phylophlan.fna is empty

[Jiffin Paulose]

Hello again!

Thanks to you, I am cranking out trees using proteomes with no problems!  However, I wanted to compare proteome-level and genomic-level analyses, and so am trying to use the supertree_nt.cfg I kept getting an error at the makeblastdb stage, so I went back to our conversations and started searching files.  I found that phylophlan.fna is empty, so I deleted the contents of phylophlan_databases, allowed the program to download the .tar and .md5 file, but the .fna file is still empty.  Any suggestions?  Thanks again!

J.

[Francesco Asnicar]

Hello Jiffin,

I think the config filename could be misleading... Sorry about that! The supertree_nt.cfg is meant to be used for a supertree approach when the marker genes in the database are nucleotides.

So, if you want to perform a phylogenomic analysis using the PhyloPhlAn database (which is amino acids) when inputs can be either/both proteomes and genomes, you simply need to make sure that the [map_dna] section is present in the configuration file.

In the case of the PhyloPhlAn database the configuration there should consider a tool able to do a translated search like, tblastn or diamond.

If you ran the phylophlan_write_default_configs.sh script the supertree_aa.cfg configuration file shuold already have the [map_dna] section.

Please, let me know if something is not clear.

Many thanks,

Francesco

--
You received this message because you are subscribed to the Google Groups "PhyloPhlAn-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phylophlan-use...@googlegroups.com.
To post to this group, send email to phylophl...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/e8e172e5-69a2-4326-8f9b-0673afd9abaa%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Kevin Lee]

Dear Francesco,

I've fallen into the same trap as well. So, if I understand correctly, supertree_aa or supermatrix_aa can actually handle nucleotide input data when using an amino acid database (e.g. phylophlan). 

So I've attempted to do:

phylophlan2.py -i input/Arthrobacter -d phylophlan --diversity low -f phylophlan_configs/supermatrix_aa.cfg --verbaes

I got the following error, but that turned out that my version of diamond was out of date (does not have --max-hsps)

[e] Command '['diamond', 'blastx', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', '/home/kevinl/phylophlan/input/Arthrobacter/B4.fna', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', 'Artobacter_phylophlan/tmp/map_dna/B4.b6o.bkp']' returned non-zero exit status 1

Once upgrading diamond to the newest version, phylophlan2 was able to map the DNA.

[Francesco Asnicar]

Dear Kevin,

Many thanks for reporting this. Can you tell me which version of Diamond was giving you trouble? I can think to add an ad-hoc check for diamond and report an error in the case of old versions.

Many thanks,

Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/d9ae3b7a-b0c9-4dcf-9ae5-e9aa38a791d8%40googlegroups.com.

[Kevin Lee]

Dear Francesco,

Unfortunately, I just overwritten the the binary (yay to messy single user system). However, according to diamond's changelog:

0.8.31 -

removed --single-domain option and replaced by --max-hsps

0.8.31 (released in 1 Jan 2017) was the first occurrence of the option.

Kind regards,

Kevin

[Francesco Asnicar]

Dear Kevin,

No problem, many thanks for checking the changelog in diamond. I'll add a check about the damond version in the next commit.

Thanks,

Francesco

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/48079eb0-61d1-4c48-a256-da7a871c14c7%40googlegroups.com.