Question: Swissprot db annotate error
0
gravatar for worarado.kan
23 months 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 • 552 views
ADD COMMENTlink modified 23 months ago by genomax80k • written 23 months ago by worarado.kan10
0
gravatar for genomax
23 months ago by
genomax80k
United States
genomax80k 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 23 months ago by genomax80k

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 23 months 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 23 months ago by lieven.sterck7.3k

Now I can run, Thank you so much

ADD REPLYlink written 23 months ago by worarado.kan10
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