Fail to assembly de-novo genome

[Dv1t]

Hello VStrains team, thank you for developing such a great tool, but while using it, I faced the following problem. I attempted to assemble the complete HIV genome from this sample: SRR29407826. I used corona-spades and it worked fine. However VStrains crashes when assembling it. First, there was an error related to rev_dict in VStrains_PE_Inference.py. It doesn't had lowercase nucleotides in it and therefore raised KeyError. I fixed it replacing: rev_dict = {"A": "T", "T": "A", "C": "G", "G": "C"} with this: rev_dict = { "A": "T", "T": "A", "C": "G", "G": "C", "a": "t", "t": "a", "c": "g", "g": "c" } But new issue occurred, after messages in CLI log:

----------------------Paired-End Information Alignment---------------------- Start aligning reads to gfa nodes Number of processed reads: 0

It freezes forever and do not proceed any further.

Worth mentioning details In the same log there is a suspicious message:

INFO - graph kmer size: 0

Also VStrains can't read _assembly_graph_aftersimplification.gfa file (which is the output of spades) without changing its version in header from 1.2 to 1.0 manually.

Steps to reproduce

1. Assembly with spades:

   spades.py --corona -1 SRR29407826_1.fastq -2 SRR29407826_2.fastq -o spades_G_SRR29407826

2. Start VStrains:

   vstrains -a spades -g spades_G_SRR29407826/assembly_graph_after_simplification.gfa \
   -p spades_G_SRR29407826/contigs.paths \
   -o vstrains_G -fwd SRR29407826_1.fastq -rve SRR29407826_2.fastq

Files with reads:. SRR29407826.zip VStrains log: vstrains.log Spades log: spades.log

[RunpengLuo]

Hi, Thanks for trying VStrains and sorry for the late reply,

1. the GFA version conflicts with the external python library for parsing GFA file (gfapy) and it is not up-to-update with GFA version 1.2, I'll try to fix it later on but currently changing the version to 1.0 manually from GFA file should work for parsing. Thanks a lot for pointing this out!

2. VStrains didn't test with coronaSPAdes but mainly on SPAdes. I've ran your dataset with SPAdes (common version) + VStrains. It might not be helpful to run VStrains with coronaSPAdes since it already report a single collapsed strain and the graph structure doesn't have edges to further process either. I've attached the result&Bandage visualization if it might be helpful.

Feel free to let me know if there are further questions, John

out_SRR29407826.zip

[Dv1t]

I've also tried --rnaviral option of spades and there are two types of outcome with VStrains in case kmer=0:

1. Strain assembled (but same as scaffold of spades)
2. VStrain runs forever

Attaching logs and files for both cases: First: vstrains_kmer_0_success.log spades_kmer_0_success.log kmer_0_success_reads.zip

Second: vstrains_kmer_0_fail.log spades_kmer_0_fail.log kmer_0_fail_reads.zip