kchen-lab / medalt Goto Github PK

Hi,

I encounter an error when running the example and my samples.
Can you help me it?
I created a conda env with python2.7 and R3.5.1

(medalt) romain@lynx:/samurlab1/RawData/Romain/Logiciel/MEDALDT/MEDALT-1.0$ python2 scTree.py -P ./ -I ./example/scDNA.CNV.txt -D D -G hg19 -O ./example/outputDNA
Transfer data to segmental level
Inferring MEDALT.
MEDALT inferrence finish.
Performing LSA.
Error: unexpected input in "3"
Execution halted
Done!

Hello,

Is there any way to use mouse mm10 scDNA or scRNA data with this tool?

Keyur

At this line:
https://github.com/KChen-lab/MEDALT/blob/master/scTree.py#L71
and also a few lines below, there is a mix of tabs and spaces. Please replace the tabs with spaces.

Hi, thanks for the nice tool, I want to try it on some scRNA-seq CNV data. I ran your example that uses "scRNA.CNV.txt", outputs to the "outputRNA" folder. I found both the singlecell.tree and LSA.tree outputs to be a bit similar but also clearly different to your provided ones in the pre-existing "outputRNA" folder. I ran it with python 2.7.16 and R 4.0.4 (I don't have the option to downgrade to 3.5) and it ran without any errors. I ran it twice and got the exact same outputs. Here are my outputs:

Are some differences expected since some of the scripts have been updated in the recent months? Thanks

Hi i'm running the MEDALT package on one of my samples (about 3,000 cells) but was met with this error below after about 8 hours of run time.

slurmstepd: error: Detected 1 oom-kill event(s) in step 802100.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.

I received this initially on a 750gb node and so i increased to our 3TB node and specified the entire node. Seems that 3TB should be more than enough for a job like this?

best,
Tyler

Hi, this is really good work!
I've installed and run scTree.py, it produce the MEDALT tree but I do get an error during the CFL calculation.
Log below:

[1] Visualization MEDALT!
null device
1
[1] LSA segmentation!
[1] Calculating CFL
Error in subCNV[, startIndex] : incorrect number of dimensions
Calls: do.call -> lapply -> lapply -> FUN
Execution halted
Done!

Any Idea on why this is happening and how can be fixed?
Thank you a lot!

Bests

Possible bug in DNAinput function - what if elements of region are not in the same order as they appear in data? Seems to be fixed if region <- region[unique(data[,1])] is added after line 7.

Thank you for the development of this very nice tool. I have a general question about how to run this on multiple samples to identify commonly amplified or deleted genes that drive tumor clone expansion as you demonstrated in your manuscript.

Do you just run it on every sample individually and then look at the overlap of significant genes? or do you combine all of the copy number analyses into one file and run it once?

Thank you,
Tyler

Hello, when I change the names of cells, the topological structure of CNV tree also would change. That is unbelievable！Can you tell me why? Thanks.

Hi Fang and Qihan,

Very grateful for your work with MEDALT! Excited to try this out.

Do you have any recommendations for running it using 10X single cell data? i.e. datasets with high N and low read depth?

So far, I'm running out of memory (currently 180gb on our institution's cluster) with anything larger than 2k cells or so.

Thanks!
Anders

Hi, this is a good work.
When I used MEDALT, i have meet this error. LOG is as follow:

[1] Visualization MEDALT!
null device
1
[1] LSA segmentation!
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
scan() expected 'an integer', got '2148562433'
Calls: eval ... import -> .local -> DataFrame -> read.table -> scan
Execution halted

"2148562433" this number is at the 3564 line in my input file. And my input file is more than 5k lines.
Then I used the first 3k lines from my input file into a new file, the new file can be worked by MEDALT.

Any Idea on why this is happening and how can be fixed?
Thank you a lot!

Best Regards