Hi there! I’m using panphlan v3.1 and I’ve noticed that many of the annotation files I downloaded from Dropbox appear to have extra headers appended to the end of some lines. For example:
$ grep “NR90” panphlan_Escherichia_coli_annot.tsv | head -n 5
NR90 NR50 GO KO KEGG Pfam EC eggNOG
UniRef90_A0A0T5XRC3 UniRef50_A0A3A1V9Q0 PF06183 NR90 NR50 GO KO KEGG Pfam EC eggNOG
UniRef90_A0A0U4J0F4 UniRef50_A0A0U4J0F4 GO:0009401,GO:0016021 PF03613 NR90 NR50 GO KO KEGG Pfam EC eggNOG
UniRef90_A0A0U4J0F4 UniRef50_A0A0U4J0F4 GO:0009401,GO:0016021 K10986 cfar:CI104_03015 PF03613 NR90 NR50 GO KO KEGG Pfam EC eggNOG
UniRef90_A0A0U4J0F4 UniRef50_A0A0U4J0F4 GO:0009401,GO:0016021 K10986 eal:EAKF1_ch2793c PF03613 NR90 NR50 GO KO KEGG Pfam EC eggNOG
panphlan_download_pangenome.py wasn’t working for me (probably due to some aspect of how our cluster is configured) so I instead downloaded pangenomes from Dropbox here: Dropbox - panphlan_3_pangenomes_tar - Simplify your life
Is this the correct Dropbox link with the most recent versions of pangenomes and the corresponding annotation files?
I’m not sure if this causes panphlan to fail as I haven’t tried with the --func_annot option yet. I only noticed when trying to read the pangenome annotation files into R
Many thanks,
Fiona