Question: Swissprot db annotate error
0
gravatar for worarado.kan
2.3 years ago by
worarado.kan10
worarado.kan10 wrote:

Hello everyone,

I'm running Trinity data with swissprot db using linux base. I already install and get file pin,phr,psq, psi. I used this command;

$ blastx -query Trinity01052018_Echota-UP_fasta_iso_ID.fasta \

-db swissprot \

-evalue 1.0e-5 \

-query_gencode 1 \

-max_target_seqs 1 \

-num_threads 4 \

 -outfmt "6 qseqid sseqid evalue stitle" \

 -out Trinity01052018_Echota-UP_swissprot_blastx_fmt6.txt \

Showed error;

BLAST Database error: No alias or index file found for protein database [swissprot] in search path [/run/media/hscience/DATA_CentOS/Bluberry/RNAseqblueberry/4_RSEM_edgeR/edgeR.genes.dir/P1e-10_C8/PickIsoform_Echota_UP/Swissprot::]

What is wrong? please let me know.

sequencing rna-seq next-gen • 614 views
ADD COMMENTlink modified 2.3 years ago by genomax87k • written 2.3 years ago by worarado.kan10
0
gravatar for genomax
2.3 years ago by
genomax87k
United States
genomax87k wrote:

Data files for swissprot database are not in your $PATH. You can set $BLASTDB to point to the directory where these files are present.

export BLASTDB=/path_to_dir_with_swissprot_files
ADD COMMENTlink written 2.3 years ago by genomax87k

Thank you so much but when I change to this command

$ blastx -query Trinity01052018_Echota-UP_fasta_iso_ID.fasta

-db /run/media/hscience/DATA_CentOS/DATABASE/db/uniPROT/swissprot

-evalue 1.0e-5

-query_gencode 1

-max_target_seqs 1

-num_threads 4 -outfmt "6 qseqid sseqid evalue stitle"

-out Trinity01052018_Echota-UP_swissprot_blastx_fmt6.tx

showed error; Command line argument error: Argument "query". File is not accessible: `Trinity01052018_Echota-UP_fasta_iso_ID.fasta'

Trinity file name not correct?

ADD REPLYlink written 2.3 years ago by worarado.kan10

Are you running this blast in the folder where the input file is located? otherwise you will also have to add the path to the input file. Do also have a look if the file permissions are OK (== are you allowed to read that file?)

ADD REPLYlink written 2.3 years ago by lieven.sterck8.3k

Now I can run, Thank you so much

ADD REPLYlink written 2.3 years ago by worarado.kan10
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