Submitting annotated metagenome to NCBI; tbl2asn

Question

[robert.waller.murdoch]

Hi folks, looking for some feedback/advice here;

Basics of the situation:

I have a large (140mb, 49,000 contigs) annotated (140,000 features) metagenome that I'd like to upload to NCBI. I ran it through prokka, then went in and added a handful of custom annotations to the *.tbl file. Consequently, the contig-fasta and tbl file need to be run through the tbl2asn gauntlet again. I'm using the following code for tbl2asn (latest version downloaded from NCBI FTP):

tbl2asn \
-i mgenome.contigs.fna \
-f annotations.tbl \
-t template.sbt -o mgenome.asn -V vbt \
-s T -m B -l paired-ends -a r10k -W T \
-y 'Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka'

Here's the issue:

As a trial, I ran thorough a trial tbl2asn using only the first contig (which includes some of the custom annotations) and went through genbank submission to the final steps; the .asn file was successfully validated and everything looks good. However, when I apply tbl2asn on the entire assembly/annotation, it simply does not complete. CPU remains 100% utilized, RAM remains occupied, but the process does not complete and there is no informative stdout feedback or logfile generated.

I have actually completed such a process before, but with a much smaller metagenome assembly.

1. Has anybody successfully run an assembly of this scale through tbl2asn succesfully?
2. Any idea why this might be getting hung up? (I can't provide the files themselves for trials unfortunately)

Any feedback or advice will be much appreciated!

[robert.waller.murdoch]

Update (sort of solved):

I ran the same command on a Macbook instead of Ubuntu laptop, both 16Gb RAM systems, just in the hope that the mac version of the program wouldn't have the same problem. There was no obvious different. I noticed that even though the RAM was not totally maxed out, it was using a good deal of virtual (swap) memory, which could explain the slowness. Therefore, I set this running on a more powerful desktop (64Gb RAM) and left it over the weekend. It finished up after ~3 days and passed NCBI asn validation checks. However, even though it had tons of RAM real-estate, it kept using a lot of swap memory and really didn't seem to process much faster.

The conclusion I suppose is that yes, it will complete, but be prepared to wait.