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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Rampart Export Reads for sample #4

Closed rjorton closed 4 years ago

rjorton commented 4 years ago

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

rambaut commented 4 years ago

This is fixed in RAMPART release v1.0.5 - do an update