Platanus_allee基因组组装器phase命令报错：SolveDBG异常求助

Let's work through this error step by step. First, let's recap what you've shared: you're trying to run the phase command in Platanus_allee v2.0.2, but hitting an Error(13) related to a SolveDBG exception.

Your Command & Error Output #

First, let's clarify the command you ran (it looks like there's some repetition/typo in the original input):

bio@bio-XPS-8700:~/Fareeha/Platanus/Platanus_allee_v2.0.2_Linux_x86_64$ ./platanus_allee phase -c out_contig.fa out_junctionKmer.fa \platanus_allee phase \ -c out_contig.fa out_junctionKmer.fa \ -IP1 /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_1_head-3000000.fq /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_2_head-3000000.fq \ 2>phase.log

The error you received:

platanus_allee version: 2.0.2
./platanus_allee phase -c out_contig.fa out_junctionKmer.fa
platanus_allee phase -c out_contig.fa out_junctionKmer.fa -IP1 /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_1_head-3000000.fq /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_2_head-3000000.fq 2
Error(13): Error, SolveDBG exception!! platanus_allee solve_DBG command failed.

Key Fixes & Troubleshooting Steps #

1. Fix the Command Syntax

Looking at your command, there's a clear repetition of platanus_allee phase -c out_contig.fa out_junctionKmer.fa and misplaced backslashes, which is almost certainly causing parameter parsing issues. Let's clean up the command to its correct form:

./platanus_allee phase -c out_contig.fa out_junctionKmer.fa -IP1 /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_1_head-3000000.fq /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_2_head-3000000.fq 2>phase.log

Make sure there are no extra backslashes or repeated command segments, and that all parameters are passed in a single, valid command line.

2. Validate Input Files

• Check contig and junction kmer files: Confirm out_contig.fa and out_junctionKmer.fa exist in your working directory, are complete (no truncation from previous steps), and are in the correct FASTA format expected by Platanus_allee. You can use head out_contig.fa to verify the file structure.
• Check sequencing reads: Ensure your paired-end FASTQ files (SDNA-270_1_head-3000000.fq and SDNA-270_2_head-3000000.fq) are readable, not corrupted, and follow standard FASTQ formatting. Run head on both files to check for valid header lines, sequences, and quality scores. Tools like fastqc can also help validate read quality and file integrity.

3. Check System Resources

The SolveDBG step is memory-intensive—if your system doesn't have enough RAM allocated, this can cause the exception.

• Run free -h to check available memory. If you're low on RAM, try closing other processes, increasing the available memory for your session, or adjusting Platanus_allee's thread/memory parameters (e.g., using -t to specify more threads if CPU is a bottleneck, though memory is more likely the issue here).

4. Dig Into the Full Log

You redirected stderr to phase.log, but the error output you shared is truncated. Check the full content of phase.log with:

cat phase.log

This may reveal more details—like a file read error, memory exhaustion message, or specific issue with the SolveDBG step that isn't shown in the truncated output.

5. Verify Version Compatibility

Platanus_allee v2.0.2 has been around for a while, and there may be bug fixes in newer versions (like v2.2.0) that address this SolveDBG exception. Check the official release notes for any fixes related to the phase command or SolveDBG, and consider upgrading to the latest stable version if possible.

内容的提问来源于stack exchange，提问作者FarihaKomal