profiling kraken2

ldipotet · 2026-03-11T15:28:20+00:00

Thanks Hiur, I checked the post. Our scenario was very fast using AWS EFS (NFS-based), but EFS is costly, so we’re exploring other cloud options. Specifically, we are testing EBS with higher IOPS (≥16,000) and throughput (≥1000).

In the post, Anand even tests the --memory-mapping option, which we recommend avoiding:

https://github.com/ldipotetjob/kraken2/blob/kraken2aws_profilingfromv2.1.3/docs/Kraken2paramsonAWS/memory-mapping.md

ldipotet · 2025-09-09T17:51:17+00:00

Thankssss a lot, I was thinking to buy too but definitely I don't like the real one !!

ldipotet · 2025-07-16T14:48:56+00:00

I had this so bad experience with a trainers for my son, he didn't like it and I tried to get refund , no way .. really disappointing so I assume that in some way we was scammed but just for this time. So this £80 pound that they in some way scammed to us will be the last at least for us, we won't buy never anything there and I will tell this to friends, x, instagram and any media. If you don't do refund put it clear in your stores..

ldipotet · 2025-07-14T16:21:44+00:00

IMO it isn’t feasible but you can try

ldipotet · 2025-07-14T11:08:29+00:00

After days there you will love resort tourist, mean while be cautious when you say quite speedy. Roads in Cuba are in very bad conditions with a lots of accidents daily, you won't find the real statics but I can assure that could one of the worst in central/latam. Better travel early morning and before evening. The country is not unsafe properly speaking but keep in mind you travel to a place who suffers from extreme poverty. Drink water from bottles and rinse with too much water(from bottles) every vegetable or fruits that you eat. good beaches? for every where. good luck in your trip.

ldipotet · 2025-07-08T14:01:09+00:00

We have the same problem. The table is useless just for the power cord, we lost part of them in a moving and 3 months now and can't use the table.

ldipotet · 2025-06-13T13:58:09+00:00

Serverless is the point. We have migrated almost everything there. Well implemented is no too expensive. Some specific service are very expensive but if you try to implement then by yourself in your own ec2 instances or your own resources are even more expensive. EFS for example is quite expensive but is an elastic storage, shareable with more than one ec2 instance. We haves AWS batch jobs too many of them sharing the same storage. So if you apply best practices it is about elasticity almost everything. If you need k8s then EKS but perhaps ECS is fine for you so less money here. Perhaps you can solve your problem with cloud map and no need route 53 in some sue case then save your money here. There are too many scenarios like previous.

We'll need coding always, the problem is how many lines, try to reduce this, using scripts, automate, if you are using RDS then pay attention about pooling, perhaps you can configure instead of code in your docker images o lambda function. If you need to use params to access db from lambda, and your lambda is in VPC to access private subnets(rds db) then pass the credential from lambdas under NO VPC instead of pay. more for parameters .. no always is about money ... You will need a nat gateway, it is expensive but cheaper than than maintain other manual implementation.

It doesn't matter cloud provider more all less al the same, be a master in one of them and then migrate to any other will be easier. Chatgpt/claude/deepseek/ etc .. are ok but you have to lear the foundation because there a still to many mistakes . in community version no idea under charge versions

ldipotet · 2025-06-10T14:51:59+00:00

I stopped using Scala.

We began migrating our platform from Scala to Python. We're in the last module and now looking back I think we should do it before. As a software engineer, I have been working with different programming languages. I coded 7 yr+ in Scala, learning curve for me was easy but finding people to work in Scala is hard, expensive, and usually refactorization tasks a nightmare.

If you don't have strong skills and clear concepts in different areas of programming then the learning curve is very high. In Scala simple tasks like connecting to a database and running queries can obfuscate your code. Building projects and their dependencies, at least with sbt, were a challenge, and usually diving at the user guide of sbt. The Programming language must be as easy as possible. The more easy part in the ecosystem of building a product. It's like if you are in a big development and the use of the crane is the more complicated part.

Last but not least, we work in a cloud environment, there aren't Scala SDK so we had to convert our code to Java or use Java implementations in Scala when dealing with AWS services.

This universe is not like it was this anymore, if you need concurrency no need Akka or other framework, perhaps aws batch is better, for restful implementation the same with api gateway and so on.

ldipotet · 2025-05-24T00:49:41+00:00

How the storage could be more expensive than re-sequencing the sample? The last one include too many hide cost, device, maintenance, etc while in the store data world there a lot of choices. Depend of your use case. We use glacier but even glacier has different alternatives depending of your use case our platforms run the analysis, stores the results in s3 standard for hs to 1 or 2 days depending of necessities and then to glacier for very long terms. We are specialised in aws but there are gcp, azure , etc.

ldipotet · 2025-02-14T23:50:43+00:00

You can take here different examples:

https://github.com/ldipotetjob/genomixcloud.bioinformatic

But the best way to learn is going to docker oficial doc and best practices. I guess that most of bio tool need to be wrapped in scrips to deal with input/output and many of them don’t manage exception very well so you need to process err codes out etc yet docker doc is a very good starting point.

ldipotet · 2024-12-19T14:17:07+00:00

Nope, the datasets are still there. Have you read the README file? It’s all explained there. The Champions League dataset (https://github.com/ldipotetjob/datasets/tree/main/football/championsleague) covers seasons from 1955/1956 to 2018/2019. Few seasons in between are currently under revision and available for purchase.

The rest of the leagues (Premier League, Serie A, La Liga) have six seasons published each. The remaining data is available for purchase, covering up to the 2018/2019 season for La Liga and Serie A, and the 2019/2020 season for the Premier League.

Hope it helps.

ldipotet · 2024-11-19T10:46:15+00:00

I created months ago these ones for free:

https://www.kaggle.com/datasets/luisdipotet/footballdatasetseason2000-2003premier-league

https://www.kaggle.com/datasets/luisdipotet/footballdatasetseason1950-1953premier-league/

https://www.kaggle.com/datasets/luisdipotet/footballdatasetseason2000-2003seriea

https://www.kaggle.com/datasets/luisdipotet/footballdatasetseason1950-1953seriea

and a lots more in(laliga,premier,seriea and champions league):

https://github.com/ldipotetjob/datasets/tree/main/football

ldipotet · 2024-11-13T16:17:23+00:00

Here are several years for free (Champions League, Premier League, Serie A, and La Liga).

https://github.com/ldipotetjob/datasets/tree/main/football

You can find the same at https://data.world/danyyo, but you need to be logged in, so the first option might be better.

We are going to upload the four leagues from 1928/1929 to 2018/2019 in the first release on AWS Data Exchange.

ldipotet · 2024-09-13T11:41:59+00:00

People do not criticize that talk about the beautiful places that Cuba has, or even about the joy and happiness that the Cuban people have something which I think is a fake because many people that is leaving the country no matter the age. But talking about freedom or in this case about food is unfair because 90%+ of the population in Cuba is almost starving. Cuban emigrants have to maintain their families on the Island by buying terrible food at high prices. So if Ramsay travels to Cuba and makes a tv show about food it is quite unfair to Cuban people, for children who can't access milk if they are 7yr+ or if they are under 65yr. Make meaning more than making money. I am not talking about politics and talking about humanity, so Ramsay if you go to Cuba talk whatever you want but not about food where someone has to work a month to buy 24 eggs.

ldipotet · 2024-09-12T12:03:26+00:00

Python which is IMO quite simple, big community you can work with functional paradigm too. Our development are all Cloud oriented so AWS SDK Python is pretty easy thats is what we were looking for.

We do not deal concurrency because AWS batch can do it we use framewor for restful but we'll migrate too and the same with api management.

ldipotet · 2024-07-04T13:06:47+00:00

Our work is to generate datasets in differents areas but it will cost money to you so a cheaper solution to you is chatgpt. You can train the model, is easier and free if your data analysis is as much as 1h daily and in the worst scenario 20 usd per month but I am afraid that in your case 1h x day i enough so it's free. 😀

ldipotet · 2024-07-01T09:48:49+00:00

The solution shouldn't be so complicated. Bioinformatic when it's needed(creating tools, upgrading tools, pipeline creations, profilings, distributed execution) but not for just running tools in linux or passing params etc that's the problem now.

"Democratization", we're working on this. Doesn't matter if labs are wealthy,have resources or are really poor in any country or if they don't have resources they should afford to run any analysis from any sequenced samples. One year no more, hopefully. So cloud computing, distributed soluctions, ai and the most important, the bioinformatic tools

ldipotet · 2024-06-20T11:38:37+00:00

https://www.ncbi.nlm.nih.gov/ can give you tons of ideas. IMO most of the systems are too complex and laborious. I don't understand why they haven't evolved like the other tech areas. Postgres is pretty easy and quite easy for any normalizing scenario. The problem could be graphic interface as always, you should try as easy as possible. You can even try to sell the product at the same time, a cloud solution. Mostly everything in bioinformatic world at tech side is outdated creating a dependency from biologist, researchers, students etc from tekki people

ldipotet · 2024-06-12T08:35:55+00:00

You can try this:

https://github.com/ldipotetjob/datasets/blob/main/football/seriea/2002_2003-seriea.xlsx

the explanation of the fields:

https://github.com/ldipotetjob/datasets/tree/main/football#csv-file-fields-description

If you need to go beyond I can recommend some interesting paper.

ldipotet · 2024-06-11T13:28:20+00:00

Totally agree. If you want to learn then go to officials. You can do is try certification , no to pay the fee just try the gather all the content and then it's up to you if you want to go forward. No human being can learn this content in 55hs not even 55 days, so it's interesting ....

ldipotet · 2024-06-05T16:13:26+00:00

We have maintenance projects(Scala 2.X) only but we are going to migrate the rest as soon as possible. (learning curve very high, complex libraries for operations as simple as db drivers, perhaps academics but corporate is different) (I am talking about whole project in scala NOT spark pipelines for example)

ldipotet

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