erikenbody
commented
1 week ago Looks like you are missing the “run” column form the sample sheet
On Fri, Jun 7, 2024 at 12:57 PM AmitSharma267 @.***> wrote:
Hi there,
when we are trying to run the command we are encountering this error. image.png (view on web) https://github.com/harvardinformatics/snpArcher/assets/158214436/ce8d2ac2-38a4-452b-986f-9068d940d5fe
the sample sheet is set up as:
BioSample,refGenome,refPath,fq1,fq2 SS3_S143,sclscl_ref,/home/sharma267/project1/GCF_000146945.2_ASM14694v2_genomic.fna,/home/sharma267/project1/SS3_S143_L008_R1_001.fastq.gz,/home/sharma267/project1/SS3_S143_L008_R2_001.fastq.gz
and config.yaml looks like this: image.png (view on web) https://github.com/harvardinformatics/snpArcher/assets/158214436/bb168292-2e79-4ff5-bc7e-5a6ff90d2448
Also tried putting the reference genome and its path to the config.yaml file but it gives the same error.
We are unable to figure out root of the problem. Could you please help me here? Please let me know if more information is needed. Thanks in advance. Amit
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AmitSharma267
Hi there,
when we are trying to run the command we are encountering this error.
the sample sheet is set up as:
and config.yaml looks like this:
Also tried putting the reference genome and its path to the config.yaml file but it gives the same error.
We are unable to figure out root of the problem. Could you please help me here? Please let me know if more information is needed. Thanks in advance. Amit