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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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fastq.smk #196

Closed atigano closed 1 month ago

atigano commented 1 month ago

Hi, I've run snpArcher on a dataset successfully before. Then, I started to work on a new dataset and nothing is working anymore, I did exactly the same everything, after copying and updating the config and sample list files. Tried to run the first dataset and it doesn't work anymore either. I've downloaded the newest version with Snakemake 8 and I get the same error below. The test dataset works though!

KeyError in file /gpfs/fs7/grdi/genarcc/wp3/annat/snpArcher/workflow/rules/fastq.smk, line 45: 'sort_reads' File "/gpfs/fs7/grdi/genarcc/wp3/annat/snpArcher/workflow/Snakefile", line 7, in File "/gpfs/fs7/grdi/genarcc/wp3/annat/snpArcher/workflow/rules/fastq.smk", line 45, in

Do you have any idea what might be going on? Here I attach my more recent sample file. Thanks! samples_chum_snparcher_cov1.8.csv

cademirch commented 1 month ago

Hi @atigano, this is because we added the option to sort reads based on read name recently. It seems like the config option "sort_reads" is missing from your YAML config file.

atigano commented 1 month ago

Thank you! It's working now.

On Fri, May 17, 2024 at 10:57 AM Cade Mirchandani @.***> wrote:

Hi @atigano https://github.com/atigano, this is because we added the option to sort reads based on read name recently. It seems like the config option "sort_reads" is missing from your YAML config file.

— Reply to this email directly, view it on GitHub https://github.com/harvardinformatics/snpArcher/issues/196#issuecomment-2118125315, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJ6ZIZMJZVINNSIUC2B7WDZCZAHJAVCNFSM6AAAAABH4RSNWOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYGEZDKMZRGU . You are receiving this because you were mentioned.Message ID: @.***>