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CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
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SnpEff can't find NC_000962.genome #20

Open elenamd opened 5 years ago

elenamd commented 5 years ago

Hi, I'm trying to install your pipeline in our HPC and after a few problems and suggestions from IT (attached at the end) I get the pipeline to finish but the annotation file is not being generated.

java -Xmx4g -jar /usr/local//snpeff/4.3t/snpEff.jar NC_000962 Results/19-1773-0027SR/19-1773-0027SR_GATK_filtered.vcf

tandard Error: java.lang.RuntimeException: Property: 'NC_000962.genome' not found

I haven't use snpeff before so I'm not sure if is a problem with the database or that the file should be somewhere in the uvp or my folders?

Any suggestions??

Thanks,

Elena

IT suggestions for HPC: (1) make it so both .fq.gz, .fastq.gz filenames work. 2) Make it so that the file given with -r can also be a gzipped file (ie if it's a .gz file, then gunzip < file.gz > Results/19-1773-0029SR/tmp/bwa/index/ref.fa" rather than the Command: cp AL123456.fasta.gz Results/19-1773-0029SR/tmp/bwa/index/ref.fa 3) place the snp.vcf file in a user writable location.)

mezewudo commented 5 years ago

Yeah,

Thanks for the suggestions, we will work on those for future revisions.

For the error, It is a problem with the snpEff database. You should look at the snpEff manual for the description on how to create custom database for your reference genome of interest. In our case we used the gbk file method for creating the database.

Let me know if you have questions.

Thanks, Matthew.

On Thu, Mar 14, 2019 at 10:47 PM elenamd notifications@github.com wrote:

Hi, I'm trying to install your pipeline in our HPC and after a few problems and suggestions from IT (attached at the end) I get the pipeline to finish but the annotation file is not being generated.

java -Xmx4g -jar /usr/local//snpeff/4.3t/snpEff.jar NC_000962 Results/19-1773-0027SR/19-1773-0027SR_GATK_filtered.vcf

tandard Error: java.lang.RuntimeException: Property: 'NC_000962.genome' not found

I haven't use snpeff before so I'm not sure if is a problem with the database or that the file should be somewhere in the uvp or my folders?

Any suggestions??

Thanks,

Elena

IT suggestions for HPC: (1) make it so both .fq.gz, .fastq.gz filenames work. 2) Make it so that the file given with -r can also be a gzipped file (ie if it's a .gz file, then gunzip < file.gz > Results/19-1773-0029SR/tmp/bwa/index/ref.fa" rather than the Command: cp AL123456.fasta.gz Results/19-1773-0029SR/tmp/bwa/index/ref.fa 3) place the snp.vcf file in a user writable location.)

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elenamd commented 5 years ago

Thanks , I will try it and see how I go.

tseemann commented 5 years ago

@elenamd did you have success? can this issue be closed?

elenamd commented 5 years ago

Yes thanks

wpf95 commented 2 years ago

i meet the same question with eleamd, so how did you did?

mezewudo commented 2 years ago

You will have to create your SnpEff database for the genome you are using. See the SnpEff manual for details on creating custom databases.

On Wed, May 25, 2022 at 9:03 AM wpf95 @.***> wrote:

i meet the same question with eleamd, so how did you did?

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