High Load Issue: dbcan_sub Creating Excessive Threads

[trx296554555]

Thank you for your hard work and recent updates. However, I wanted to bring to your attention an ongoing issue with the latest version of run_dbcan-4.1.1. When processing large input sequence files, dbcan_sub tends to create an excessive number of threads, resulting in high system load. #117

This issue persists even when specifying parameters such as --dbcan_thread and --hmm_cpu, as there seems to be no effective limitation on the number of threads being created.

After reviewing the code of run_dbcan.py, I have identified that the issue lies within the function split_uniInput. This section of code directly launches as many subprocesses as the number of small files generated by splitting the large input file.https://github.com/linnabrown/run_dbcan/blob/707aed21a0ef455828126f1afb5820963e8274ca/dbcan/cli/run_dbcan.py#L139C1-L157C22

I made modifications to this specific code section to prevent excessive load when I used it myself. I implemented a simple ThreadPool, but I'm unsure if this could potentially affect other parts of the program. Therefore, I offer it as a reference only.

from concurrent.futures import ThreadPoolExecutor, as_completed

def run_command(cmd):
    hmmer = Popen(cmd)
    hmmer.wait()
    return cmd

max_workers = dbcan_thread  
cmds = []
for j in split_files:
    cmds.append(["hmmsearch", "--domtblout", f"{outPath}d{j}", "--cpu", "2", "-o", "/dev/null",
                 f"{dbDir}dbCAN_sub.hmm", f"{outPath}{j}"])

with ThreadPoolExecutor(max_workers=max_workers) as executor:
    futures = [executor.submit(run_command, cmd) for cmd in cmds]
    for future in as_completed(futures):
        try:
            command = future.result()
            print(f"Command: {' '.join(command)} already completed.")
        except Exception as e:
            print(f"An error occurred: {e}")

Best, Robin

[linnabrown]

Hi Robin,

Thank you so much for bringing this out. We previously utilized this manner due to hmmscan does not support multithreads but hmmsearch does. Therefore, we will remove the multi-processing part and just use the multi-threading butil-in function from hmmsearch.

Let me just delete and test codes and I will put 4.1.2 version. Thank you so much!

Best, Le

[HaidYi]

Our 4.1.2 version is already issued. Problem solved.