analysis does not start

[sbgonenc]

Hi greta Team!

Thank you so much for the benchmark suite you have developed. I really think we need a standard for benchmarking GRNs on different datasets, and your tool delivers that, so thanks!

I am interested in performing benchmark study on heart dataset and compare with the model I am using. Right now, I am having issues with setting up and running the greta. So far I managed to download datasets on the HPC cluster with singularity containers, but not able to run analysis. Could you please point out where I might be missing?

snakemake --profile config/slurm/ anl/metrics/pbmc10k.all.csv

_______________________________________________________________
Using profile config/slurm/ for setting default command line arguments.
Building DAG of jobs...
MissingRuleException:
No rule to produce anl/metrics/pbmc10k.all.csv (if you use input functions make sure that they don't raise unexpected exceptions).

snakemake --profile config/slurm/ anl/metrics/heart.all.csv

_____________________________________________________________
Using profile config/slurm/ for setting default command line arguments.
Building DAG of jobs...
MissingRuleException:
No rule to produce anl/metrics/heart.all.csv (if you use input functions make sure that they don't raise unexpected exceptions).

You can find the Snakemake environment here:
greta_env.txt

and the system it runs:

NAME="Red Hat Enterprise Linux"
VERSION="9.6 (Plow)"
ID="rhel"
ID_LIKE="fedora"
VERSION_ID="9.6"
PLATFORM_ID="platform:el9"
PRETTY_NAME="Red Hat Enterprise Linux 9.6 (Plow)"
ANSI_COLOR="0;31"
LOGO="fedora-logo-icon"
CPE_NAME="cpe:/o:redhat:enterprise_linux:9::baseos"
HOME_URL="https://www.redhat.com/"
DOCUMENTATION_URL="https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/9"
BUG_REPORT_URL="https://issues.redhat.com/"

REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 9"
REDHAT_BUGZILLA_PRODUCT_VERSION=9.6
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="9.6"
Red Hat Enterprise Linux release 9.6 (Plow)
Red Hat Enterprise Linux release 9.6 (Plow)

Thanks for your time.

Sincere regards,
Berk

[PauBadiaM]

Hi @sbgonenc,

Apologies, the correct command is:

snakemake --profile config/slurm/ anl/metrics/summary/heart.all.csv

I've updated the README accordingly. Just a note, currently there will be two methods (scmtni and scdori) that will most likely fail, we are working on it.