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artic-network / rampart

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
GNU General Public License v3.0
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Export reads Error #60

Closed zhuying412 closed 4 years ago

zhuying412 commented 4 years ago

When click the "Export reads", I got error:

NameError in line 38 of /opt/rampart/default_protocol/pipelines/bin_to_fastq/Snakefile: name 'yaml' is not defined File "/opt/rampart/default_protocol/pipelines/bin_to_fastq/Snakefile", line 38, in module

Then, I inserted import yaml in the first line of bin_to_fastq/Snakefile, I got error:

snakemake --snakefile /opt/rampart/default_protocol/pipelines/bin_to_fastq/Snakefile --configfile /opt/rampart/default_protocol/pipelines/bin_to_fastq/config.yaml --config sample_name=Mayinga barcodes=NB01 annotated_path=/opt/rampart/example_data/20181008_1405_EBOV/annotations/ basecalled_path=/opt/rampart/example_data/20181008_1405_EBOV/fastq/pass/ output_path=/opt/rampart/example_data/20181008_1405_EBOV --nolock --rerun-incomplete AttributeError in line 39 of /opt/rampart/default_protocol/pipelines/bin_to_fastq/Snakefile: 'collections.OrderedDict' object has no attribute 'read' File "/opt/rampart/default_protocol/pipelines/bin_to_fastq/Snakefile", line 39, in File "/opt/conda/envs/artic-rampart/lib/python3.7/site-packages/yaml/init.py", line 162, in safe_load File "/opt/conda/envs/artic-rampart/lib/python3.7/site-packages/yaml/init.py", line 112, in load File "/opt/conda/envs/artic-rampart/lib/python3.7/site-packages/yaml/loader.py", line 34, in init File "/opt/conda/envs/artic-rampart/lib/python3.7/site-packages/yaml/reader.py", line 85, in init File "/opt/conda/envs/artic-rampart/lib/python3.7/site-packages/yaml/reader.py", line 124, in determine_encoding File "/opt/conda/envs/artic-rampart/lib/python3.7/site-packages/yaml/reader.py", line 178, in update_raw

rambaut commented 4 years ago

I just released v1.0.5 which should fix this issue. Also uploaded to conda if you are using that to install.

rambaut commented 4 years ago

Also you don’t need to use the export reads from RAMPART if you use the ARTIC protocol for consensus generation as it will do demultiplexing for you.