Error while building new database for SnpEff

Question

[mjones1337]

Greetings! I'm a beginner when it comes to next-gen sequencing and analysis and I'm working with my first data set. Currently I'm using the public instance of Galaxy for my analysis. I'm comparing two malaria genomes and attempting to look for important SNPs between them via SnpEff. However my genome of interest is not one of the databases readily available. Thus, I'm working through the command line version of SnpEff to create my database from scratch. I'm following the directions from the SnpEff website but when I attempt to run the tool I get the error/output found below. Does anyone have any ideas as to what I'm doing wrong? I should also state that I'm equally new to command line usage so it could be something very simple. I've tried doing this in both the windows command line and also a Linux-like environment (using cygwin). In each case the output was the same.

If there is any additional information I can provide to help the diagnosis please let me know! Thanks in advance for any help you can offer!

 /SnpEff
$ java -jar snpEff.jar build -gff3 -v Pchabaudi28
00:00:00        SnpEff version SnpEff 4.3 (build 2016-06-14 18:42), by Pablo Cingolani
00:00:00        Command: 'build'
00:00:00        Building database for 'Pchabaudi28'
00:00:00        Reading configuration file 'snpEff.config'. Genome: 'Pchabaudi28'
00:00:00        Reading config file: C:\Users\mjj16\snpEff\snpEff.config
00:00:00        done
Reading GFF3 data file  : 'C:\Users\mjj16\snpEff/./data/                                                                                    /Pchabaudi28/genes.gff'
java.lang.RuntimeException: File not found 'C:\Users\mjj16\snpEff/./data/                                                                   /Pchabaudi28/genes.gff'
        at org.snpeff.util.Gpr.reader(Gpr.java:519)
        at org.snpeff.util.Gpr.reader(Gpr.java:490)
        at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.readGff(SnpEffPredictorFactoryGff.java:486)
        at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:337)
        at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor(SnpEffCmdBuild.java:116)
        at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:345)
        at org.snpeff.SnpEff.run(SnpEff.java:1009)
        at org.snpeff.SnpEff.main(SnpEff.java:155)
java.lang.RuntimeException: Error reading file 'C:\Users\mjj16\snpEff/./data/                                                               /Pchabaudi28/genes.gff'
java.lang.RuntimeException: File not found 'C:\Users\mjj16\snpEff/./data/                                                                   /Pchabaudi28/genes.gff'
        at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:353)
        at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.createSnpEffPredictor(SnpEffCmdBuild.java:116)
        at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:345)
        at org.snpeff.SnpEff.run(SnpEff.java:1009)
        at org.snpeff.SnpEff.main(SnpEff.java:155)
00:00:00        Logging
00:00:01        Checking for updates...

[WouterDeCoster]

While being unfamiliar with the tool, to me this looks like a confusion between unix-style and windows-style file paths, considering the '\' for Windows and '/' for unix. Your GFF3 data file path uses a combination: C:\Users\mjj16\snpEff/./data/ /Pchabaudi28/genes.gff' (which is unlikely to pass without errors)

[mjones1337]

Do you know of any way to fix this issue?

[GenoMax]

Can you include the command line you are using?

[mjones1337]

I'm using the basic command prompt in windows to attempt all this. I believe that is what you're asking.

[HannahT]

Were you able to solve your problem? I too am having the same problem.

[Andhikafm.afm]

can you solve that problem? can you explain to me?

[bioinfo8]

I also have same issue snpEFF Database building error, did anyone of you solve it?

Thanks.

[HannahT]

Hello,

Thanks to some friends that have done this before I have come to a solution that the problem with building my database was from the gff file. I did not have both the gene and exon information. There was only gene information.

[Anastasia A.]

I'm currently running on the same issue. How were you able to fix it? Is it that it requires the CDS and protein seqs? Thanks!

Answer 1

[Santosh Anand]

I am not sure you are following all the steps mentioned at http://snpeff.sourceforge.net/SnpEff_manual.html#buildAddConfig

Since you have a GFF file, you need to follow: Option 2: Building a database from GFF files

Specifically,

1. Move to SnpEff/data directory. There you should create Pchabaudi28 directory.

2. In Pchabaudi28 directory, you need to have a file named genes.gff, with the GFF annotation. Then follow the rest of the steps.

Note regarding filepath: Windows follows back-slash as path separator (\), while Unix/Linux systems use forward slash (/) https://stackoverflow.com/questions/38428561/difference-between-forward-slash-and-backslash-in-file-path/38428899

You should never mix the two types of file-path seperators. The thumb rule is that when working with Linux/Unix-like system (eg. Cygwin), use forward slash (/).

[bioinfo8]

Thanks Santosh. I have gtf file and not gff. I followed all the steps and used /. I think its because of some java error in cygwin, still figuring out. :P

[Santosh Anand]

Oh Sorry! I did not see that it is an old post that you dug it out of the grave. Yeah, mixing of slashes is weird and it might be a problem related to Cygwin itself. Another thing you can do is to build the database on a linux machine, and port it from there. If you don't have any linux machine at your disposal, you may try running a lightweight Linux (say PuppyLinux or Lubuntu) under a VM (like VirtualBox https://www.virtualbox.org/wiki/VirtualBox)