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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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Error when Blasting against Custom Database #5

Open MountainFace opened 5 years ago

MountainFace commented 5 years ago

Hi,

Sorry for this basic level question, I am still a novice with bioinformatics. When I attempt to run 3UTR_orf_20170816.pl as:

perl 3UTR_orf_20170816.pl -i test.fa -d /home/hayden/Downloads/ExUTR-master/bin/db -a 2 -o Test -l un

It runs but returns the following:

Starting to translate potential ORFs......

Finish ORF translation.

Done

Now Blasting the translated ORFs to Swissprot...... Blast and report analysis.

Done

Annotating the transcripts......

Extracting ORF sequences with the stop codon......

cat: '*sp.fa': No such file or directory

I am using a database that I made using 'makeblastdb' from these files:

https://www.uniprot.org/uniprot/?query=reviewed:yes%20taxonomy:35237

as: makeblastdb -in uniprot-reviewed%3Ayes+taxonomy%3A35237.fasta -dbtype prot

The error log then reads: BLAST Database error: No alias or index file found for nucleotide database [tmp_transcripts_with_orf.fa] in search path [/home/hayden/Downloads/ExUTR-master/bin:db:]

I have tried:

Any help you can give would be greatly appreciated.

MountainFace commented 5 years ago

Also, the Test_orfs.fa and Test_transcripts.fa are created but are empty.

Is it possibly to run 3UTR_ext.pl against a virus database? I notice that UTRdb mostly has eukaryote entries.

Kind regards Hayden

s-rana0 commented 5 years ago

Hi Hayden,

Did you ever find a solution for this error? I recently downloaded the ExUTR and tried to test it in the test.fa file and I get the same error.

Thanks, Sam

s-rana0 commented 5 years ago

Ok solved the problem.

When you are specifying the path to the swissprot database add the filename of the .pal file in the path too (here my .pal file is swissprot.pal, so I will add 'swissprot' at the end of the path, but no extension)

i.e. perl 3UTR_orf_20170816.pl -i test.fa -d /home/xxxxx/Downloads/ExUTR/swissprot/swissprot -a 2 -o Test -l un

Rease123 commented 5 years ago

hello! how to resolve the problem?

------------- EXCEPTION ------------- MSG: Could not read file 'tmp_blast_orf1': No such file or directory STACK Bio::Root::IO::_initialize_io /Users/xxx/perl5/perlbrew/perls/perl-5.28.0/lib/site_perl/5.28.0/Bio/Root/IO.pm:268 STACK Bio::Root::IO::new /Users/xxx/perl5/perlbrew/perls/perl-5.28.0/lib/site_perl/5.28.0/Bio/Root/IO.pm:163 STACK Bio::SearchIO::new /Users/xxx/perl5/perlbrew/perls/perl-5.28.0/lib/site_perl/5.28.0/Bio/SearchIO.pm:185 STACK main::PARSE_BLAST_REPORT 3UTR_orf_20170816.pl:208 STACK toplevel 3UTR_orf_20170816.pl:261

emma23ed commented 4 years ago

Hi @s-rana0 Where did you get your swissprot database from? I am just curious as the version I obtained doesn't have the .pal file so I can't run ExUTR. Thanks a lot!!

Shukla04 commented 8 months ago

Hi @s-rana0 Where did you get your swissprot database from? I am just curious as the version I obtained doesn't have the .pal file so I can't run ExUTR. Thanks a lot!!

Hello, were you able to resolve the issue? I have the same issue when I tried to run ExUTR, but all in vain. Please help to find a solution. I am working with de-novo assembly on a non-model system.

Shukla04 commented 8 months ago

the bin folder does not contain any "db" folder or database file. I downloaded protein reference sequences from uniprot, however, it does not contain any ".pal" file. it has only the sequence file in fasta format. Any help is appreciated. Thanks Neha