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JiekaiLab / scTE

MIT License
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Error when running scTEATAC: 'genome required' #29

Open mathosi opened 2 years ago

mathosi commented 2 years ago

Hi,

I have a problem running the command 'scTEATAC': When runnning scTEATAC -i input.bam -o outfile -x mm10.te.atac.idx I receive the error

scTE_scatacseq: error: the following arguments are required: -g/--genome

However, when running the command scTEATAC -i input.bam -o outfile -x mm10.te.atac.idx -g mm10 another error occurs:

TypeError: Readanno() got an unexpected keyword argument 'genome'

Could you please provide an example on how to run scTE on the output from Cellranger-atac (10x scATAC-seq data)? The example provided in the README does not work for me.

Thanks and best wishes, Malte

JBreunig commented 2 years ago

Also having same issue using -g or --genome mm10 or leaving it out as above.

mathosi commented 2 years ago

Dear developers, do you have any suggestions on this? In the current state, the software does not seem to be usable.

Sokratis5 commented 1 year ago

First, thank you for creating scTE, it has been very useful in my research. I have had the same problem with scTEATAC as the above users. I just wanted to bump this issue, and see if any resolution can be provided. I also get if I don't specify the genome: scTE_scatacseq: error: the following arguments are required: -g/--genome and if I do specify it: TypeError: Readanno() got an unexpected keyword argument 'genome'

Thanks