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
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.
Try addressing: