Swissprot db annotate error

Question

[worarado.kan]

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.

Answer 1

[GenoMax]

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

[worarado.kan]

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?

[lieven.sterck]

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?)

[worarado.kan]

Now I can run, Thank you so much