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stajichlab / FGMP

Fungal Genome Mapping Pipeline
MIT License
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makeblastdb directory not found #24

Open kyleschutz opened 2 years ago

kyleschutz commented 2 years ago

Hi,

I'm having some trouble running this on even the sample data. I continue to get an error around tblastn. It's the same error when I run my own data. I am running blast v. 2.12.0.

Error message after running:

./fgmp.pl -g sample_test.dna -T 3 --tag OMA

[ 30-06-2022 02:25:27 PM ] Finding candidate regions cannot execute makeblastdb -in sample_test.dna -dbtype nucl -out sample_test.dna.db > /dev/null 2>&1:No such file or directory at /Users/kyleschutz/FGMP/src/fgmp.pl line 436.

Any thoughts?

hyphaltip commented 2 years ago

seems like the blast executables are not in your path when running this. when you installed blast, are these all in your path? What’s do you see when you run $ which makeblastdb

Jason E Stajich, PhD Professor, Dept of Microbiology and Plant Pathology Chair, Academic Senate, Riverside Division University of California, Riverside

Fellow, CIFAR Fungal Kingdom: Threats and Opportunities https://www.cifar.ca/research/program/fungal-kingdom email: @.*** twitter: @stajichlab http://twitter.com/stajichlab @hyphaltip http://twitter.com/hyphaltip @zygolife http://twitter.com/zygolife website: http://lab.stajich.org office: +1 951.827.2363 mobile: +1 909.333.6709

On Thu, Jun 30, 2022 at 4:30 PM kyleschutz @.***> wrote:

Hi,

I'm having some trouble running this on even the sample data. I continue to get an error around tblastn. It's the same error when I run my own data. I am running blast v. 2.12.0.

Error message after running:

./fgmp.pl -g sample_test.dna -T 3 --tag OMA

[ 30-06-2022 02:25:27 PM ] Finding candidate regions cannot execute makeblastdb -in sample_test.dna -dbtype nucl -out sample_test.dna.db > /dev/null 2>&1:No such file or directory at /Users/kyleschutz/FGMP/src/fgmp.pl line 436.

Any thoughts?

— Reply to this email directly, view it on GitHub https://github.com/stajichlab/FGMP/issues/24, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL5OYNXBNYO4GABCJLP5LVRX7VNANCNFSM52KSKLQA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

kyleschutz commented 2 years ago

Hi Jason,

I see /Users/kyleschutz/miniconda3/bin/makeblastdb

ocisse commented 1 year ago

Can check that your blast installation is functional?

Thanks

On Thu, Jun 30, 2022 at 4:30 PM kyleschutz @.***> wrote:

Hi,

I'm having some trouble running this on even the sample data. I continue to get an error around tblastn. It's the same error when I run my own data. I am running blast v. 2.12.0.

Error message after running:

./fgmp.pl -g sample_test.dna -T 3 --tag OMA

[ 30-06-2022 02:25:27 PM ] Finding candidate regions cannot execute makeblastdb -in sample_test.dna -dbtype nucl -out sample_test.dna.db > /dev/null 2>&1:No such file or directory at /Users/kyleschutz/FGMP/src/fgmp.pl line 436.

Any thoughts?

— Reply to this email directly, view it on GitHub https://github.com/stajichlab/FGMP/issues/24, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABPSZLBE2C4UOUTEGKZTMFTVRX7VNANCNFSM52KSKLQA . You are receiving this because you are subscribed to this thread.Message ID: @.***>