Disclaimer

The story, all names, characters, genomes and incidents portrayed in this blog post are fictitious.
No identification with actual persons (living, dead or undead), places, companies, and processes is intended or should be inferred.
No animals were harmed in the making of this blog post.

Let’s try answering a question:

why are there many incomplete/draft bacterial genomes, and much fewer complete genomes?

The answer is simple: insufficient value/cost ratio.
This can also be summarized as the good enough principle: if something is good enough, it does not get improved.

Sample scenario 1.
Players: Principal Investigator (PI), Bacterial Genome (BG), Biologist (B), Sequencing Company (SC), (optional) Bioinformatician (oBI), Genomes Database (GD).

B is interested to work with BG, and gets PI‘s approval to sequence it.
Biomaterial is sent to SC, which sequences and even assembles the BG.
BG looks overall great and comes in just a handful fragments.
oBI is (optionally) involved, to annotate and describe the BG.
B works happily with the BG, describing and characterizing all the interesting biosynthetic features it contains.
An article is prepared, and oBI is (optionally) involved again, to prepare and submit the BG to the GD.
Preparing the BG, oBI has to answer a question if this BG contains any plasmids.
Upon closer examination, oBI finds that one of the fragments is actually the complete chromosome, and all others are just unplaced fragments of it.
oBI knows that this genome could probably be merged into a single draft scaffold
using bioinformatics tools and manual examination in maybe a few days (or a week… or two? ).
oBI also knows that with a little bit of B‘s help (a few primer walking experiments) it should be possible to have the complete BG within a month or two.
However, BG stays a draft, and is not going to be complete any time soon.

Why?

Let’s look at motivations of all the players, and see if any of the players wants the complete BG:

• PI wants publications; spending extra time/effort to make BG complete does not present any obvious benefits;
• BG wants to be left alone;
• B wants to publish exciting new findings; they are already supported by the draft BG, so there is clearly no need for a complete BG;
• SC was happy to get payment in time; SC is also proud to be able to provide genome assembly as an extra service with its (primary) sequencing offers;
• oBI has interest in finishing the BG: it will then be complete; however, there are 5 more other BGs awaiting processing, and the backlog of semi-written manuscripts only keeps growing… finishing this specific BG will not result in a perceived benefit to oBI;
• GD stores genomes; it doesn’t care much if the genome submitted could have been better.

Surprise!
Looks like none of the players sees benefits in actually finishing the BG,
simply because efforts spent (or time waited) does not bring any perceived benefits to any of the players.

Sample scenario 2.
Players: Bacterial Genome (BG), Biologist (B), Sequencing Company (SC), non-optional Bioinformatician (noBI), Genomes Database (GD).

This time, B (who is interested in quickly publishing a short genome announcement) asks for noBI‘s help from the moment the BG is provided by the SC.
noBI has a cursory look at the BG, and although there is a huge discrepancy between thousands of contigs on the one hand and insanely high coverage on the other,
the BG otherwise appears good enough for further work, especially after scaffolding; after all, this is just a genome announcement, not a full-blown article!
There is also some weirdness about the coverage distribution of the BG, but noBI carelessly ignores that.
The BG is worked on: annotated, examined, described, prepared for submission to the GD.
Meanwhile, the announcement article is also nearly complete.
Genome is submitted, and GD‘s response comes back: some scaffolds contain orangutan and human DNA, and some scaffolds contain known adapter sequences in the middle…
“Oh crap“, thinks noBI, “I should have checked the raw reads for adapters and contamination, in spite of having the BG assembly already…”
The GD also kindly offers an easy way out: just remove the obviously-orangutan scaffolds, and remove/mask/discard adapter sequences.
This is the easy way, leading to a quicker genome announcement, and a slight bump to the personal publication records of both B and noBI.

The right way is, of course, to clean raw reads from adapters and contamination, re-assemble, re-scaffold, re-annotate, re-describe the BG,
then prepare again for submission. This can delay the quick genome announcement by about a week,
but will highly likely result in a more contiguous and more correct BG – although still not complete.

As we have learned from Scenario 1, perceived benefits of going the right way (as opposed to the easy way) are nearly non-existent…

There was a genome I have finalized manually a few years ago.
I had some good quality data, obtained a 300-something contigs initial assembly,
then scaffolded and manually finalized to about 10 scaffolds.
There was simply not enough evidence (data) to keep merging scaffolds, so I had to stop.

Nowadays, as bacterial genome sequencing prices are akin to weekend supermarket shopping expenses,
nobody is going the extra mile to produce a better quality, more contiguous, or even a complete genome.
And this feels sad…

On the other hand, consumer markets function like that for decades.
An old water heater with a failed heating element is not repaired: it is replaced by a new water heater,
because human time cost to repair the old one is higher than just buying a new one.

Funnily, universal basic income might change that: without the need to spend 40+ hours a week at work
(and thus being unable to repair that water heater on one’s own),
one might just order that heating element and fix it – instead of buying the new one.

Would universal basic income have the same effect on draft and incomplete bacterial genomes? I have no idea.

I buy a lot on amazon.de – this is easy and convenient. Most of the time it also works good, with items arriving as promised or (mostly) earlier. Sometimes there are minor problems, but nothing worth remembering or mentioning. However, my latest order, “delivered” by Hermes Paketversand, was such a spectacular failure, that it deserves a blog post.

My item was expected to arrive on Tuesday, the 5th of August. In the evening of that day we found an important message from Hermes in our mailbox, saying that We were unable to deliver your package, we come again tomorrow, on the 6th of August. Hmmm. That is strange. My wife was at home in the 1st half of the day, when Hermes, supposedly, was delivering my package (I learned about their delivery time later from delivery tracking page). This is what I would call a minor problem, not really an issue. Maybe, for some reason, the door bell wasn’t heard, and our delivery did not reach us. But it comes next day, right? Right?…

There was absolutely nothing – not even a note – delivered in the following 4 days. On Saturday I started worrying. I checked Amazon package delivery status (detailed), which said that we have missed 3 (!) delivery attempts between 9:00 and 13:00 on August 5-7. I could have believed one miss, but three in a row, with my wife at home… that is extremely strange, to say the least. Anyway, I was ready to forgive this, as long as I get the package.

Previous packages, when their delivery failed, were usually left at the nearest Paketshop (pickup place), which is about 7 minutes walking from where I live. There were absolutely no notes left about the whereabouts of my package, so I assumed it is in that Paketshop, and walked there. But the package was not there.

I then explored the Hermes Paketversand website, and did find a form to ask about the location of the package. I had thoroughly, as I usually do, filled in the form, including my email and phone number. I have explained the absence of any notification about the package whereabouts, and asked to deliver the package to that Paketshop not far from me. I have never received any response to that form.

To be extra safe, I also enabled Amazon‘s SMS notifications about delivery status changes. Never needed them before, but this was already a special case.

After a day or two, I received an SMS from Amazon, saying that delivery requires my interaction to proceed. On the amazon.de I was told that delivery failed and I need to contact Hermes to resolve the issue. Amazon does give the phone number. Interestingly, on the Hermes Paketversand website there are no phone numbers, only the (apparently ignored or dysfunctional) feedback form.

The phone number costs up to 0.6 EUR to call from cell phone. I had already paid for shipping when ordering, so it is really surprising that I have to pay again to ask where the shiny paradise my package is.

Anyway, it was a small gift for a friend, so I called and arranged the delivery to that Paketshop I like.

I was already deeply unsatisfied with Hermes, but had this failure ended here, I would have never written this piece.

On the 14th of August I get 2 SMSs from Amamzon saying that my package is ready to be picked up. “Hurray!”, I think. Next day was a holiday, so I planned the pickup for early Saturday. After getting the package I intended to have a haircut, and then depart for my vacations.

The package was not there. Not in the Paketshop I was told it will arrive to, making a toll phone call.

I had no choice other than to call Hermes again. (Hermes seems to enjoy leaving customers no choice.) This time, I was told that the package is in a different Paketshop. I kept, in vain, asking “But why is it in a different Paketshop?…”, only to be told again that I can take it there. In response to my complaint that I go on vacations today and, thus, may have no time to get the package, I was informed that the package will then be returned to the sender, and was suggested to print some proxy/trust form from Hermes website for someone else to get the package. Well, thanks! 2 hours before I leave, and I need to think about some stupid form, and where to print it, and who could get the package – all because of Hermes delivering the package to a wrong Paketshop.

I ended up walking to that other Paketshop (~3km further from where I had already been) and getting the package.

Obviously, I no longer had enough time for a haircut. I was also quite angry and destabilized – just what I needed before a day-long trip. Thanks, Hermes.

I will be contacting Amazon and the specific shop to report this failure of Hermes, and to ask to never use Hermes for my deliveries.

A friend of mine had similar experiences with Hermes, so I guess this is not a one in a thousand failure.

I have three simple questions to Hermes, if it ever bothers to answer them:

1. Why do I have to seek contact with Hermes to find my package? Why Hermes delivery left absolutely no notifications about the package whereabouts when it failed to deliver for the 3rd time?
2. Why was there absolutely no response to my feedback form?
3. Why was the package delivered to a different Paketshop? Why wasn’t I notified about the change?

I have come to a conclusion never to use Hermes, even if the alternative is more expensive.

I wish you timely and successful deliveries.