Error in species, strain inference

[priyatamapandey]

Hi, I got the error while just running the given command in manual. Please help me to understand why I am getting these errors.

Thank you, Priya

[zwdzwd]

Hi Priya,

Sounds like you are running the older release of sesame following the latter examples. SigSet is what we use previously. If you type packageVersion("sesame") and saw anything < 1.10 that's the issue. I suggest updating to 1.12+.

[priyatamapandey]

Hi, Yes, It shows

packageVersion("sesame") [1] ‘1.10.5’

I used the following command to install it. BiocManager::install('zwdzwd/sesameData') BiocManager::install('zwdzwd/sesame') How to install the 1.12+ version?

Thank you, Priya

[priyatamapandey]

Hi, I have installed the higher version of the sesame. Now it returned the following error. Please suggest how to solve this. Here is the screenshot

Thank you,

Priya

[zwdzwd]

My guess is that your ExperimentHub is still not updated (I think 1.12+ should be good.). That bited me in the past: the experimentHub version strictly pairs with all the tools that depend on it.

[priyatamapandey]

Thank you for the suggestion. I checked it is showing version 2.

.

Thank you, Priya

[priyatamapandey]

Hi, When I checked tried to check the MM285.address file in the cache. It returned the following

Thank you, Priya

[zwdzwd]

I think for sesame 1.13 we need 2.1.* for ExperimentHub. Could you try update ExperimentHub and let me know if that solves your problem?

[priyatamapandey]

Hi, Sorry for the late reply. I was on vacation. I have tried installing the ExperimentHub 2.1.4 but it returning error so I have install the latest version 2.2.0 thought it should work too but it is still returning error. Do you think, it only work with 2.1.4 version o f experiment hub, if yes what command I should use to install this version? I used the following command to install the ExperimentHub version 2.2.0 and it work but the same command did not work with the experimentHub 2.1.4. install.packages("https://bioconductor.org/packages/release/bioc/src/contrib/ExperimentHub_2.2.0.tar.gz", repo=NULL, type="source")

Here is the error:

Please suggest, Priya

[priyatamapandey]

Hi, I did install the experimentHub version 2.1.4 but there is still the same problem. It does not find the MM285. I want to apply DML or DMR on my mouse data. I am new in the project too. Is there any way to proceed with the differential CpGs for my mouse samples?

Thank you, Priya

[zwdzwd]

Have you run 'sesameCacheAll()' after you install the new ExperimentHub? What do you get if you type

sesameDataGet("MM285.address")

[priyatamapandey]

I removed ExperimentHub from my cache and again install the experimentHub 2.2.0 and then run the sesameCacheAll(). I noticed it says metadata N=70 but only run till 28/70 and then print true. Here is the screenshot for both returned sesameCacheAll() and sesameDataGet("MM285.address").

[zwdzwd]

Could you also check your R version? Is it 4.1? also BiocVersion 3.14? What if you update all of them? I tried 2.2.0 ExperimentHub on my end it seems to work.

[priyatamapandey]

Hi, My R version is 4.1.1 and BiocVersion is 3.13. Is it too old? I am working on HPC and I am afraid that I could update the r version, not sure about the BiocVersion though.

Thank you, Priya

[zwdzwd]

I think the ExperimentHub 2.2 is with BiocVersion 3.14. Should be easy to update. Can you try BiocManager::install("sesame") The issue might be because you were installing using install.packages.

[priyatamapandey]

Hi Wanding,

YAY! finally it worked. Thank you so much for bearing with me. It worked on my computer. FYI, I updated R to 4.1.2 and Bioc Version 3.14 and installed sesame BiocManager::install("sesame", force = TRUE)

I am still afraid that whether it will work on HPC too because I am loading module R/4.1.0 on HPC.

Thank you, Priya