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chung-lab / SCAFE

Single Cell Analysis of Five'Ends
MIT License
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bam_to_ctss throws error with demo data #7

Closed semrau-regeneron closed 3 years ago

semrau-regeneron commented 3 years ago

I downloaded the genome reference using "scafe.download.resources.genome --genome=hg19.gencode_v32lift37", but get an error when I try to run the demo data with scafe.workflow.sc.solo. I reran prep_genome, as instructed, but the error remains.

#===========================#
Start running bam_to_ctss
#===========================#

=========================================================================
[2021-04-29 17:27] starts running ...... 
=========================================================================

[2021-04-29 17:27] Checking all SCAFE executables          
[2021-04-29 17:27] Checking: bedtools version: 2.30.0
[2021-04-29 17:27] Checking: samtools version: Version: 1.3.1
[2021-04-29 17:27] Checking: paraclu found.
[2021-04-29 17:27] Checking: paraclu-cut found.
[2021-04-29 17:27] Checking: bedGraphToBigWig version: 2.8
[2021-04-29 17:27] Checking: bigWigAverageOverBed version: 2
genome hg19.gencode_v32lift37 does not have chrom_name_path. Please rerun prep_genome step
semrau-regeneron commented 3 years ago

My bad, must have been due to an interrupted download. I downloaded the reference again and now it works. Thanks for developing this great tool! Looking forward to running it on our own data.

houruiyan commented 3 years ago

hello, I also get the same question. But even if I downloaded the reference again, I also get the same error. Hope to get your help. Thank you in advance!