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chung-lab / SCAFE

Single Cell Analysis of Five'Ends
MIT License
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Results of count not found. Quitting #13

Closed houruiyan closed 2 years ago

houruiyan commented 2 years ago

Hello Dr. Chung, I am really really sorry. But I cannot fix it. I still run the scafe.workflow.sc.pool My lib is like this: S17765-F11_S33 33 ./S33_SCAFE_out/bam_to_ctss/S17765-F11_S33/bed/S17765-F11_S33.UMI_CB.ctss.bed.gz ./S17765-F11_S33_out/outs/filtered_feature_bc_matrix/S17765-F11_S33.barcodes.tsv.gz ./S33_SCAFE_out/bam_to_ctss/S17765-F11_S33/bed/S17765-F11_S33.CB.ctss.bed.gz S17765-F11_S34 34 ./S34_SCAFE_out/bam_to_ctss/S17765-F11_S34/bed/S17765-F11_S34.UMI_CB.ctss.bed.gz ./S17765-F11_S34_out/outs/filtered_feature_bc_matrix/S17765-F11_S34.barcodes.tsv.gz ./S34_SCAFE_out/bam_to_ctss/S17765-F11_S34/bed/S17765-F11_S34.CB.ctss.bed.gz S17765-F11_S35 35 ./S35_SCAFE_out/bam_to_ctss/S17765-F11_S35/bed/S17765-F11_S35.UMI_CB.ctss.bed.gz ./S17765-F11_S35_out/outs/filtered_feature_bc_matrix/S17765-F11_S35.barcodes.tsv.gz ./S35_SCAFE_out/bam_to_ctss/S17765-F11_S35/bed/S17765-F11_S35.CB.ctss.bed.gz S17765-F11_S36 36 ./S36_SCAFE_out/bam_to_ctss/S17765-F11_S36/bed/S17765-F11_S36.UMI_CB.ctss.bed.gz ./S17765-F11_S36_out/outs/filtered_feature_bc_matrix/S17765-F11_S36.barcodes.tsv.gz ./S36_SCAFE_out/bam_to_ctss/S17765-F11_S36/bed/S17765-F11_S36.CB.ctss.bed.gz

My code is nohup scafe.workflow.sc.pool --overwrite=yes --lib_list_path=./lib_list_path.txt --genome=hg38.gencode_v32 --run_tag=demo --run_outDir=./sc.pool &

However it gives me this error. image

This time, I already check the lib_list_path clearly. However, it still throw this error. Hope to get your help. Thank you!

chung-lab commented 2 years ago

try to use full path in ./lib_list_path.txt and the file has to be tab delimited