Hi! I'm trying the code out on a subsample of 10X data and I'm getting this error:
Inspecting and pre-processing input data
Unzipping files (temporary)
Running Dropseq_subgraphs
Args:{
"output_dir": "subsample",
"reads": "/tmp/tmp45lkyjyw",
"index_depth": 0.1,
"threads": 32,
"umi_end": 34,
"min_dist": 1,
"breadth": 10000,
"kmer_size": 9,
"barcodes": "/tmp/tmpu2zufo2d",
"depth": 10,
"barcode_start": 0,
"umi_start": 26,
"barcode_end": 26
}
Initializing redis-db server
Indexing reads by circularized kmers
10089 reads indexed
141944 kmers indexed
Finding cyclic paths
15 cyclic paths found
Thresholding paths
Traceback (most recent call last):
File "/home/aaron/bin/sircel/sircel/Sircel_master.py", line 318, in
output_files = run_all(args)
File "/home/aaron/bin/sircel/sircel/Sircel_master.py", line 83, in run_all
output_files, elapsed_time = Split_reads.run_all(split_args)
File "/home/aaron/bin/sircel/sircel/Split_reads.py", line 81, in run_all
(threshold, top_paths, fit_out) = threshold_paths(output_dir, cyclic_paths)
File "/home/aaron/bin/sircel/sircel/Split_reads.py", line 301, in threshold_paths
savgol = signal.savgol_filter(slopes, 251, 4)
File "/usr/local/lib/python3.5/dist-packages/scipy/signal/_savitzky_golay.py", line 344, in savgol_filter
_fit_edges_polyfit(x, window_length, polyorder, deriv, delta, axis, y)
File "/usr/local/lib/python3.5/dist-packages/scipy/signal/_savitzky_golay.py", line 222, in _fit_edges_polyfit
polyorder, deriv, delta, y)
File "/usr/local/lib/python3.5/dist-packages/scipy/signal/_savitzky_golay.py", line 187, in _fit_edge
xx_edge = xx_edge.reshape(xx_edge.shape[0], -1)
ValueError: cannot reshape array of size 0 into shape (0,newaxis)
Also, I had to fix some typos in the merge_barcodefiles_10x code to get it to work at all:
indexq should be index1 and 'writer = open(out_file, 'wb')' should be 'writer = open(out_file_name, 'wb')'
Hi! I'm trying the code out on a subsample of 10X data and I'm getting this error:
Inspecting and pre-processing input data Unzipping files (temporary)
Running Dropseq_subgraphs Args:{ "output_dir": "subsample", "reads": "/tmp/tmp45lkyjyw", "index_depth": 0.1, "threads": 32, "umi_end": 34, "min_dist": 1, "breadth": 10000, "kmer_size": 9, "barcodes": "/tmp/tmpu2zufo2d", "depth": 10, "barcode_start": 0, "umi_start": 26, "barcode_end": 26 } Initializing redis-db server Indexing reads by circularized kmers 10089 reads indexed 141944 kmers indexed Finding cyclic paths 15 cyclic paths found Thresholding paths Traceback (most recent call last): File "/home/aaron/bin/sircel/sircel/Sircel_master.py", line 318, in
output_files = run_all(args)
File "/home/aaron/bin/sircel/sircel/Sircel_master.py", line 83, in run_all
output_files, elapsed_time = Split_reads.run_all(split_args)
File "/home/aaron/bin/sircel/sircel/Split_reads.py", line 81, in run_all
(threshold, top_paths, fit_out) = threshold_paths(output_dir, cyclic_paths)
File "/home/aaron/bin/sircel/sircel/Split_reads.py", line 301, in threshold_paths
savgol = signal.savgol_filter(slopes, 251, 4)
File "/usr/local/lib/python3.5/dist-packages/scipy/signal/_savitzky_golay.py", line 344, in savgol_filter
_fit_edges_polyfit(x, window_length, polyorder, deriv, delta, axis, y)
File "/usr/local/lib/python3.5/dist-packages/scipy/signal/_savitzky_golay.py", line 222, in _fit_edges_polyfit
polyorder, deriv, delta, y)
File "/usr/local/lib/python3.5/dist-packages/scipy/signal/_savitzky_golay.py", line 187, in _fit_edge
xx_edge = xx_edge.reshape(xx_edge.shape[0], -1)
ValueError: cannot reshape array of size 0 into shape (0,newaxis)
Also, I had to fix some typos in the merge_barcodefiles_10x code to get it to work at all: indexq should be index1 and 'writer = open(out_file, 'wb')' should be 'writer = open(out_file_name, 'wb')'
paramaters: python3 ~/bin/sircel/sircel/Sircel_master.py --threads 32 \ --10xgenomics \ --output_dir subsample \ --reads 100k_R2_001.fastq.gz \ --barcodes 100k_R1_001.fastq.gz \ --umis 100k_I1_001.fastq.gz \ --kallisto_idx mus.rel79.idx