export2graphlan error

[ZhangMin-123]

Hi,

I'm trying to use export2graphlan on my humann3 abundance table output. but when I RUN:
"Traceback (most recent call last):
File "/home/meta/miniconda2/envs/meta/bin/export2graphlan.py", line 768, in
main()
File "/home/meta/miniconda2/envs/meta/bin/export2graphlan.py", line 511, in main
lefse_input = DataMatrix(args.lefse_input, args)
File "/home/meta/miniconda2/envs/meta/bin/hclust2.py", line 149, in init
index_col = self.args.sname_row if self.args.sname_row > -1 else None
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 678, in parser_f
return _read(filepath_or_buffer, kwds)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 446, in _read
data = parser.read(nrows)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 1036, in read
ret = self._engine.read(nrows)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 1886, in read
values = data.pop(self.index_col[i])
IndexError: list index out of range".
物种.xlsx

Any ideas what's going wrong?
Thanks in advance!

[fasnicar]

Hi, can you please provide the full command and also the input file(s) you're using?

[ZhangMin-123]

export2graphlan.py --skip_rows 1,2 -i taxonomy.tsv \

  --tree temp/merged_abundance.tree.txt \
  --annotation temp/merged_abundance.annot.txt \
  --most_abundant 1000 --abundance_threshold 20 --least_biomarkers 10 \
  --annotations 3,4 --external_annotations 7

Traceback (most recent call last):
File "/home/meta/miniconda2/envs/meta/bin/export2graphlan.py", line 768, in
main()
File "/home/meta/miniconda2/envs/meta/bin/export2graphlan.py", line 511, in main
lefse_input = DataMatrix(args.lefse_input, args)
File "/home/meta/miniconda2/envs/meta/bin/hclust2.py", line 149, in init
index_col = self.args.sname_row if self.args.sname_row > -1 else None
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 678, in parser_f
return _read(filepath_or_buffer, kwds)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 446, in _read
data = parser.read(nrows)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 1036, in read
ret = self._engine.read(nrows)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 1886, in read
values = data.pop(self.index_col[i])
IndexErrotaxonomy.xlsx

[timj6599]

i got the same error. any fixes?

[fasnicar]

It could be due to the presence of the NCBI_tax_ID column. Can you check if removing it will solve it? In this case, I can implement a code fix for this case.

Thanks,
Francesco