BLAST Database error: No alias or index file found for nucleotide database [tmp_transcripts_with_orf.fa] in search path [/gpfs/scratch/ml0094::]

huangzixia / ExUTR

ExUTR is a practical and powerful tool that enables rapid genome-wide 3'-UTR prediction from massive RNA-Seq data

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BLAST Database error: No alias or index file found for nucleotide database [tmp_transcripts_with_orf.fa] in search path [/gpfs/scratch/ml0094::] #8

Closed ml0094 closed 2 years ago

ml0094 commented 2 years ago

Hello, so I've been trying to run this for several days. I am having an issue where it's failing to produce any tmp_blast files. Any file beginning with that prefix is blank. As a result it is failing when it gets to the above. I am using a modern unitprot database. Perl script has been edited and looks like this 3UTR_orf_20170816.txt

This is using your test data set. .

ml0094 commented 2 years ago

Issue was resolved by changing the file in the run script to not refer to an extension for the swissprot fasta (directory/swissport v.s. directory/swissprot.fasta)

r0ark commented 2 years ago

Hi @ml0094 , did you upload your forked version of the script? I would like to be able to use a modern swissprot database to use this as well. Thanks in advance!

ml0094 commented 2 years ago

Hi @ml0094 , did you upload your forked version of the script? I would like to be able to use a modern swissprot database to use this as well. Thanks in advance!

I actually couldn't get the ORF prediction script to function on my data, so I resorted to manually following the steps instituted in the paper as I only had a very small number of genes of interest. I can look for my ORF prediction script but it was not funcitoning.