Question: I need help to create 2 SNPEFF databases (v1.01/v2.01) of Pinus taeda
0
gravatar for nie shuai
12 months ago by
nie shuai0
nie shuai0 wrote:

In recent days, I have been trying to create two databases (v1.01/v2.01) of Pinus taeda , but I don’t know why it failed. So ,I need your help to create their database.

The required information is as follows:

<h6>#</h6>

v1.01: Name of the species Pinus taeda L Reference genome version v101 A link to the reference genome sequence https://treegenesdb.org/FTP/Genomes/Pita/v1.01/ptaeda.v1.01.scaffolds.fasta.gz A link to a gene and transcript definition file low quality:https://treegenesdb.org/FTP/Genomes/Pita/v1.01/annotation/pita.LQgenes.gff3.gz   high quality:https://treegenesdb.org/FTP/Genomes/Pita/v1.01/annotation/pita.HQgenes.gff3.gz A link to the protein sequences low quality:https://treegenesdb.org/FTP/Genomes/Pita/v1.01/annotation/pita.LQgenes.proteins.fasta.gz   high quality:https://treegenesdb.org/FTP/Genomes/Pita/v1.01/annotation/pita.HQgenes.proteins.fasta.gz Codon table information The Standard Code

<h6>#</h6>

v2.01: Name of the species Pinus taeda L Reference genome version v201 A link to the reference genome sequence https://treegenesdb.org/FTP/Genomes/Pita/v2.01/genome/Pita.2_01.fa.gz A link to a gene and transcript definition file https://treegenesdb.org/FTP/Genomes/Pita/v2.01/annotation2.0/pita2.01_allGeneModels_renamed.gff3 A link to the protein sequences https://treegenesdb.org/FTP/Genomes/Pita/v2.01/annotation2.0/pita2.01_allGeneModels_prots_renamed.fasta Codon table information The Standard Code

<h6>#</h6>

It's my code to build databases, and I don't know why it failed:

1.pita_101

1.1.Configure

vim snpEff.config

pita,version pita_101

pita_101.genome:pita

1.2. build path

mkdir ~/src/snpEff/snpEff/data
mkdir ~/src/snpEff/snpEff/data/genomes
mkdir ~/src/snpEff/snpEff/data/pita_101

1.3.Get the reference genome sequence (it's so large that I used soft connections. )

cd ~/src/snpEff/snpEff/data/genomes
ln -s mypath/ptaeda.v1.01.scaffolds.fasta pita_101.fa

1.4.Get genome annotations.we merge HQgenes and LQgenes into pita_gene.

gff

cd ~/src/snpEff/snpEff/data/pita_101
cp mypath/pita_gene.gff3 ~/src/snpEff/snpEff/data/pita_101
mv pita_gene.gff3 genes.gff

protein.fa

cp mypath/pita.proteins.fasta ~/src/snpEff/snpEff/data/pita_101
mv pita.proteins.fasta protein.fa

1.5.create the database

cd ~/src/snpEff/snpEff
java -jar snpEff.jar build -gff3 -v pita_101

1.6.run

java -Xmx30g -jar snpEff.jar pita_101

ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_pita_101.zip

<h6>#</h6>

2.pita_201

2.1.Configure

cd ~/src/snpEff/snpEff/ vim snpEff.config

pita,version pita_201

pita_201.genome:pita

2.2. build path

mkdir ~/src/snpEff/snpEff/data/pita_201

2.3.Get the reference genome sequence (it's so large that I used soft connections. )

cd ~/src/snpEff/snpEff/data/genomes
ln -s mypath/pita_2.0/Pita.2_01.fa pita_201.fa

2.4.Get genome annotations.we merge HQgenes and LQgenes into pita_gene.

gff

cd ~/src/snpEff/snpEff/data/pita_201
wget http://treegenesdb.org/FTP/Genomes/Pita/v2.01/annotation/Pita.2_01.gff.gz
gzip -d Pita.2_01.gff.gz
mv Pita.2_01.gff genes.gff

2.5.create the database

cd ~/src/snpEff/snpEff
java -Xmx64g -jar snpEff.jar build -gff3 -v pita_201

2.6.run

java -Xmx30g -jar snpEff.jar pita_201

ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_pita_201.zip

snpeff • 466 views
ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 12 months ago by nie shuai0

Please, add proper formatting to your post, in particular (but not limited to) by using the code button. I've done some formatting for you, but your post still needs attention.

Be aware BioStars uses markdown, so some characters add formatting to the post - as you may have noted. For example, # at the beginning of a line is not a comment, it formats text as heading:

bigger text here (here I wrote # bigger text here)

And not:

# comment (here I wrote \# comment)

P.S.: you are trying to perform a task twice and failing both times for the same reason, you could keep your post shorter and easier to read by posting the problem for only one database - once you solve for one case, you will solve for the other.

ADD REPLYlink modified 12 months ago • written 12 months ago by h.mon26k

Try addressing:

ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_pita_101.zip
ADD REPLYlink written 12 months ago by cpad011211k
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