Problem trying to run VariationHunter

[alig]

Hi,

I'm just trying to run the program VariationHunter, but I get the following error.

There doesn't seem to be any instructions for install & make just returns
make: Nothing to be done for `all'.

Can anyone help

thanks alig

:~/Documents/VariationHunter/test$ VariationHunter_SC
Please enter the minimum paired-end insert size:
100
Please enter the maximum paired-end insert size:
400
Please enter the pre-processing mapping prune probability:
0
Please enter the name of the input file:
output_DIVET.vh
Please enter the minimum support for a cluster:
1
sh: ./sortString: not found
sh: ./calProbMinEditRead: not found
sh: ./convertToInvLRProbMinEditDist: not found
sh: ./createSetsDelAsInsNoGapInvRLProb.alpha: not found
sh: ./combineRR_FF.Prob: not found
sh: ./createSetsDelAsInsNoGapInvRLProb.alpha: not found
sh: ./combineRR_FF.Prob: not found
sh: ./createSetsDelAsInsNoGapInvRLProb.alpha: not found
sh: ./combineRR_FF.Prob: not found
etc...

[john_mu]

I haven't used that program before, but judging from the errors you might want to check if all your program files are in the same path.

Do you know how to do that?

[alig]

Probs trying to run variationhunter

Hi john,

I forgot to say that I'd put the path to the program executables in my bash shell. They all reside in the same directory. So when I echo $PATH

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/neuro/Documents/VariationHunter/Package/ForRelease_v0.3

All the executables are in ForRelease_v0.3 but it seems that only the VariationHunter_SC is recognised

thanks

alig

[fhormozd]

Hi Alig.

I have seen this error before when try to us the current Version of VariationHunter. For this version to work without any problems, you have to run the program from its directory that is /home/neuro/Documents/VariationHunter/Package/ForRelease_v0.3

I hope this helps you.

[plichel]

non human reference

could you advice how to run variation hunter with arbitrary reference genome. I have the impression that it assumes a certain hg assembly.
When running with the output of mrfast I get files like this. All are empty:

2.Chr10.RR_FF 2.Chr13.RR_FF 2.Chr16.RR_FF 2.Chr19.RR_FF 2.Chr21.RR_FF 2.Chr24.RR_FF 2.Chr4.RR_FF 2.Chr7.RR_FF 2.FullChr.RR_FF 2.Prob.Clean 2.SV.Deletion
2.Chr11.RR_FF 2.Chr14.RR_FF 2.Chr17.RR_FF 2.Chr1.RR_FF 2.Chr22.RR_FF 2.Chr2.RR_FF 2.Chr5.RR_FF 2.Chr8.RR_FF 2.Name.Edit.Prob 2.Prob.Full 2.SV.Insertion
2.Chr12.RR_FF 2.Chr15.RR_FF 2.Chr18.RR_FF 2.Chr20.RR_FF 2.Chr23.RR_FF 2.Chr3.RR_FF 2.Chr6.RR_FF 2.Chr9.RR_FF 2.Name.MinEdit.TotalProb 2.SV 2.SV.Inversion

My input (generated with mrfast) is like:

test_sv_805942_806358_0:0:0_1:0:0_3 test 805941 806040 F 806258 806357 R D 1 17 2.095262e-02
test_sv_107994_108275_0:0:0_1:0:0_4 test 107993 108092 F 108175 108274 R I 1 17 2.095262e-02
test_sv_336499_336897_1:0:0_1:0:0_8 test 336498 336597 F 336797 336896 R D 2 17 4.390124e-04

my commandline running VariationHunter: (for pe reads, with outer distance of 350)

./VariationHunter_SC <<EOF
140
160
0
mrfast_DIVET.vh
1
EOF

[milesgr]

I tried to simply run the makefile and got the following...any help would be appreciated...I'm kind of new to this.

./makefile
./makefile: line 1: all:: command not found
./makefile: line 3: calProbMinEditRead: command not found
./makefile: line 5: combineRR_FF.Prob: command not found
./makefile: line 7: convertToInvLRProbMinEditDist: command not found
./makefile: line 9: createSetsDelAsInsNoGapInvRLProb.alpha: command not found
./makefile: line 11: parserQualWReadPrunWSatellite: command not found
./makefile: line 13: setCoverProbWeighted: command not found
./makefile: line 15: sortString: command not found
./makefile: line 17: VariationHunter_SC: command not found

[plichel]

you are trying to execute the makefile as a shellscript. this doesnt work. you have run it using make. to build the (any) project using make, you usually do simply:

make

make will automatically detect the makefile, when it is appropriately named.

[milesgr]

Thanks for the quick response. I actually did that as well and got the exact same result. Any other thoughts?

[milesgr]

Actually I misspoke, this is the result of running make:

make: Nothing to be done for `all'.

[plichel]

Then you are pobably done with building/compiling variationHunter.

After I builded the project I can find these binaries:
calProbMinEditRead
convertToInvLRProbMinEditDist
sortString
VariationHunter_SC
combineRR_FF.Prob
createSetsDelAsInsNoGapInvRLProb.alpha
parserQualWReadPrunWSatellite
setCoverProbWeighted

Do you see those files ?

[milesgr]

I will look a little later...but if I do see those files, do you know how to use the software? It seems like the manual is sparse. I wanted to find CNV between twins...I wanted to see CNV that differ between both twins and the reference genome, but more importantly I wanted to see instances where one twin has a CNV and the other does not (or has a different variation). I already have the aligned files. Any help would be greatly appreciated. Thanks.

[bubblesppf]

I have been trying to run the code given for Variation hunter (the set cover) version 3. When I run the VariationHunter_SC file I happen to get empty output files. I tried to make an input file out of the example given in the ReadMe file. I kindly request you to guide through it since I'm new to computing.

Regards
Nandy

[plichel]

I will look a little later...but if I do see those files, do you know how to use the software? It seems like the manual is sparse. I wanted to find CNV between twins...I wanted to see CNV that differ between both twins and the reference genome, but more importantly I wanted to see instances where one twin has a CNV and the other does not (or has a different variation). I already have the aligned files. Any help would be greatly appreciated. Thanks.

Not entirely sure, but I think for cnv detection this software is not suited.

[seqpig100]

I have been trying to run the code given for Variation hunter (the set cover) version 3. When I run the VariationHunter_SC file I happen to get empty output files. I tried to make an input file out of the example given in the ReadMe file. I kindly request you to guide through it since I'm new to computing.

Regards
Nandy

I get the same problem..empty output no matter what input i loaded in. Can anyone kindly help?

[Sponge]

VariationHunter with a non-human reference

Hi,

I too am trying to use VariationHunter with a non-human reference.

Is there an easy way to adapt the tool to work with other genomes?