When I try the "Export Reads" for a sample from the rampart webpage, I get the following error:
[warning] pipeline (Export reads) finished with exit code 1. Error messages:
[warning] AttributeError in line 40 of /home/orto01r/anaconda3/envs/artic-ncov2019/lib/node_modules/artic-rampart/default_protocol/pipelines/bin_to_fastq/Snakefile:
'collections.OrderedDict' object has no attribute 'read'
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/node_modules/artic-rampart/default_protocol/pipelines/bin_to_fastq/Snakefile", line 40, in
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/init.py", line 162, in safe_load
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/init.py", line 112, in load
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/loader.py", line 34, in init
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/reader.py", line 85, in init
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/reader.py", line 124, in determine_encoding
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/reader.py", line 178, in update_raw
I'm on Ubuntu 18, mozilla firefox. The visualisations seems to have worked fine, and there are plenty of reads for each of the samples
When I try the "Export Reads" for a sample from the rampart webpage, I get the following error:
[warning] pipeline (Export reads) finished with exit code 1. Error messages: [warning] AttributeError in line 40 of /home/orto01r/anaconda3/envs/artic-ncov2019/lib/node_modules/artic-rampart/default_protocol/pipelines/bin_to_fastq/Snakefile: 'collections.OrderedDict' object has no attribute 'read' File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/node_modules/artic-rampart/default_protocol/pipelines/bin_to_fastq/Snakefile", line 40, in
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/init.py", line 162, in safe_load
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/init.py", line 112, in load
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/loader.py", line 34, in init
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/reader.py", line 85, in init
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/reader.py", line 124, in determine_encoding
File "/home/orto01r/anaconda3/envs/artic-ncov2019/lib/python3.6/site-packages/yaml/reader.py", line 178, in update_raw
I'm on Ubuntu 18, mozilla firefox. The visualisations seems to have worked fine, and there are plenty of reads for each of the samples