a solution. In this article, we've provided a Q&A section to help you troubleshoot and resolve the "rule untip" step issue.