Panphlan duplicate sequences

Microbial community profiling PanPhlAn
1

Hi there, I am running panphlan v3.1 installed via conda, and when I profile samples with the Prevotella_copri pangenome, I get the following duplicated sequence warnings after panphlan_map.py (the step appears to finish correctly and produce output):

[W::sam_hdr_parse] Duplicated sequence 'GG703878.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703877.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703876.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703875.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703874.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703873.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703872.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703871.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703870.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703869.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703868.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703867.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703866.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703865.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703864.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703863.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703862.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703861.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703860.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703859.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703858.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703857.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703856.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703855.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703854.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703853.1'
[W::sam_hdr_parse] Duplicated sequence 'GG703852.1'

Indeed, several sequences in Prevotella_copri_pangenome_contigs.fna appear to be duplicated: is this a concern for the reliability of the resulting output?

Thanks!
Fiona

2

Hello Fiona,

indeed this kind of warning appear for some species, sometimes as warning, sometimes it makes the mapping fail (kind of a random issue yet to be fixed).
It is not a problem for the analysis since the issue is anyway neutralized by the normalization during the profiling process. However, if this is a problem anyhow (with other species for example, or to prevent the flood of warnings messages :smile:), I’ve recently added a small script in the PanPhlAn repository on GitHub called panphlan_clean_pangenome.py that will regenerate a “clean” pangenome. Just use :
panphlan_clean_pangenome.py --species Prevotella_copri --pangenome [path to the pangenome folder]

Hope this will be helpful.
Léonard

3

Thanks Léonard, I appreciate your reply! That’s helpful to know, thanks for linking to the cleaning script!

Best,
Fiona