mini_sprot.pep

[Alecrim24]

Hi brian im having issue using the mini_sprot.pep.

here is my error

BLAST Database error: No alias or index file found for protein database [/nobackup/qkdf72/Trinity/mini_sprot.pep] in search path [/nobackup/qkdf72/Trinity::]

here is my script

#!/bin/bash

#SBATCH -p shared
#SBATCH -c 64
#SBATCH --mem=100G
#SBATCH --gres=tmp:400G
#SBATCH -t 71:00:00

cd /nobackup/qkdf72/Trinity

module purge

module load bioinformatics

module load blast/2.13.0

blastx -db /nobackup/qkdf72/Trinity/mini_sprot.pep
-query trinity_assembly-H.m.Trinity.fasta -num_threads 2
-max_target_seqs 1 -outfmt 6 -evalue 1e-5
> swissprot.blastx_H.m.outfmt6

thanks

[brianjohnhaas]

Hi, You might need to first make the database blastable via: makeblastdb -in /nobackup/qkdf72/Trinity/mini_sprot.pep -dbtype prot let's see if that helps. best, ~b

…

On Sat, Sep 30, 2023 at 4:52 PM Alecrim24 ***@***.***> wrote: Hi brian im having issue using the mini_sprot.pep. here is my error BLAST Database error: No alias or index file found for protein database [/nobackup/qkdf72/Trinity/mini_sprot.pep] in search path [/nobackup/qkdf72/Trinity::] here is my script #!/bin/bash #SBATCH -p shared #SBATCH -c 64 #SBATCH --mem=100G #SBATCH --gres=tmp:400G #SBATCH -t 71:00:00 cd /nobackup/qkdf72/Trinity module purge module load bioinformatics module load blast/2.13.0 blastx -db /nobackup/qkdf72/Trinity/mini_sprot.pep -query trinity_assembly-H.m.Trinity.fasta -num_threads 2 -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > swissprot.blastx_H.m.outfmt6 thanks — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXZT6MUPMDHX2FDADNDX5CBBTANCNFSM6AAAAAA5NZJF7A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[Alecrim24]

Hi Brian Yes it worked Thanks George Sent from Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Brian Haas ***@***.***> Sent: Saturday, September 30, 2023 11:12:36 PM To: trinityrnaseq/KrumlovTrinityWorkshopJan2018 ***@***.***> Cc: Alecrim24 ***@***.***>; Author ***@***.***> Subject: Re: [trinityrnaseq/KrumlovTrinityWorkshopJan2018] mini_sprot.pep (Issue #2) Hi, You might need to first make the database blastable via: makeblastdb -in /nobackup/qkdf72/Trinity/mini_sprot.pep -dbtype prot let's see if that helps. best, ~b

On Sat, Sep 30, 2023 at 4:52 PM Alecrim24 ***@***.***> wrote: Hi brian im having issue using the mini_sprot.pep. here is my error BLAST Database error: No alias or index file found for protein database [/nobackup/qkdf72/Trinity/mini_sprot.pep] in search path [/nobackup/qkdf72/Trinity::] here is my script #!/bin/bash #SBATCH -p shared #SBATCH -c 64 #SBATCH --mem=100G #SBATCH --gres=tmp:400G #SBATCH -t 71:00:00 cd /nobackup/qkdf72/Trinity module purge module load bioinformatics module load blast/2.13.0 blastx -db /nobackup/qkdf72/Trinity/mini_sprot.pep -query trinity_assembly-H.m.Trinity.fasta -num_threads 2 -max_target_seqs 1 -outfmt 6 -evalue 1e-5 > swissprot.blastx_H.m.outfmt6 thanks — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKXZT6MUPMDHX2FDADNDX5CBBTANCNFSM6AAAAAA5NZJF7A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> — Reply to this email directly, view it on GitHub<#2 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7ZSXO3EE4CD4422TTFSLXTX5CKNJANCNFSM6AAAAAA5NZJF7A>. You are receiving this because you authored the thread.Message ID: ***@***.***>