Body: <p>I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data.</p>
  <p>I have the file contigs.fa from short reads but phasing step with PacBio reads gives the following error after running for couple of hours</p>
  <blockquote>
  <p>Error(13): Error, SolveDBG exception!! platanus_allee solve_DBG
  command failed.</p>
  </blockquote>
  <p>Here is the script used for contig assembly and phasing</p>
  <pre><code>num_threads=20 
  tmp_dir=/path-to-/tem/platanus_allee 
  memory_GB=100 
  out_prefix=out
  minimap2_path=minimap2
  
  # Input reads
  
  PE=trimmed_L1_*.fq
  PacBio=pacbio???.fastq.gz
  
  # Contig assembly commands
  platanus_allee assemble -t <span class="math-container">${num_threads} -tmp $</span>{tmp_dir} -m <span class="math-container">${memory_GB} -o $</span>{out_prefix} \
  -f <span class="math-container">$PE \
  2&gt;$</span>{out_prefix}.assembleLog
  
  # phasing commands 
  platanus_allee phase -t <span class="math-container">${num_threads} -tmp $</span>{tmp_dir} -o <span class="math-container">${out_prefix} -mapper $</span>{minimap2_path} \
  -c out_contig.fa \
  -IP1 <span class="math-container">$PE -p $</span>PacBio \ 
  2&gt;${out_prefix}.phaseLog
  </code></pre>
  <p>cat out.phaseLog</p>
  <pre><code>platanus_allee version: 2.2.2
  platanus_allee phase -t 20 -tmp /path-to-/tem/platanus_allee -o out -mapper minimap2 -c out_contig.fa -IP1 trimmed_L1_1.fq trimmed_L1_2.fq -p /path-to-/pacbio*.fastq.gz 
  
  Error(13): Error, SolveDBG exception!!
  platanus_allee solve_DBG command failed.
  </code></pre>
  <p>tail -n 15 path-to-/out_intermediateResults/round1/out.solveDBGLog</p>
  <pre><code>dividing nodes based on bubbles ...
  dividing scaffolds to adjust bubble-breakpoints...
  dividing indonsistent bubble-ends...
  pairing bubble nodes...
  dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
  NUM_DIVISION = 1832
  dividing scaffolds to adjust bubble-breakpoints...
  dividing indonsistent bubble-ends...
  pairing bubble nodes...
  dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
  NUM_DIVISION = 0
  TOTAL_NUM_DIVISIONS =1832
  
  dividing erroneous scaffolds based on base-level coverages ...
  Segmentation fault (core dumped)
  </code></pre>
  <p>A bug causing the segmentation fault seems issue on <a href="http://platanus.bio.titech.ac.jp/platanus2" rel="nofollow noreferrer">Platanus-allee v2.0.0 and earlier</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-08T09:30:40.613Z
Comments.Text: I would suggest talking to the platanus authors. A segfault without any accompanying error message or informative logging suggests an unforeseen bug, and this is really not much information for us to work from. It does not look like it is related to the previously fixed bug that causes a segfault. As usual of course it is a good idea to check all your input files but it does not appear that that is an issue.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-08T10:50:51.307Z
Comments.Text: Thanks @MaximilianPress. I wrote to correspondent author of Platanus-allee and didn't get response!
Comments.UserDisplayName: Enset
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-08T17:18:25.757Z
Comments.Text: That isn't good! I hope they get back to you. In the meantime, you might look into alternatives for assemblers/scaffolders. I hesitate to recommend because I don't know what your goals are, though.
Comments.UserDisplayName: Maximilian Press
Tags: <phylogenetics><assembly><software-recommendation><long-reads><pacbio>
Title: Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!
ThreadText: # Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!
  
  (Asked by: username_0 on 2020-04-08)
  
  I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data.
  
  I have the file contigs.fa from short reads but phasing step with PacBio reads gives the following error after running for couple of hours
  
  > Error(13): Error, SolveDBG exception!! platanus\_allee solve\_DBG
  > command failed.
  
  Here is the script used for contig assembly and phasing
  
  ```
  num_threads=20 
  tmp_dir=/path-to-/tem/platanus_allee 
  memory_GB=100 
  out_prefix=out
  minimap2_path=minimap2
  
  # Input reads
  
  PE=trimmed_L1_*.fq
  PacBio=pacbio???.fastq.gz
  
  # Contig assembly commands
  platanus_allee assemble -t ${num_threads} -tmp ${tmp_dir} -m ${memory_GB} -o ${out_prefix} \
  -f $PE \
  2>${out_prefix}.assembleLog
  
  # phasing commands 
  platanus_allee phase -t ${num_threads} -tmp ${tmp_dir} -o ${out_prefix} -mapper ${minimap2_path} \
  -c out_contig.fa \
  -IP1 $PE -p $PacBio \ 
  2>${out_prefix}.phaseLog
  
  ```
  
  cat out.phaseLog
  
  ```
  platanus_allee version: 2.2.2
  platanus_allee phase -t 20 -tmp /path-to-/tem/platanus_allee -o out -mapper minimap2 -c out_contig.fa -IP1 trimmed_L1_1.fq trimmed_L1_2.fq -p /path-to-/pacbio*.fastq.gz 
  
  Error(13): Error, SolveDBG exception!!
  platanus_allee solve_DBG command failed.
  
  ```
  
  tail -n 15 path-to-/out\_intermediateResults/round1/out.solveDBGLog
  
  ```
  dividing nodes based on bubbles ...
  dividing scaffolds to adjust bubble-breakpoints...
  dividing indonsistent bubble-ends...
  pairing bubble nodes...
  dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
  NUM_DIVISION = 1832
  dividing scaffolds to adjust bubble-breakpoints...
  dividing indonsistent bubble-ends...
  pairing bubble nodes...
  dividing scaffolds to adjust bubble-breakpoints distiguishing strands ...
  NUM_DIVISION = 0
  TOTAL_NUM_DIVISIONS =1832
  
  dividing erroneous scaffolds based on base-level coverages ...
  Segmentation fault (core dumped)
  
  ```
  
  A bug causing the segmentation fault seems issue on [Platanus-allee v2.0.0 and earlier](http://platanus.bio.titech.ac.jp/platanus2)
  
  **Tags:** phylogenetics, assembly, software-recommendation, long-reads, pacbio
  
  > **Comments:**
  > **username_1**: I would suggest talking to the platanus authors. A segfault without any accompanying error message or informative logging suggests an unforeseen bug, and this is really not much information for us to work from. It does not look like it is related to the previously fixed bug that causes a segfault. As usual of course it is a good idea to check all your input files but it does not appear that that is an issue.  
  > **username_0**: Thanks @username_1. I wrote to correspondent author of Platanus-allee and didn't get response!  
  > **username_1**: That isn't good! I hope they get back to you. In the meantime, you might look into alternatives for assemblers/scaffolders. I hesitate to recommend because I don't know what your goals are, though.  
  
  ---
  
  ## 0 answers
  
  