Hi,

I'm trying to run a fresh conda installation with unicycler, but have issues with the spades assembly as all but the 127 k-mer assembly is listed as failed. I had this issue previously as well, and then feeding the assembler the spades path worked, but since installing it again this doesn't solve the issue. I've tested spades separately and it works as it should so this can't be the issue.

I run the following command

unicycler -1 R1.fastq.gz -2 R2.fastq.gz -l assembly.fasta -o uni_out -t 16 --keep 0 --spades_path /home/user/tools/SPAdes-3.13.1-Linux/bin/spades.py --mode bold

And my problem is this:
SPAdes assemblies (2019-12-03 14:36:52)

Unicycler now uses SPAdes to assemble the short reads. It scores the assembly graph for each k-mer using the number of contigs (fewer is better) and the number of dead ends (fewer is better). The score function is 1/(c*(d+2)), where c is the contig count and d is the dead end count.

K-mer Contigs Dead ends Score
27 failed
47 failed
63 failed
77 failed
89 failed
99 failed
107 failed
115 failed
121 failed
127 203 203 2.40e-05 <-best

Any ideas as what might solve this issue?

Thanks in advance!