# Unable to merge virus profile.txt files into table
**URL:** https://forum.biobakery.org/t/unable-to-merge-virus-profile-txt-files-into-table/6848
**Category:** MetaPhlAn
**Created:** [March 26, 2024, 1:32am UTC](https://forum.biobakery.org/t/unable-to-merge-virus-profile-txt-files-into-table/6848 "2024-03-26T01:32:51Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@young\_doktor](https://forum.biobakery.org/u/young_doktor)
#### Post date: [March 26, 2024, 1:32am UTC](https://forum.biobakery.org/t/unable-to-merge-virus-profile-txt-files-into-table/6848/1 "2024-03-26T01:32:51Z")
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
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!
---
### Author:  [@young\_doktor](https://forum.biobakery.org/u/young_doktor)
#### Post date: [March 26, 2024, 11:56pm UTC](https://forum.biobakery.org/t/unable-to-merge-virus-profile-txt-files-into-table/6848/2 "2024-03-26T23:56:42Z")
I found this tutorial: [MetaPhlAn 4.1 · biobakery/biobakery Wiki · GitHub](https://github.com/biobakery/biobakery/wiki/MetaPhlAn-4.1#3-metaphlan-viral-module-tutorial)
However, the code provided: ```
# Merge multiple tables
merge\_vsc\_tables.py -o OUT.vsc.txt \*\_vsc.txt
```auto
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
```
---
### Author:  [@fconstancias](https://forum.biobakery.org/u/fconstancias)
#### Post date: [November 24, 2025, 8:37pm UTC](https://forum.biobakery.org/t/unable-to-merge-virus-profile-txt-files-into-table/6848/3 "2025-11-24T20:37:38Z")
Hello,
I am also facing an error when trying to merge the VSC tables:
merge\_vsc\_tables.py X204SC250\*/S\_\*/\*\*\_vsc\_metagenome.txt -o merged\_vsc\_tables.txt
Traceback (most recent call last):
File “/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2/bin/merge\_vsc\_tables.py”, line 10, in
sys.exit(main())
^^^^^^
File “/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2/lib/python3.12/site-packages/metaphlan/utils/merge\_vsc\_tables.py”, line 99, in main
merge(args.aistms, fout, options)
File “/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2/lib/python3.12/site-packages/metaphlan/utils/merge\_vsc\_tables.py”, line 69, in merge
out\_table = pd.pivot\_table(
merged\_tables,
index=indexes\_for\_pivot,
columns=‘sampleID’,
values=groupby\_field
)
File “/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2/lib/python3.12/site-packages/pandas/core/reshape/pivot.py”, line 102, in pivot\_table
table = \_\_internal\_pivot\_table(
File “/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2/lib/python3.12/site-packages/pandas/core/reshape/pivot.py”, line 172, in \_\_internal\_pivot\_table
grouped = data.groupby(keys, observed=observed\_bool, sort=sort, dropna=dropna)
File “/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2/lib/python3.12/site-packages/pandas/core/frame.py”, line 9190, in groupby
return DataFrameGroupBy(
File “/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2/lib/python3.12/site-packages/pandas/core/groupby/groupby.py”, line 1329, in **init**
grouper, exclusions, obj = get\_grouper(
File “/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2/lib/python3.12/site-packages/pandas/core/groupby/grouper.py”, line 1043, in get\_grouper
raise KeyError(gpr)
KeyError: ‘Annotation’
(/work/FAC/FBM/DBC/slehtine/stool\_sampling/tools/mpa4.2.2) metaphlan --version
MetaPhlAn version 4.2.2 (4 Jun 2025)
Any help would be appreciated !
---
### Author:  [@lindacova](https://forum.biobakery.org/u/lindacova)
#### Post date: [November 27, 2025, 10:00am UTC](https://forum.biobakery.org/t/unable-to-merge-virus-profile-txt-files-into-table/6848/4 "2025-11-27T10:00:49Z")
Hi @fconstancias ,
I think there was a bug in the `merge_vsc_tables` script in MetaPhlAn version 4.2.2, which has been fixed in the newer versions.
You can either update the whole MetaPhlAn package or find the fixed script for merging vsc tables here: [https://github.com/biobakery/MetaPhlAn/blob/master/metaphlan/utils/merge\_vsc\_tables.py](https://github.com/biobakery/MetaPhlAn/blob/master/metaphlan/utils/merge_vsc_tables.py)
Hope this was helpful!
Linda