spades_options flag in Unicycler v0.5; valid input?

[tomdeman-bio]

It seems like only certain SPAdes options can be passed on to SPAdes via Unicycler 0.5 using the --spades_options flag. Is there a list of these valid options?

are -m and --phred-offset the only valid options for this flag? I have tried to pass on SPAdes option -k (even though one should use --kmers in the main Unicycler UI) but that one generates a SPAdes error. --spades_options "--untrusted-contigs test.fa" also leads to a fatal error.

[valzip]

Hi! I have similar troubles passing option not to correct reads:

unicycler -1 G01_val_1.fq.gz -2 G01_val_2.fq.gz -s unpairedALL.fastq.gz --keep 3 --min_fasta_length 200 -o G01_UnicyclerOUT --spades_options "--only-assembler" ends up with error: unicycler: error: argument --spades_options: expected one argument Any idea what to do?

[lxsteiner]

For whatever reason, I think you need a space character at the end of the spades argument for it to work... so:

--spades_options "--untrusted-contigs test.fa "
and
--spades_options "--only-assembler "

try it and see if it works for you. I had a similar problem and this seemed to do the trick ;)

[valzip]

Thanks @lxsteiner! Extra space at the end of flag worked and options are passing to SPAdes.

Just to add a bit of my knowledge - I tried to pass --threads 24 directly to SPAdes but Unicycler default (8) overruled this option.