Question: build databses for genome using snpEff
0
gravatar for StudentBio
15 months ago by
StudentBio0
StudentBio0 wrote:

hello, please i got this error when i try building a database for date plam genome

        Total: 363391 markers added.

    Create exons from CDS (if needed): ..................................................................+......................................................................................................................
    Exons created for 138 transcripts.

    Deleting redundant exons (if needed): 
        Total transcripts with deleted exons: 0

    Collapsing zero length introns (if needed): 
        Total collapsed transcripts: 0
    Reading sequences   :
    FASTA file: '/home/inra/snpEff/./data/genomes/dpv01.fa' not found.
    FASTA file: '/home/inra/snpEff/./data/dpv01/sequences.fa' not found.
java.lang.RuntimeException: Cannot find reference sequence.
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.readExonSequences(SnpEffPredictorFactory.java:692)
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.readExonSequences(SnpEffPredictorFactoryGff.java:428)
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:342)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)
java.lang.RuntimeException: Error reading file '/home/inra/snpEff/./data/dpv01/genes.gff'
java.lang.RuntimeException: Cannot find reference sequence.
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:353)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:21    Logging
00:00:26    Checking for updates...
00:00:27    Done.
snp snpeff annotation • 652 views
ADD COMMENTlink modified 15 months ago by finswimmer12k • written 15 months ago by StudentBio0
1

Hello StudentBio,

what was the exact command you use?

Read the error message carefuly. It clearly stated out what the problem is:

FASTA file: '/home/inra/snpEff/./data/genomes/dpv01.fa' not found.
FASTA file: '/home/inra/snpEff/./data/dpv01/sequences.fa' not found.
java.lang.RuntimeException: Error reading file '/home/inra/snpEff/./data/dpv01/genes.gff'
java.lang.RuntimeException: Cannot find reference sequence.

So there is a mistake in how you tell snpEff where it will find the data needed.

fin swimmer

ADD REPLYlink modified 15 months ago • written 15 months ago by finswimmer12k
java -jar snpEff.jar build -gff3 -v dpv01
ADD REPLYlink modified 15 months ago by finswimmer12k • written 15 months ago by StudentBio0

And how does your config file look like?

ADD REPLYlink written 15 months ago by finswimmer12k
#phoenix dactylifera
dpv01.genome : phoenix_dactylifera
ADD REPLYlink modified 15 months ago by finswimmer12k • written 15 months ago by StudentBio0

Hello,

this cannot be the full config file. There must be at least a line about the data dir, because that's your problem. snpEff appends ./data but it should be just /data. You can:

  1. modify your config file setting an absolute path to the data dir
  2. use the -dataDir <path> option in your build command

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

ADD REPLYlink modified 15 months ago • written 15 months ago by finswimmer12k
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