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Swissprot db annotate error

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.

rna-seq sequencing next-gen
• 1,720 views • link
updated by GenoMax GenoMax • written by worarado.kan • worarado.kan

1 answer

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
• 1 views • link
written by GenoMax GenoMax

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?

• 1 views • link
written by worarado.kan • worarado.kan

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?)

• 1 views • link
written by lieven.sterck lieven.sterck

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