I think [300 will be parsed as 0.
You can check what Ray did by reading LibraryStatistics.txt
I added a ticket for that, as user-provided should contain floating numbers
or integers and not
anything else.
Sébastien
Adrian Platts a écrit :
> Hi Sebastien
>
> A trivial observation on the Ray command syntax.
>
> A new user here was using Ray 1.7 for the first time to run some test
> assemblies. However they misunderstood the optional parameter notation in
> the manual and included
> brackets around the insert size& SD. They then re-ran the alignment with
> essentially the same options except without the brackets:
>
> mpiexec -n 40 Ray \
> -k \
> 31 \
> -p \
> xxx_forward_pairs.fastq \
> xxx_reverse_pairs.fastq \
> [300 \
> 30] \
> -p \
> xxx_forward_pairs.fastq \
> xxx_reverse_pairs.fastq \
> [300 \
> 30] \
> -p \
> xxx_forward_pairs.fastq \
> xxx_pairs.fastq \
> [300 \
> 30] \
> -o \
> Ray-build-k31-PE-endfilQ30L40_jun_11_2012
>
> and then
>
> mpiexec -n 40 Ray \
> -k \
> 31 \
> -p \
> xxx_forward_pairs.fastq \
> xxx_reverse_pairs.fastq \
> 300 \
> 30 \
> -p \
> xxx_forward_pairs.fastq \
> xxx_reverse_pairs.fastq \
> 300 \
> 30 \
> -p \
> xxx_forward_pairs.fastq \
> xxx_reverse_pairs.fastq \
> 300 \
> 30 \
> -o \
> Ray-build-k31-PE-endfilQ30L40_jun_13_2012
>
> They thought that if they had the syntax incorrect, then Ray would simply
> return an error. However in this case Ray ran both assemblies
> however the outcomes were very different. The first generated:
>
> N50 scaffold length 1911
>
> While the second generated:
>
> N50 scaffold length 16602
>
> Since it's an easy mistake I wondered if you may want to try to catch this in
> the command parser? I'm also slightly curious as to how Ray interpreted the
> first
> command. Did it assume insert size=0 or attempt to estimate the insert size.
> The former I hope...
>
> Best
>
> Adrian
>
>
>
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