Error when running scTEATAC

[cnk113]

Hello,

I'm trying to run this on my scATAC-seq sample and I'm running into this issue: `TypeError: Readanno() got an unexpected keyword argument 'genome' I built the hg38 index using the same method you did with you mm10 genome on the README. scTEATAC -i filtered.bam -x hg38.te.atac.idx -p 16 -CB -g hg38 Any ideas why this is an issue?

Thanks, Chang

[leeyoyohku]

I remember the updated scTE doesn't need genome flag. Perhaps try without '--genome hg38'?

[cnk113]

So when I do it without it, I get

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

[leeyoyohku]

Oh, I see it. It's because you put-g hg38after -CB flag. You should specify CR,CB, or False after -CB.

[cnk113]

I'm back to the original error now:

File "/home/chang/miniconda3/envs/venv/lib/python3.7/site-packages/scTE-1.0-py3.7.egg/EGG-INFO/scripts/scTEATAC", line 216, in <module>
    main()
  File "/home/chang/miniconda3/envs/venv/lib/python3.7/site-packages/scTE-1.0-py3.7.egg/EGG-INFO/scripts/scTEATAC", line 144, in main
    allelement, chr_list, all_annot, glannot = Readanno(filename=outname, annoglb=args.annoglb[0], genome=args.genome)
TypeError: Readanno() got an unexpected keyword argument 'genome'

[cnk113]

I just fixed this by commenting out the genome parameter in the line of Readanno.

[funpys]

@cnk113 Thank you. I had the same issue. And I fixed it in the same way.

[funpys]

I got another error.

INFO : Calculating expression... 2021-07-30 08:06:59 Traceback (most recent call last): File "/home/bskim/anaconda3/bin/scTEATAC", line 4, in import('pkg_resources').run_script('scTE==1.0', 'scTEATAC') File "/home/bskim/anaconda3/lib/python3.8/site-packages/pkg_resources/init.py", line 665, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/bskim/anaconda3/lib/python3.8/site-packages/pkg_resources/init.py", line 1463, in run_script exec(code, namespace, namespace) File "/home/bskim/anaconda3/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTEATAC", line 216, in main() File "/home/bskim/anaconda3/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTEATAC", line 198, in main len_res, genenumber, filename = Countexpression(filename=args.out, allelement=allelement, genenumber=args.genenumber, cellnumber=args.cellnumber,hdf5=args.hdf5) File "/home/bskim/anaconda3/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/scTE/base.py", line 505, in Countexpression adata = ad.AnnData(np.asarray(data),var = var,obs = obs) File "/home/bskim/anaconda3/lib/python3.8/site-packages/anndata-0.7.6-py3.8.egg/anndata/_core/anndata.py", line 308, in init self._init_as_actual( File "/home/bskim/anaconda3/lib/python3.8/site-packages/anndata-0.7.6-py3.8.egg/anndata/_core/anndata.py", line 463, in _init_as_actual _check_2d_shape(X) File "/home/bskim/anaconda3/lib/python3.8/site-packages/anndata-0.7.6-py3.8.egg/anndata/_core/anndata.py", line 97, in _check_2d_shape raise ValueError( ValueError: X needs to be 2-dimensional, not 1-dimensional.

[ApolloWuu]

Hi,

Have you fixed the Readanno error? I was wondering how to fix it.

Best, Apollo

[funpys]

@ApolloWuu No, I couldn't fix it. I just analyzed the data by Signac with the TE annotation file.

[sabrinacamp2]

@funpys How did you use the TE annotation file in Signac? And did you calculate counts over TEs using the GeneActivity function? I'm also looking for a workaround here!

[funpys]

@sabrinacamp2 No. I just checked whether region of interest in scATAC data is TE or not.