Closed wangdi2016 closed 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?
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'
Thanks!
Thank you, Difei!
Copying file locally and running ./pgap.py .... -g ASM2732v1.annotation.nucleotide.1.fasta
should work
Thanks Azat!
It worked after I copied the fasta file in the local directory and run the command as directed.
Have a great weekend!
I am glad it worked, Difei!
We will work on fixing the documentation.
Have a great weekend!
You too!
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.