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NCBI Prokaryotic Genome Annotation Pipeline
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[BUG] test example failed #260

Closed wangdi2016 closed 1 year ago

wangdi2016 commented 1 year ago

I installed docker image and downloaded input files etc under the user home folder. When I run the test example using the following command

./pgap.py -r -o mg37_results -g .pgap/test_genomes/MG37/ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasmoides genitalium'

I got the following error message saying

No such file or directory: '/pgap/user_input/.pgap/test_genomes/MG37/ASM2732v1.annotation.nucleotide.1.fasta'

The fasta file is located in the following folder. /home/wangdi/.pgap/test_genomes/MG37/ASM2732v1.annotation.nucleotide.1.fasta

Thanks.

azat-badretdin commented 1 year ago

Thanks for reporting this, Difei!

This is a mistake in documentation. We presume that user's current directory is $HOME, which clearly not the case.

Could you please try this by specifying full path?

wangdi2016 commented 1 year ago

Thanks Azat for your response!

I just tried using the full path. It is the same error message. See the log file here and the command.

./pgap.py -r -o mg37_results -g /home/wangdi/.pgap/test_genomes/MG37/ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasmoides genitalium'

run.log

Thanks!

azat-badretdin commented 1 year ago

Thank you, Difei!

Copying file locally and running ./pgap.py .... -g ASM2732v1.annotation.nucleotide.1.fasta should work

wangdi2016 commented 1 year ago

Thanks Azat!

It worked after I copied the fasta file in the local directory and run the command as directed.

Have a great weekend!

azat-badretdin commented 1 year ago

I am glad it worked, Difei!

We will work on fixing the documentation.

Have a great weekend!

You too!