reat2tree run seems to go well but species not added to the tree.

[mathildeparis]

Hi,

I've tried to run the read2tree pipeline but got no results.
The installation and run test were fine. I tried the Multiple species mode with two samples species1 and species2. The procedure seemed to go well (it ran with no errors) but the files species1_Lib_all_sc.txt and species1_Lib_all_cov.txt did not contain any numerical values (just the name of the different fields). Same for species2. The merged tree did not include species1 and species2.

Do you have an idea of what went wrong?

Thank you in advance,

Mathilde

[sinamajidian]

Hi Mathilde,

Thanks for using Read2Tree. Could you please share the output log of all steps with us. It should tell us which version of read2tree you are using and some other stats which helps us to debug.

Also, I'm wondering how many species and gene markers you downloaded from OMA browser. We also need to know how close species1/2 is to the species in the reference gene marker. At some point it might be useful to know the sequencing coverage of the sample? sth like cov= (number of reads)*(read length)/ (genome size).

Best,
Sina

[mathildeparis]

Thanks for the quick answer!
I'll need to rerun the pipeline for the output.
The read2tree version is 2.0.1.
I downloaded 200 markers and 73 species (all Hexapoda + Crustacea).
species1/2 are hyalid amphipods (Crustaceans), but not particularly close to the species in the reference markers (several hundreds of millions of years apart).
I just did a low coverage run for my first run (coverage around 1.5x).

Thank you!
Mathilde

[sinamajidian]

I see. Are there any closer species to "hyalid amphipods" in the OMA browser?
Probably these two reasons (distant reference and low coverage) resulted in no mapped reads on gene markers and thus MSA without species1/2, and no tree.
If you are not limited in computation resources, adding more gene markers (e.g. 500 or 1000), closer species, more coverage (>20x or 40x) should help in general. I hope this would be the case here as well.
It would be useful to include one or 2 outgroups in gene markers, so we could do rooting of the final tree (The output of Read2Tree/IqTree is unrooted).

You could use this at the end of your command line to save the full log.

read2tree ...     >> r2t.log 2>&1  

[mathildeparis]

I took all the (pancruscea) species available on OMA.
I'll try with more gene markers and reads, thanks for the advice (and I'll let you know if it worked)!