AttributeError: 'str' object has no attribute 'id'

[oona...@gmail.com]

Hi,

I installed PhyloPhlAn with correct versions and run the example successfully, but when i run my own data, something was wrong with it, here is the result

./phylophlan.py -u shiyan11

All usearch runs already performed!

Mapping finished in 0 secs.

All alignments already computed!

Aligning finished in 0 secs (0 total time).

Traceback (most recent call last):

  File "./phylophlan.py", line 803, in <module>

    aln_merge(projn,pars['integrate'])

  File "./phylophlan.py", line 525, in aln_merge

    v.id = k

AttributeError: 'str' object has no attribute 'id'

but i use the 16S rDNA V3-V4 sequence instead of whole-genome sequence, i wonder if that is why i can't run it successfully

Thanks

Ou

[Francesco Asnicar]

Hi Ou,
unfortunately PhyloPhlAn won't work on 16S data, because PhyloPhlAn tries
to extract the phylogenetic signal from the inputs, using the markers in
the database. The markers however, are proteins and they do not cover the
16S.
For your 16S data you can simply align you input sequences (shouldn't be
too long, ~500 nt) and build a phylogeny from the alignment using FastTree
or RAxML, or you can use some other standard pipeline from QIIME, for
instance.

Many thanks,
Francesco

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[ou ou]

Hi Francesco,

Oh, i see and thanks for your advice!

Thanks again for your patient!

Ou

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