Open LeonCharlesTranchevent opened 11 months ago
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".
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?
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:
When spades is run on its own, the log file is a bit more explicit and reports:
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).