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Description
I am running into the following error when searching the SRA for all Staphylococcus aureus sequences:
Command executed:
bionode-ncbi search sra "Staphylococcus aureus" > results.txt
Command exit status:
1
Command output:
(empty)
Command error:
events.js:165
throw er; // Unhandled 'error' event
^
TypeError: Cannot create property 'Run' on string ' '
at /home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/nested-property/index.js:54:27
at Array.reduce (<anonymous>)
at Object.setNestedProperty [as set] (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/nested-property/index.js:53:26)
at Transform.cb [as _transform] (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/lib/tool-stream.js:136:49)
at Transform._read (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/readable-stream/lib/_stream_transform.js:184:10)
at Transform._write (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/readable-stream/lib/_stream_transform.js:172:12)
at doWrite (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/readable-stream/lib/_stream_writable.js:237:10)
at writeOrBuffer (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/readable-stream/lib/_stream_writable.js:227:5)
at Transform.Writable.write (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/readable-stream/lib/_stream_writable.js:194:11)
at Pumpify.Duplexify._write (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/duplexify/index.js:214:22)
Emitted 'error' event at:
at Parser.exports.Parser.Parser.parseString (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/xml2js/lib/parser.js:326:16)
at /home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/xml2js/lib/parser.js:5:59
at parseXMLString (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/lib/tool-stream.js:399:5)
at parseXMLProperty (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/lib/tool-stream.js:386:7)
at /home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/async/lib/async.js:122:13
at _each (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/async/lib/async.js:46:13)
at Object.async.each (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/async/lib/async.js:121:9)
at Transform.parser [as _transform] (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/lib/tool-stream.js:379:11)
at Transform._read (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/readable-stream/lib/_stream_transform.js:184:10)
at Transform._write (/home/esteinig/miniconda3/envs/nextflow/lib/node_modules/bionode-ncbi/node_modules/tool-stream/node_modules/readable-stream/lib/_stream_transform.js:172:12)
.command.stub: line 98: 106508 Terminated nxf_trace "$pid" .command.trace
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