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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

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  • $\begingroup$ 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. $\endgroup$ Apr 8 '20 at 9:30
  • $\begingroup$ Thanks @MaximilianPress. I wrote to correspondent author of Platanus-allee and didn't get response! $\endgroup$
    – Enset
    Apr 8 '20 at 10:50
  • $\begingroup$ 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. $\endgroup$ Apr 8 '20 at 17:18

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