Problem with metaphlan2krona.py

Hi,

I fed the Metaphlan output to metaphlan2krona.py but I got the following error. Is there anything I need to do with the output file from metaphlan?

Thanks!

Error:

Traceback (most recent call last):
  File "/pub59/jingk/miniconda3/envs/metaphlan4/bin/metaphlan2krona.py", line 10, in <module>
    sys.exit(main())
  File "/pub59/jingk/miniconda3/envs/metaphlan4/lib/python3.10/site-packages/metaphlan/utils/metaphlan2krona.py", line 42, in main
    abundance = float(x_cells[-2].rstrip('\n')) 
ValueError: could not convert string to float: 'Bradyrhizobium'
(metaphlan4) jingk@ada18:/pub59/jingk/04_chigger_mito01/07_metaphlan$ metaphlan2krona.py -p metaphlan4_out.txt -k R9P_metaphlan4_krona.out 
Traceback (most recent call last):
  File "/pub59/jingk/miniconda3/envs/metaphlan4/bin/metaphlan2krona.py", line 10, in <module>
    sys.exit(main())
  File "/pub59/jingk/miniconda3/envs/metaphlan4/lib/python3.10/site-packages/metaphlan/utils/metaphlan2krona.py", line 42, in main
    abundance = float(x_cells[-2].rstrip('\n')) 
ValueError: could not convert string to float: 'Bradyrhizobium'
(metaphlan4) jingk@ada18:/pub59/jingk/04_chigger_mito01/07_metaphlan$ metaphlan2krona.py -p metaphlan4_out.txt -k R9P_metaphlan4_krona.out 
Traceback (most recent call last):
  File "/pub59/jingk/miniconda3/envs/metaphlan4/bin/metaphlan2krona.py", line 10, in <module>
    sys.exit(main())
  File "/pub59/jingk/miniconda3/envs/metaphlan4/lib/python3.10/site-packages/metaphlan/utils/metaphlan2krona.py", line 42, in main
    abundance = float(x_cells[-2].rstrip('\n')) 
ValueError: could not convert string to float: 'Bradyrhizobium'

More info if it helps:

$ metaphlan --version
MetaPhlAn version 4.0.3 (24 Oct 2022)

Command used to run Metaphlan:

metaphlan R1.fastq.gz,R2.fastq.gz --bowtie2out R1.bowtie2.bz2,R2.bowtie2.bz2 --nproc 5 --input_type fastq --unclassified_estimation -o metaphlan4_out.txt &

Command used to run metaphlan2krona.py:

metaphlan2krona.py -p metaphlan4_out.txt -k R9P_metaphlan4_krona.out 

Hi @khoojj
I will have a look into the problem (it seems some changes in the code when moving to version 4 had affected the konda exporter script) I will keep you updated when the new version fixing this issue is available

That will be great! Thanks!