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chung-lab / SCAFE

Single Cell Analysis of Five'Ends
MIT License
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genome does not have chrom_name_path #11

Closed houruiyan closed 3 years ago

houruiyan commented 3 years ago

Hello, thank you for developing this awesome tool. I meet trouble when I use it. When I use the scafe.workflow.sc.solo, it always tell me that genome does not have chrom_name_path. My code is looking like this. scafe.workflow.sc.solo --run_bam_path ./S17765-F11_S33_out/outs/possorted_genome_bam.bam --run_cellbarcode_path ./S17765-F11_S34_out/outs/filtered_feature_bc_matrix --genome /storage/yhhuang/users/ruiyan/software/SCAFE/resources/genome/my_hg38_encode --run_tag S17765-F11_S33 --run_outDir ./S33_SCAFE_out

However, I got the error. image

Hope to get your help. I found that some people have the same questions. But he solved it by re-downloading the reference genome. However, I did it according to his analysis. I found that it is not helpful to me. On the one hand, I download the resources.genome. ./scafe.download.resources.genome --genome hg38.gencode_v32 On the other hand, I run the scafe.tool.cm.prep_genome. All of them do not work for me.

Thank you in advance.

jenchien commented 3 years ago

The --genome parameter takes the genome name installed in the SCAFE/resources/genome/ folder, not the path. In your code, --genome my_hg38_encode should work. We may modify it in the future to make it more general. Thanks.

houruiyan commented 3 years ago

Thank you very much!