I am attempting to run the human PBMC example analysis and am running into an error when I run the script run_conga.py.
I have downloaded the datasets using the "conga_example_datasets_v1" Dropbox folder here.
I run the script setup_10x_for_conga.py with the appropriate filtered_contig_annotations.csv file and run into no errors and the appropriate output files.
However, when I run the script run_conga.py, I am greeted with the following error:
Session information updated at 2022-09-23 18:31
reading: ./conga/conga_example_datasets_v1/vdj_v1_hs_pbmc3_5gex_filtered_gene_bc_matrices_h5.h5 of type 10x_h5
Variable names are not unique. To make them unique, call .var_names_make_unique.
./conga/conga/preprocess.py:233: DeprecationWarning: Use is_view instead of isview, isview will be removed in the future.
if adata.isview: # ran into trouble with AnnData views vs copies
total barcodes: 7231 (7231, 33555)
reading: ./conga/conga_example_datasets_v1/vdj_v1_hs_pbmc3_t_filtered_contig_annotations_tcrdist_clones.tsv
reading: ./conga/conga_example_datasets_v1/vdj_v1_hs_pbmc3_t_filtered_contig_annotations_tcrdist_clones_AB.dist_50_kpcs
Reducing to the 3176 barcodes (out of 7231) with paired TCR sequence data
Traceback (most recent call last):
File "./conga/scripts/run_conga.py", line 483, in
print(adata)
UnicodeEncodeError: 'ascii' codec can't encode character '\xd7' in position 26: ordinal not in range(128)
This identical error replicates after multiple attempts to run run_conga.py and after re-runs of setup_10x_for_conga.py. The error also replicates when using data downloaded individually using the link here.
Below is my command (copied from the example) for running run_conga.py:
I am attempting to run the human PBMC example analysis and am running into an error when I run the script run_conga.py.
I have downloaded the datasets using the "conga_example_datasets_v1" Dropbox folder here.
I run the script setup_10x_for_conga.py with the appropriate filtered_contig_annotations.csv file and run into no errors and the appropriate output files.
However, when I run the script run_conga.py, I am greeted with the following error:
Session information updated at 2022-09-23 18:31
reading: ./conga/conga_example_datasets_v1/vdj_v1_hs_pbmc3_5gex_filtered_gene_bc_matrices_h5.h5 of type 10x_h5 Variable names are not unique. To make them unique, call
print(adata)
UnicodeEncodeError: 'ascii' codec can't encode character '\xd7' in position 26: ordinal not in range(128)
.var_names_make_unique. ./conga/conga/preprocess.py:233: DeprecationWarning: Use is_view instead of isview, isview will be removed in the future. if adata.isview: # ran into trouble with AnnData views vs copies total barcodes: 7231 (7231, 33555) reading: ./conga/conga_example_datasets_v1/vdj_v1_hs_pbmc3_t_filtered_contig_annotations_tcrdist_clones.tsv reading: ./conga/conga_example_datasets_v1/vdj_v1_hs_pbmc3_t_filtered_contig_annotations_tcrdist_clones_AB.dist_50_kpcs Reducing to the 3176 barcodes (out of 7231) with paired TCR sequence data Traceback (most recent call last): File "./conga/scripts/run_conga.py", line 483, inThis identical error replicates after multiple attempts to run run_conga.py and after re-runs of setup_10x_for_conga.py. The error also replicates when using data downloaded individually using the link here.
Below is my command (copied from the example) for running run_conga.py:
python ./conga/scripts/run_conga.py --all --organism human --clones_file ./conga/conga_example_datasets_v1/vdj_v1_hs_pbmc3_t_filtered_contig_annotations_tcrdist_clones.tsv --gex_data ./conga/conga_example_datasets_v1/vdj_v1_hs_pbmc3_5gex_filtered_gene_bc_matrices_h5.h5 --gex_data_type 10x_h5 --outfile_prefix tcr_hs_pbmc
Thank you for any advice!