Unable to merge virus profile.txt files into table

Microbial community profiling MetaPhlAn
1

I am using metaphlan4 with mpa_vJun23_CHOCOPhlAnSGB_202307

I obtained profiled.vsc files for virus using this command:
SampleName.r1.fastq --input_type fastq --bowtie2out SampleName.r1.bowtie2.bz2 --profile_vsc --vsc_out profiled_Sample Name.vsc.txt

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I am running this command

merge_metaphlan_tables.py profiled_*.txt > -o merged_abundance_table.txt

I am getting this error:
Traceback (most recent call last):
File “MYPATH/.conda/envs/metaphlan4/lib/python3.10/site-packages/pandas/core/indexes/base.py”, line 3805, in get_loc
return self._engine.get_loc(casted_key)
File “index.pyx”, line 167, in pandas._libs.index.IndexEngine.get_loc
File “index.pyx”, line 196, in pandas._libs.index.IndexEngine.get_loc
File “pandas/_libs/hashtable_class_helper.pxi”, line 7081, in pandas._libs.hashtable.PyObjectHashTable.get_item
File “pandas/_libs/hashtable_class_helper.pxi”, line 7089, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: ‘relative_abundance’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “MYPATH/.conda/envs/metaphlan4/bin/merge_metaphlan_tables.py”, line 10, in
sys.exit(main())
File “MYPATH/.conda/envs/metaphlan4/lib/python3.10/site-packages/metaphlan/utils/merge_metaphlan_tables.py”, line 73, in main
merge(args.aistms, open(args.o, ‘w’) if args.o else sys.stdout, args.gtdb_profiles)
File “MYPATH/.conda/envs/metaphlan4/lib/python3.10/site-packages/metaphlan/utils/merge_metaphlan_tables.py”, line 36, in merge
profiles_list.append(pd.Series(data=iIn[‘relative_abundance’], index=iIn.index,
File “MYAPTH/.conda/envs/metaphlan4/lib/python3.10/site-packages/pandas/core/frame.py”, line 4090, in getitem
indexer = self.columns.get_loc(key)
File “MYPATH/.conda/envs/metaphlan4/lib/python3.10/site-packages/pandas/core/indexes/base.py”, line 3812, in get_loc
raise KeyError(key) from err
KeyError: ‘relative_abundance’

Any thoughts of how I can troubleshoot this?

Thanks!

2

I found this tutorial: MetaPhlAn 4.1 · biobakery/biobakery Wiki · GitHub

However, the code provided: ```

Merge multiple tables

merge_vsc_tables.py -o OUT.vsc.txt *_vsc.txt


Did not work.

I tried modeling the code after how the merge command is written for relative abundance. This is what worked for me: 

merge_vsc_tables.py profiled_*.txt > OUT.vsc.txt