Question

build databses for genome using snpEff

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5.7 years ago

StudentBio • 0

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.

annotation SNP snpEff • 3.3k views

ADD COMMENT • link updated 8 months ago by nehakhilwani18 • 0 • written 5.7 years ago by StudentBio • 0

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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 REPLY • link 5.7 years ago by finswimmer 16k

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java -jar snpEff.jar build -gff3 -v dpv01

ADD REPLY • link updated 5.7 years ago by finswimmer 16k • written 5.7 years ago by StudentBio • 0

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And how does your config file look like?

ADD REPLY • link 5.7 years ago by finswimmer 16k

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#phoenix dactylifera
dpv01.genome : phoenix_dactylifera

ADD REPLY • link updated 5.7 years ago by finswimmer 16k • written 5.7 years ago by StudentBio • 0

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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:

modify your config file setting an absolute path to the data dir
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 REPLY • link 5.7 years ago by finswimmer 16k

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Hey, I am going through the same problem while building database

00:00:41 Reading sequences : 00:00:41 FASTA file: '/mnt/d/snpEff/data/Asian_seabass_v1/genomes/Asian_seabass_v1.fa' not found. 00:00:41 FASTA file: '/mnt/d/snpEff/data/Asian_seabass_v1/Asian_seabass_v1/sequences.fa' not found. java.lang.RuntimeException: Cannot find reference sequence. at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.readExonSequences(SnpEffPredictorFactory.java:702) at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.readExonSequences(SnpEffPredictorFactoryGff.java:450) at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:347) at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:416) at org.snpeff.SnpEff.run(SnpEff.java:1141) at org.snpeff.SnpEff.main(SnpEff.java:160) java.lang.RuntimeException: Error reading file '/mnt/d/snpEff/data/Asian_seabass_v1/Asian_seabass_v1/genes.gff' java.lang.RuntimeException: Cannot find reference sequence. at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:359) at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:416) at org.snpeff.SnpEff.run(SnpEff.java:1141) at org.snpeff.SnpEff.main(SnpEff.java:160) 00:00:41 Logging

could you suggest me how can I resolve this???

ADD REPLY • link 24 months ago by aabhordia ▴ 30

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hey, i am having error while building the database please suggest the solution for this how can i solve it

 java.lang.RuntimeException: Cannot find reference sequence.
    at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:362)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
    at org.snpeff.SnpEff.run(SnpEff.java:1173)
    at org.snpeff.SnpEff.main(SnpEff.java:163)

this the command i am using

java -Xmx1G -jar snpEff.jar  build -gff3 dbase

for building the database

ADD REPLY • link updated 8 months ago by GenoMax 141k • written 8 months ago by nehakhilwani18 • 0

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Error is clearly noted:

Cannot find reference sequence

ADD REPLY • link 8 months ago by GenoMax 141k

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reference sequence is already there in the folder

ADD REPLY • link 8 months ago by nehakhilwani18 • 0