AMALGKIT version: 0.9.22
AMALGKIT command: /opt/conda/envs/biotools/bin/amalgkit metadata --out_dir ./ --config_dir ./config
AMALGKIT bug report: https://github.com/kfuku52/amalgkit/issues
amalgkit metadata: start
Creating directory: ./metadata
Creating directory: ./metadata/tmp
Config file found: search_term_exclusion.config
Config file found: search_term_other.config
Config file found: search_term_species.config
Config file found: search_term_keyword.config
Number of species for Entrez search: 0
Number of free keywords for Entrez search: 1
Number of other conditions for Entrez search: 3
Number of excluded conditions for Entrez search: 2
Entrez search species: All
Entrez search term: (PRJNA350297) AND "platform illumina"[Properties] AND "type rnaseq"[Filter] AND "sra biosample"[Filter] NOT ("strategy mirna seq"[Properties] OR "strategy rip seq"[Properties])
Number of SRA records: 0
stderr
Traceback (most recent call last):
File "/opt/conda/envs/biotools/bin/amalgkit", line 368, in <module>
args.handler(args)
File "/opt/conda/envs/biotools/bin/amalgkit", line 18, in command_metadata
metadata_main(args)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/amalgkit/metadata.py", line 170, in metadata_main
metadata_species[sp_print] = Metadata.from_xml(xml_root=root).df
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/amalgkit/util.py", line 176, in from_xml
df = pandas.concat(df_list, ignore_index=True, sort=False)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 372, in concat
op = _Concatenator(
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 429, in __init__
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
PRJNA350297
stdout
stderr