Unable to run test after installation

[qt37t247]

Dear authors,

I installed snpArcher and snakemake last week and it works well. Today, I installed them on another device and ran:

snakemake -d .test/ecoli --cores 1 --use-conda

it gives me:

File "/home/users/nus/dbstq/.conda/envs/snparcher/lib/python3.12/site-packages/snakemake/cli.py", line 1895, in args_to_api dag_api = workflow_api.dag( ^^^^^^^^^^^^^^^^^ File "/home/users/nus/dbstq/.conda/envs/snparcher/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag return DAGApi( ^^^^^^^ File "", line 6, in init File "/home/users/nus/dbstq/.conda/envs/snparcher/lib/python3.12/site-packages/snakemake/api.py", line 421, in __post_init__ self.workflow_api._workflow.dag_settings = self.dag_settings ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/users/nus/dbstq/.conda/envs/snparcher/lib/python3.12/site-packages/snakemake/api.py", line 372, in _workflow workflow.include( File "/home/users/nus/dbstq/.conda/envs/snparcher/lib/python3.12/site-packages/snakemake/workflow.py", line 1363, in include exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals) File "/scratch/users/nus/dbstq/snpArcher/workflow/Snakefile", line 13, in else: File "/home/users/nus/dbstq/.conda/envs/snparcher/lib/python3.12/site-packages/snakemake/workflow.py", line 1363, in include exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals) File "/scratch/users/nus/dbstq/snpArcher/workflow/rules/fastq.smk", line 10, in resources['get_fastq_pe']['threads'] ^^^^^^^^^^^^^ AttributeError: 'Workflow' object has no attribute 'default_remote_prefix'

I wonder if this is an issue caused by a recent update of snakemake...

Many thanks and best regards,

Qian

[cademirch]

Hi @qt37t247, could you check and report what version of Snakemake produced this error? You can run snakemake --version to print that info.

[qt37t247]

Hi @qt37t247, could you check and report what version of Snakemake produced this error? You can run snakemake --version to print that info.

It is 8.0.1. The one works is 7.32.4.

[cademirch]

Hi @qt37t247, could you check and report what version of Snakemake produced this error? You can run snakemake --version to print that info.

It is 8.0.1. The one works is 7.32.4.

Okay, that's likely the issue, there was some big changes in Snakemake 8.0. I'll take a look and see what we need to change in snparcher to support these changes, but the in the meantime you'll need to use an older version.

[qt37t247]

Hi @qt37t247, could you check and report what version of Snakemake produced this error? You can run snakemake --version to print that info.

It is 8.0.1. The one works is 7.32.4.

Okay, that's likely the issue, there was some big changes in Snakemake 8.0. I'll take a look and see what we need to change in snparcher to support these changes, but the in the meantime you'll need to use an older version.

Sounds good. I'll follow your updates too. Thanks!

[cademirch]

closing for now. will create new issue for support snakemake >= 8.0

[siberianhigh]

Hi,

just to confirm exactly the same issue for me with snakemake 8.0.1.

best, Evgeniy