Genome storage for genomes with no HMM sources

[ShaiberAlon]

I tried running anvi-gen-genomes-storage on two phage genomes that have no hmm hits. And I got the following error:

Running command: anvi-gen-genomes-storage -e external_genomes.txt -o phage-GENOMES.h5

WARNING
===============================================
None of your genomes seem to have any functional annotation. No biggie. Things
will continue to work. But then your genomes have no functional annotation. SAD.

Internal genomes .............................: 0 have been initialized.
External genomes .............................: 2 found.

Config Error: There are no HMM sources among your external genomes that occur in every genome
              :/

I don't understand why it cares whether there are HMM sources among your external genomes that occur in every genome or not.

[meren]

Hi @ShaiberAlon, I hope this fixes it :)

[ShaiberAlon]

Thank you very much Meren, I'm re-running now, and will let you know if I run into trouble.

On Sat, Aug 12, 2017 at 5:22 PM, A. Murat Eren notifications@github.com wrote:

Hi @ShaiberAlon https://github.com/shaiberalon, I hope this fixes it :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/573#issuecomment-322009526, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ18dNrd6yc1OGtEiQZncrKV6QJH57JMks5sXiWQgaJpZM4O1dYK .

[ShaiberAlon]

Actually,

I still got this error:

Running command: anvi-gen-genomes-storage -e external_genomes.txt -o
crassphage-GENOMES.h5

WARNING
===============================================
None of your genomes seem to have any functional annotation. No biggie.
Things
will continue to work. But then your genomes have no functional annotation.
SAD.

Internal genomes .............................: 0 have been initialized.
External genomes .............................: 2 found.

Config Error: Some of the genomes you have for this analysis are missing
HMM hits for SCGs (1
              of 2 of them, to be precise). You can run `anvi-run-hmms` on
them to recover
              from this. Here is the list: crassphage

Job exit status: 255
Warning: job exited non-zero: 255

On Sat, Aug 12, 2017 at 10:47 PM, Alon Shaiber alon.shaiber@gmail.com wrote:

Thank you very much Meren, I'm re-running now, and will let you know if I run into trouble.

On Sat, Aug 12, 2017 at 5:22 PM, A. Murat Eren notifications@github.com wrote:

Hi @ShaiberAlon https://github.com/shaiberalon, I hope this fixes it :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/573#issuecomment-322009526, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ18dNrd6yc1OGtEiQZncrKV6QJH57JMks5sXiWQgaJpZM4O1dYK .

[meren]

Hi Alon,

As a temporary workaround, can you please not run anvi-run-hmms on these genomes at all?

Sorry about this.

[ShaiberAlon]

Of course !

Thanks!

On Sat, Aug 12, 2017 at 10:51 PM, A. Murat Eren notifications@github.com wrote:

Hi Alon,

As a temporary workaround, can you please not run anvi-run-hmms on these genomes at all?

Sorry about this.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/573#issuecomment-322020125, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ18dHRhAQ-x-wH8Pm55FCh9_N1kL9knks5sXnKvgaJpZM4O1dYK .