encountered same error when setting cores and executing snpArcher on my local machine

[yuan-circle-long]

the environment is ok when using "snakemake -d .test/ecoli --cores 1 --use-conda" to test.

I tried to set up the cores using "snakemake --cores 8 --use-conda" and encountered an error. l also executed my own data, and the same error was happened. The error message relates to three files: reference.smk, common.smk, and Snakefile. However, I did not change these files. l only changed the parameters of resources.ymal.

The code is on the main disk and the sequencing files are on another disk. For testing purposes, I chose three samples to build the sample table.

Best wishes

[yuan-circle-long]

Building DAG of jobs... InputFunctionException in rule download_reference in file /home/aiworkstation/snpArcher/workflow/rules/reference.smk, line 3: Error: IndexError: list index out of range Wildcards: refGenome=ref Traceback: File "/home/aiworkstation/snpArcher/workflow/rules/common.smk", line 79, in get_ref

[tsackton]

This looks like an error parsing your sample sheet. Can you confirm that your sample sheet is comma-separated and looks the same as the example sample sheet?

[yuan-circle-long]

Thanks for your help very much! Compared with the example sample sheet, the ref path in my sample sheet is a directory not a fasta file. l modify the sample sheet and the code runs no problem.

[yuan-circle-long]

Sorry to bother you again.

In my project, the cores number is set to 48, and the memory is 100000. But using the top command shows the cpu used is just 100%，is this condition is normal？

the resource file the cpu used

My computer hardware About my data, the reference genome is about 8GB, and each sample is about 3GB. l used the GBS sequencing method.

[yuan-circle-long]

Memory usage seems to be normal now.

[cademirch]

Hi @yuan-circle-long, glad its working as expected.