BUG: HMMER Version Conflict Causes Crash with '--cut_tc' (Strict Error Handling)

[ystone1101]

Summary
The main.py bin subcommand crashes during the seed generation phase because the hmmsearch command uses the problematic --cut_tc flag. This error is triggered by the strict error handling introduced in newer HMMER versions (v3.3.x and later).

Setting	Value
OS/Architecture	Linux/ARM64
System Type	NVIDIA DGX Spark
HMMER Version	v3.3.x or later (Strict behavior)
Working Environment	HMMER 3.1b2 (Legacy/amd64) works without issue

The process fails when executing the hmmsearch command with the following error reported in the .err file:

Warning

Error: TC bit thresholds unavailable on model BA00001

Technical Root Cause: The marker file (bacar_marker.hmm) is missing the required TC (Trusted Cutoff) scores.
We confirmed that the uploaded .hmm file does not contain these thresholds.
The legacy HMMER version ignored this absence, while the modern version aborts the process as a fatal error.

Proposed Fix: The necessary flag must be removed and replaced with a standard E-value cutoff.

The fix is required because the database lacks the necessary metadata.
File: COMEBin/utils.py
Modification: Find the hmmCmd variable inside the gen_seed function (around line 166) and replace the command structure.

# [Fix: Remove --cut_tc and add -E 1e-5 (Standard Filter)]
hmmCmd = hmmExeURL + " --domtblout " + hmmResultURL + " -E 1e-5 --cpu " + str(
    threads) + " " + markerURL + " " + fragResultURL + " 1>" + hmmResultURL + ".out 2>" + hmmResultURL + ".err"

Notes on Other Compatibility Issues (Crucial for ARM64)
Scikit-learn Version: The KMeans initialization in cluster.py must be updated (remove n_jobs=-1 and change algorithm="full" $\rightarrow$ algorithm="lloyd").
Perl Regex: The contig name parsing regex in the auxiliary Perl script required adding an OR condition (||) due to varying FragGeneScan output formats on ARM64.