CheckM merge: empty merger.tsv file

[domenico-simone]

Hello,

I am trying to run checkm merge on some data but it returns an empty merger.tsv file, while all the other output files look normal. The bins I'm trying to merge as supposed to belong to the same species, based on ANI/AAI values and their placement on phylogenetic tree. What can be the problem?

Many thanks for your kind support,

Domenico

[donovan-h-parks]

Is the merge file completely empty or just has a header line in it?

[domenico-simone]

Hi, it has just the header. Thanks Domenico 2017-11-29 16:59 GMT+01:00 Donovan Parks <notifications@github.com>:

…

Is the merge file completely empty or just has a header line in it? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#125 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKwX3Lml3deMJY5w08VtoAq0Fnv8JDRyks5s7X91gaJpZM4QvIfa> .

-- Domenico Simone, PhD Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS) Department of Biology and Environmental Science Barlastgatan 11 392 31 Kalmar Sweden Skype: berliner_08

[domenico-simone]

Hi again, I forgot to mention that I'm working on an Ubuntu 16.04.2 LTS machine, if that can be useful. 2017-11-29 17:33 GMT+01:00 Domenico Simone <domenico.simone@lnu.se>:

…

Hi, it has just the header. Thanks Domenico 2017-11-29 16:59 GMT+01:00 Donovan Parks ***@***.***>: > Is the merge file completely empty or just has a header line in it? > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#125 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AKwX3Lml3deMJY5w08VtoAq0Fnv8JDRyks5s7X91gaJpZM4QvIfa> > . > -- Domenico Simone, PhD Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS) Department of Biology and Environmental Science Barlastgatan 11 392 31 Kalmar Sweden Skype: berliner_08

-- Domenico Simone, PhD Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS) Department of Biology and Environmental Science Barlastgatan 11 392 31 Kalmar Sweden Skype: berliner_08

[donovan-h-parks]

This indicates that CheckM did not find any bins that it could merge together. You can try loosening the criteria CheckM uses to allow two bins to be merged together, though I don't recommend this as it can easily lead to chimeric bins.