DiscoSnp++ Installation Problem

Question

[solhan2000]

I downloaded the DiscoSnp++ latest version and tried compiling it in my mac OS. I tried the ./compile as suggested. Did not work. I installed cMake and compiled it. It runs the first module but then can not find the kissnp2 or kissnpreads. Says "file not found" and can't run starting the second module when I used the example files. Why is the simple ./compile as suggested in the program not working in my case and why wouldn't a cMake compiled file wont install the complete files. Is there anything I am missing in installing Discosnp++ to my mac OS? I downloaded the darwin binary as well as the source. Can't solve the issue. Please let me know what you guys think. Thanks

[acros]

Hi, I'm trying to install DiscoSnp++2.2.4 on a Mac OS 10.11.2. I'm having the same issues as Solhan2000 withe compilation error. Has this been resolved? Is it an issue in the CMakeLists?

Thanks for the help,

Annick

[pierre.peterlongo]

Hi Annick,

Sorry for the trouble; Would you mind copying the compilation error message here?

[acros]

Hi Pierre, here it is

Compiling discoSnp, from directory /Users/annickcros/programs/DiscoSNP++-2.2.4-Darwin
mkdir: build: File exists ===> CMAKE_MODULE_PATH=
CMake Error at CMakeLists.txt:33 (include): 
include could not find load file: GatbCore
CMake Error at CMakeLists.txt:72 (INCLUDE):
include could not find load file: Delivery -- Configuring incomplete, errors occurred!
See also "/Users/annickcros/programs/DiscoSNP++-2.2.4-Darwin/build/CMakeFiles/CMakeOutput.log".
make: *** No targets specified and no makefile found. Stop.

[acros]

Hi Pierre, I found the issue! My path changes when I move the folder.

Thanks,
Annick

[solhan2000]

Correction: Missing "kissnp2 and kissreads" files

[h.mon]

Did you move or rename the folder after compiling discoSnp++? Which version of discoSnp++?

[solhan2000]

I didn't move it after installation. It did not compile with ./compile command so I had to compile it with CMake as I mentioned. The version is - Last stable version: DiscoSNP++-2.1.7.

[gadicherla.ramya]

Hi

I am totally new to using the DiscoSNp++ tool.

Can I use it for two data sets generated from Ion Torrent?

I am trying to install the latest version 2.1.7, but encountering an error. Do I have to use the binaries file as well. ? as in link the binaries file? can anyone help me out with this?

Thanks in advance,
Ramya.

[pierre.peterlongo]

Hi Ramya,

I copy here the other questions you raised by email

1. can I use this tool for calling SNP's from data generated from Iontorrent platform?

We do not have feedback nor experience with ion torrent data. I'm curious and interested by results I'll obtain.

2. Should I cal SNP's from one sample and then compare it with others or all the sample's data can be combined and called for SNP's?

and

3. I get a format when I use a single sample file and a different profile if I using more datasets of different samples?

Yes read sets can be combined. The documentation should help you for understanding the output format

4. how do I infer the generated data?i mean the interpretation.

As far as I understand, you've a reference file. You may indicate it using the -G option. So a VCF file will be created, showing up the loci of the predicted mapped variants. Such VCF could be used for downstream analysis.

I hope this helps.

Best regards,
Pierre

[gadicherla.ramya]

Hi Pierre,

Thanks for your reply.

Let me be more clear in what I am looking for. We have a draft sequence. I will be using this draft sequence as a reference and comparing this sequence to other sample sequences.

So now the command line would be

./run_discoSnp++,sh -G name_of_reference_file.fasta -T

I should get an output in VCF file format and .fa file. I take these reads and then compare it with remaining reads with following command:

./run_discoSnp++,sh -G variants.fasta -r sample1.fasta sample2. fasta sample3.fasta -T

Please let me know if this is how the command line should be or any changes needs to be made so that I can workout and let you know the output.

Regards,
Ramya.

[pierre.peterlongo]

Hi,

You've found the best way to proceed. Don't forget the " sign surrounding the read files:

./run_discoSnp++.sh -G variants.fasta -r "sample1.fasta sample2. fasta sample3.fasta" -T

Best,
Pierre

[acros]

Hi Pierre, here it is

Compiling discoSnp, from directory /Users/annickcros/programs/DiscoSNP++-2.2.4-Darwin
mkdir: build: File exists ===> CMAKE_MODULE_PATH= CMake
Error at CMakeLists.txt:33 (include): include could not find load file: GatbCore CMake
Error at CMakeLists.txt:72 (INCLUDE): include could not find load file: Delivery -- Configuring incomplete, errors occurred! 
See also "/Users/annickcros/programs/DiscoSNP++-2.2.4-Darwin/build/CMakeFiles/CMakeOutput.log". 
make: *** No targets specified and no makefile found. Stop.

[acros]

I think I found the issue. I'm moving my folder after unzipping it and it seems to change some of the path. I unzipped where I wanted the program to be and it works.

[pierre.peterlongo]

Hi!

I'm discovering both your problem and its solution! Happy you fixed the issue, and sorry for this late reply :)

Pierre

Answer 1

[h.mon]

The "compile_discoSnp++.sh" also compiles the programs kissnp2 and kissreads, they should be located at ./build/tools/{kissnp2,kissreads}. I think you may compile them independently with cmake as well.

If you installed cmake after trying and failing with "compile_discoSnp++.sh", you should try again: the script call cmake to compile all programs.

[solhan2000]

Dear h.mon, Thank you for your feedback.

I would have assumed if the ./compile_discoSnp++.sh command to do all that but that doesn't run in my mac. As such after I compiled the program with cMake, I checked the folders. I do find the folders you mentioned ./build/tools/{kissnp2,kissreads} being created. But when I run the test script

./run_discoSnp++.sh -r "data_sample/reads_sequence1.fasta.gz data_sample/reads_sequence2.fasta.gz" -T

it runs the first section "GRAPH CREATION" fine then when it reaches the module "KISSNP2 MODULE" I encounter this error message

"/Users/sghailu/DiscoSNP++-2.1.7-Source/build//tools/kissnp2/kissnp2 -in discoRes_k_31_c_4.h5 -out discoRes_k_31_c_4_D_0_P_1_b_0_withlow  -b 0 -l -P 1  -D 0 -T
./run_discoSnp++.sh: line 330: /Users/sghailu/DiscoSNP++-2.1.7-Source/build//tools/kissnp2/kissnp2: No such file or directory"

Apparently CMake is not able to create the files necessary for kissnp2 to work properly. Now the installation command nor the CMake compiled files are running properly. I am using 10.8.4 Mac OS version.

Why wouldn't ./compile_discoSnp++.sh work in my system to begin with? I am confused.

[h.mon]

I am on linux, and can't test on Os X, so I have no idea why it did not work. Did you check if the kissnp and and kissreads executables are found on the folders I mentioned?

[solhan2000]

Sorry for late reply. I could not find the files in the folders. It is empty. It didn't compile it. I tried using galaxy and automatically install it as well. It failed saying installation error.