Running shovill 1.1.0 and passing the option '--plasmid' to spades

[LeonCharlesTranchevent]

I have identified a problem when running shovill 1.1.0 and passing the option '--plasmid' to spades.

How to reproduce the problem

shovill --outdir {output_folder} --R1 {R1_file} --R2 {R2_file} --trim --mincov 3.00 --opts '--plasmid' --force
The input files do not really matter as long as the spades step is reached, as this is ultimately only a problem of having incompatible spades options.

Error reported

The shovill log reports:

[shovill] Assembling reads with 'spades'
[shovill] Running: spades.py -1 flash.notCombined_1.fastq.gz -2 flash.notCombined_2.fastq.gz --isolate --threads 8 --memory 16 -o spades --tmp-dir /tmp -k 21,27,33 --plasmid --merged flash.extendedFrags.fastq.gz 2>&1 | sed 's/^/[spades] /' | tee -a shovill.log
[spades]
[spades]
[spades] == Error == Specified mode combination is not supported! Check out user manual for available modes.
[spades]
[spades] In case you have troubles running SPAdes, you can write to [email protected]
[spades] or report an issue on our GitHub repository github.com/ablab/spades
[spades] Please provide us with params.txt and spades.log files from the output directory.
[shovill] Assembly failed - spades.fasta has zero contigs!

When spades is run on its own, the log file is a bit more explicit and reports:

== Error == you cannot simultaneously use more than one mode out of Isolate, Metagenomic, Large genome, Illumina TruSeq, RNA-Seq, Plasmid, and Single-cell (except combining Metagenomic and Plasmid)!
In case you have troubles running SPAdes, you can write to [email protected]
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

Explanation

The reason is that shovill uses the --isolate option of spades by default, which is not compatible with '--plasmid'.
Prior to version 1.1.0, shovill used the spades option --only-assembler by default, which was, and still is, compatible with '--plasmid'.

Potential fix

Use the spades option --isolate by default, but switch to --only-assembler when the spades option '--plasmid' is also provided to shovill. The same problem will also happen with other spades options (as per the spades logs above).

[wvnicholson]

After going to a new version of Shovill, I have run into a similar problem. I have --opts "--careful" passed to Spades and this clashes with Shovill selecting "--isolate".

[Zjianglin]

After going to a new version of Shovill, I have run into a similar problem. I have --opts "--careful" passed to Spades and this clashes with Shovill selecting "--isolate".

I encountered a similar problem, Did you solve the problem?