format of the usePhysical file

[Angus Davison]

Hi Pasi

I am struggling to include the usePhysical command in making a linkage map. Could you clarify the precise format? I have tried the following format (and various others) but without success. Taken a look but cant find precise instructions in the documentation

OZ073235.1_85384 OZ073235.1 85384
OZ073235.1_154247 OZ073235.1 154247
OZ073235.1_192828 OZ073235.1 192828
OZ073235.1_225077 OZ073235.1 225077
OZ073235.1_226497 OZ073235.1 226497

Exemplar command is

java -Xmx5g -cp /gpfs01/home/plzad/lep-map3-code/bin SeparateChromosomes2 \
data=$FILT_OUTPUT lodLimit=10 sizeLimit=50 informativeMask=3 grandparentPhase=1 usePhysical=1 0.01 map=$PHY_MAP \
numThreads=1 distortionLod=1 > $MAP_OUTPUT 2> separate.log

Error is as follows. I realise that this indicates that it does not like the string in the first column but not sure otherwise how to fix it!

Exception in thread "main" java.lang.NumberFormatException: For input string: "OZ073235.1_85384"
at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67)
at java.base/java.lang.Integer.parseInt(Integer.java:668)
at java.base/java.lang.Integer.parseInt(Integer.java:786)
at LGMap2.loadLGMap(LGMap2.java:199)
at SeparateChromosomes2.main(SeparateChromosomes2.java:60)

   Thanks, Angus

[Pasi Rastas]

Dear Angus,

The second column of the input data must be numeric in order for the usePhysical to work. So the format with contig and pos as the first two columns should work.

Cheers,
Pasi