Roary seemed to have stopped prematurely; any way to continue the run?

[sentausa]

Hi,

I don't know why, my roary run seemed to have stopped too soon after producing gene_presence_absence.Rtab file. Is there a way to continue the run from this point?

This is the command that I used to run it:
roary -p 14 -e --mafft -r -o pan-bacteria -v ./gff/*.gff

And these are the output that I have:
-rw-r--r-- 1 es249628 big 6,5G janv. 11 21:16 gene_presence_absence.Rtab
-rw-r--r-- 1 es249628 big 11G janv. 11 20:10 gene_presence_absence.csv
-rw-r--r-- 1 es249628 big 96M janv. 11 18:34 core_accessory_graph.dot
-rw-r--r-- 1 es249628 big 96M janv. 11 18:21 accessory_graph.dot
-rw-r--r-- 1 es249628 big 123K janv. 11 16:01 _accessory_clusters.clstr
-rw-r--r-- 1 es249628 big 594K janv. 11 16:01 _accessory_clusters
-rw-r--r-- 1 es249628 big 115K janv. 11 15:54 accessory_binary_genes.fa.newick
-rw-r--r-- 1 es249628 big 13M janv. 11 15:51 accessory_binary_genes.fa
-rw-r--r-- 1 es249628 big 368M janv. 11 10:01 pan-bacteria
-rw-r--r-- 1 es249628 big 368M janv. 11 08:45 _labeled_mcl_groups
-rw-r--r-- 1 es249628 big 354M janv. 11 08:45 _inflated_mcl_groups
drwx------ 2 es249628 big 4,0K janv. 11 08:43 2agvKs2tFr
drwx------ 2 es249628 big 188K janv. 11 08:23 07NXVoFAfK
-rw-r--r-- 1 es249628 big 354M janv. 11 07:12 _inflated_unsplit_mcl_groups
-rw-r--r-- 1 es249628 big 43M janv. 11 07:11 _uninflated_mcl_groups
-rw-r--r-- 1 es249628 big 65 janv. 11 06:15 blast_identity_frequency.Rtab
-rw-r--r-- 1 es249628 big 819M déc. 26 10:33 _clustered.clstr
-rw-r--r-- 1 es249628 big 635M déc. 26 10:32 _clustered
-rw-r--r-- 1 es249628 big 6,2G déc. 26 00:47 _combined_files
-rw-r--r-- 1 es249628 big 0 déc. 24 12:45 _combined_files.groups

The 07NXVoFAfK directory contains .gff.proteome.faa files, while 2agvKs2tFr contains "group" files.

Thanks in advance for your kind help.

[andrewjpage]

Hi, It can sometimes be possible to restart and run the other roary scripts (roary-*), however looking at the enormous file sizes for your gene_presense_absense.Rtab file I suspect theres something up with your input data. I would double check that all your samples are from the same species and QC the input data. Regards, Andrew

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On 12 January 2018 at 09:44, sentausa ***@***.***> wrote: Hi, I don't know why, my roary run seemed to have stopped too soon after producing gene_presence_absence.Rtab file. Is there a way to continue the run from this point? This is the command that I used to run it: roary -p 14 -e --mafft -r -o pan-bacteria -v ./gff/*.gff And these are the output that I have: -rw-r--r-- 1 es249628 big 6,5G janv. 11 21:16 gene_presence_absence.Rtab -rw-r--r-- 1 es249628 big 11G janv. 11 20:10 gene_presence_absence.csv -rw-r--r-- 1 es249628 big 96M janv. 11 18:34 core_accessory_graph.dot -rw-r--r-- 1 es249628 big 96M janv. 11 18:21 accessory_graph.dot -rw-r--r-- 1 es249628 big 123K janv. 11 16:01 _accessory_clusters.clstr -rw-r--r-- 1 es249628 big 594K janv. 11 16:01 _accessory_clusters -rw-r--r-- 1 es249628 big 115K janv. 11 15:54 accessory_binary_genes.fa. newick -rw-r--r-- 1 es249628 big 13M janv. 11 15:51 accessory_binary_genes.fa -rw-r--r-- 1 es249628 big 368M janv. 11 10:01 pan-bacteria -rw-r--r-- 1 es249628 big 368M janv. 11 08:45 _labeled_mcl_groups -rw-r--r-- 1 es249628 big 354M janv. 11 08:45 _inflated_mcl_groups drwx------ 2 es249628 big 4,0K janv. 11 08:43 2agvKs2tFr drwx------ 2 es249628 big 188K janv. 11 08:23 07NXVoFAfK -rw-r--r-- 1 es249628 big 354M janv. 11 07:12 _inflated_unsplit_mcl_groups -rw-r--r-- 1 es249628 big 43M janv. 11 07:11 _uninflated_mcl_groups -rw-r--r-- 1 es249628 big 65 janv. 11 06:15 blast_identity_frequency.Rtab -rw-r--r-- 1 es249628 big 819M déc. 26 10:33 _clustered.clstr -rw-r--r-- 1 es249628 big 635M déc. 26 10:32 _clustered -rw-r--r-- 1 es249628 big 6,2G déc. 26 00:47 _combined_files -rw-r--r-- 1 es249628 big 0 déc. 24 12:45 _combined_files.groups The 07NXVoFAfK directory contains .gff.proteome.faa files, while 2agvKs2tFr contains "group" files. Thanks in advance for your kind help. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#380>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeV8PFCYI496WlJUseAjvh0D4NN2vIks5tJylugaJpZM4RcCnM> .

[sentausa]

Actually they are from the same genus, different species. The whole genus. Roary doesn't like that?

If I want to continue anyway, how to run the other roary scripts? Where can I find them? I just want to get the core_gene_alignment.aln file to make tree later.

Thanks very much.

[andrewjpage]

Roary is is tuned for the same species. For more diverse datasets you'll need to play around with the the identity and the inflation factor (different for every genus). I wouldn't try to continue in this instance ( the scripts are probably in your path if you type roary- then tab complete). I would recommend you QC your assemblies first, then test a small subset (its quick) and go from there.

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On 12 January 2018 at 09:57, sentausa ***@***.***> wrote: Actually they are from the same genus, different species. The whole genus. Roary doesn't like that? If I want to continue anyway, how to run the other roary scripts? Where can I find them? Thanks very much. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#380 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeVwzN7yOOUIwGOCfInyLPMHIwoC7jks5tJyx6gaJpZM4RcCnM> .

[sentausa]

So you mean that roary failed to produce the alignment? Because I couldn't see anything that indicates that it was done during the run.

[andrewjpage]

It failed before producing an alignment. The cause is likely to be your input data.

[sentausa]

Does it have anything to do with the fact that there are many draft genomes in my data? Do you think it'll be better if I use only complete genomes?

Thank you again.

[andrewjpage]

I use draft genomes all of the time and its not a problem. Have you QC'd your assemblies? For example removing highly fragmented assemblies, assemblies that are too big/small, checked the species is as expected or if there is contamination etc...

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On 12 January 2018 at 13:34, sentausa ***@***.***> wrote: Does it have anything to do with the fact that there are many draft genomes in my data? Do you think it'll be better if I use only complete genomes? Thank you again. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#380 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeVwV9r90xDwT3ag6nTJSN-h8YVPupks5tJ19YgaJpZM4RcCnM> .

[sentausa]

I'm reusing publicly available genomes from a whole genus, and it's true that there are highly fragmented assemblies. So well, I think I'll try to remove them. Or it might be easier to just ignore the draft genomes.... I just need a global picture of the genus anyway.

Thank you for all your help!

Regards,