Open ManoloYoda89 opened 3 years ago
Hey,
I get the same error as in one the former Issues even though I use chemistry v1. The last few lines look like this:
Processed 1900000 aligned reads... Processed 1900000 aligned reads... Processed 1900000 aligned reads... 2021-09-07 12:16:45.949065 Generating digital gene expression matrix... Traceback (most recent call last): File "/home/mrank/miniconda3/envs/Lotus_split/bin/split-seq", line 87, in analysis.generate_all_dge_reports(args.output_dir, args.genome_dir, args.chemistry, args.sample, read_thresh=args.umi_threshold) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/split_seq/analysis.py", line 211, in generate_all_dge_reports generate_single_dge_report(output_dir,genome_dir,chemistry,sample_name=sample_name,sub_wells=sub_wells,sublibraries=sublibraries, read_thresh=read_thresh) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/split_seq/analysis.py", line 276, in generate_single_dge_report fig,ax,read_thresh = plot_read_thresh(read_counts, read_thresh=read_thresh) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/split_seq/analysis.py", line 140, in plot_read_thresh read_threshold = get_read_threshold(read_counts[read_counts>2]) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/split_seq/analysis.py", line 125, in get_read_threshold f = scipy.interpolate.interp1d(x, y,kind='linear') File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/scipy/interpolate/interpolate.py", line 474, in init self._y = self._reshape_yi(self.y) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/scipy/interpolate/polyint.py", line 110, in _reshape_yi return yi.reshape((yi.shape[0], -1)) ValueError: cannot reshape array of size 0 into shape (0,newaxis)
I am using the most recent version of the required packages. Could it be that these cause problems?
Thx for your help!
Hey,
I get the same error as in one the former Issues even though I use chemistry v1. The last few lines look like this:
Processed 1900000 aligned reads... Processed 1900000 aligned reads... Processed 1900000 aligned reads... 2021-09-07 12:16:45.949065 Generating digital gene expression matrix... Traceback (most recent call last): File "/home/mrank/miniconda3/envs/Lotus_split/bin/split-seq", line 87, in analysis.generate_all_dge_reports(args.output_dir, args.genome_dir, args.chemistry, args.sample, read_thresh=args.umi_threshold) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/split_seq/analysis.py", line 211, in generate_all_dge_reports generate_single_dge_report(output_dir,genome_dir,chemistry,sample_name=sample_name,sub_wells=sub_wells,sublibraries=sublibraries, read_thresh=read_thresh) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/split_seq/analysis.py", line 276, in generate_single_dge_report fig,ax,read_thresh = plot_read_thresh(read_counts, read_thresh=read_thresh) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/split_seq/analysis.py", line 140, in plot_read_thresh read_threshold = get_read_threshold(read_counts[read_counts>2]) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/split_seq/analysis.py", line 125, in get_read_threshold f = scipy.interpolate.interp1d(x, y,kind='linear') File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/scipy/interpolate/interpolate.py", line 474, in init self._y = self._reshape_yi(self.y) File "/home/mrank/miniconda3/envs/Lotus_split/lib/python3.9/site-packages/scipy/interpolate/polyint.py", line 110, in _reshape_yi return yi.reshape((yi.shape[0], -1)) ValueError: cannot reshape array of size 0 into shape (0,newaxis)
I am using the most recent version of the required packages. Could it be that these cause problems?
Thx for your help!