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xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
MIT License
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this software had met mistake, i had changed the blastn version, diamond version， how can i solve it ? #65

Open pl19940314 opened 2 months ago

pl19940314 commented 2 months ago

WARNING: Output folder </home/meta/mdisk/pl/earthworm/megahit/cd-hit/L1HHH0200300/MGE_new> contains and/or <.filtered.>, they/it will be overwritten. [2024-05-09 14:50:21] INFO: Processing </home/meta/mdisk/pl/earthworm/megahit/cd-hit/L1HHH0200300/MGE_new/extracted.fa> ... [2024-05-09 14:50:21] INFO: Extracting target sequences using BLAST ... [2024-05-09 14:50:21] INFO: BLAST settings: 1260675 bps, 8355 reads, 10 threads, mt_mode 0. [2024-05-09 14:50:24] INFO: Merging files ... Traceback (most recent call last): File "/home/meta/miniconda3/envs/args_oap/bin/args_oap", line 10, in sys.exit(main()) ^^^^^^ File "/home/meta/miniconda3/envs/args_oap/lib/python3.12/site-packages/args_oap/args_oap.py", line 232, in main options.func(options) File "/home/meta/miniconda3/envs/args_oap/lib/python3.12/site-packages/args_oap/stage_two.py", line 213, in run_stage_two StageTwo(vars(options)).run() File "/home/meta/miniconda3/envs/args_oap/lib/python3.12/site-packages/args_oap/stage_two.py", line 208, in run self.merge_files() File "/home/meta/miniconda3/envs/args_oap/lib/python3.12/site-packages/args_oap/stage_two.py", line 191, in merge_files out = pd.merge(self.metadata, result, on='sample') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/meta/miniconda3/envs/args_oap/lib/python3.12/site-packages/pandas/core/reshape/merge.py", line 170, in merge op = _MergeOperation( ^^^^^^^^^^^^^^^^ File "/home/meta/miniconda3/envs/args_oap/lib/python3.12/site-packages/pandas/core/reshape/merge.py", line 794, in init ) = self._get_merge_keys() ^^^^^^^^^^^^^^^^^^^^^^ File "/home/meta/miniconda3/envs/args_oap/lib/python3.12/site-packages/pandas/core/reshape/merge.py", line 1310, in _get_merge_keys left_keys.append(left._get_label_or_level_values(lk)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/meta/miniconda3/envs/args_oap/lib/python3.12/site-packages/pandas/core/generic.py", line 1911, in _get_label_or_level_values raise KeyError(key) KeyError: 'sample'

xinehc commented 2 months ago

Did you modified the metadata.txt file?

Can you confirm that the first entry of the file is sample using:

grep sample metadata.txt
pl19940314 commented 2 months ago

image

pl19940314 commented 2 months ago

i have rerun the stage_one, after, the stage_two had not make mistake and had sucessfully run again