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wandreopoulos / deeplasmid

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Output file not generated #7

Open fabrizziom99 opened 1 year ago

fabrizziom99 commented 1 year ago

Hi!

I was wandering if someone could help me. I´m running deeplasmid and everything seems to perform as expected (as I can see the scores generated to each of my assembled contigs) but after it ends running i can´t find the output files : samplescore_hist.png, scaffscore_hist.png and predictions.txt. Is it something I did wrong on the installation process?

Here is the installation command line that I used:

docker pull billandreo/deeplasmid-cpu-ubuntu2

and the command to run the program (I created an outdir folder at my user´s home one):

sudo /usr/bin/docker run -it -v ~/Rs1.4Eclo/scaffolds.fasta:/srv/jgi-ml/classifier/dl/in.fasta -v ~/outdir/srv/jgi-ml/classifier/dl/outdir billandreo/deeplasmid-cpu-ubuntu2 deeplasmid.sh in.fasta outdir

wandreopoulos commented 1 year ago

Hi

The output path you are giving for the Docker volume does not seem correct (syntactically): ~/outdir:/srv/jgi-ml/classifier/dl/outdir you need to separate the two with a colon : because it maps your local output directory to the Volume for the container.

Let me know if it works

On Sat, Feb 11, 2023 at 12:33 PM fabrizziom99 @.***> wrote:

Hi!

I was wandering if someone could help me. I´m running deeplasmid and everything seems to perform as expected (as I can see the scores generated to each of my assembled contigs) but after it ends running i can´t find the output files : samplescore_hist.png, scaffscore_hist.png and predictions.txt. Is it something I did wrong on the installation process?

Here is the installation I command line that I used:

docker pull billandreo/deeplasmid-cpu-ubuntu2

and the command to run the program (I created an outdir folder at my user´s home one):

sudo /usr/bin/docker run -it -v ~/Rs1.4Eclo/scaffolds.fasta:/srv/jgi-ml/classifier/dl/in.fasta -v ~/outdir/srv/jgi-ml/classifier/dl/outdir billandreo/deeplasmid-cpu-ubuntu2 deeplasmid.sh in.fasta outdir

— Reply to this email directly, view it on GitHub https://github.com/wandreopoulos/deeplasmid/issues/7, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANGW5N24NE7CSSCH3KSHELWW7ZS3ANCNFSM6AAAAAAUY4KAEE . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Thanks, Bill

William B. Andreopoulos, Ph.D. Joint Genome Institute LBNL

fabrizziom99 commented 1 year ago

Thanks a lot, i apologize for my late answer. It was a typing error.