No output result, and keeps showing "Nothing to be done Building DAG of jobs..."

[fcbayern31]

Hello Dr. Zheng,

When I run NGS data using

snakemake -j 40 --reason --printshellcmds -s config.NGS.yaml ,

it always shows

"Nothing to be done. Building DAG of jobs... Nothing to be done (all requested files are present and up to date). ”

The same happens when running the example NGS workflow:

Building DAG of jobs... Nothing to be done (all requested files are present and up to date). Complete log: ../../.snakemake/log/2024-04-09T163028.914719.snakemake.log

I haven't found any other errors. What could be the reason for this?

[starskyzheng]

Can you list files in your workdir?

[fcbayern31]

Here are files in my workdir:

Ref.gfa ##softlink sample.reads.list ##softlink ASX-1.2.fq.gz ##softlink ASX-1.1.fq.gz ##softlink JPN_DS.1.fq.gz ##softlink JPN_DS.2.fq.gz ##softlink ...

Below is my sample.reads.list(The separator is a space):

ASX-1 ASX-1.1.fq.gz ASX-1.2.fq.gz JPN_DS JPN_DS.1.fq.gz JPN_DS.2.fq.gz ...

Below is my config.NGS.yaml:

workdir: "/home/***/panpop"
sample_reads_list_file: "sample.reads.list"
Default is True.
split_chr: True
mode: "genotype"
graph: 'Ref'
mapper: 'gaffe'

And the result was :

Building DAG of jobs... Nothing to be done (all requested files are present and up to date). Complete log: ../.snakemake/log/2024-04-10T084544.593329.snakemake.log

I got same result running example in example/example_short_reads.

[starskyzheng]

May be a full file list of workdir will helps. Was there exists some dirs?

[fcbayern31]

Thank you! I have solved the problem. It was caused by the incorrect snakefile.