Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105 about beer

[jumphone]

Hi, we have tested BEER by using over 100,000 cells.
Could you please tell me the total number of cells in your input file?
If the number is not "too big", you may need to try a computer with a larger memory size.
Best,
Feng

[yueli8]

Hello jumphone,

Thank you so much for your quick response!

I ran the program in the server, not my local computer. The size of the combined eight samples are almost 3-4 GB.

Would you please help me to test in your computer?

There are also another two files too large to be uploaded. Is that possible I can send to your 163 email?

Thank you again and really appreciated!

Best,

Yue

donor_82_01.zip
donor_85_02.zip
donor_87_03.zip
donor_89_04.zip
donor_91_05.zip
donor_93_06.zip
donor_95_07.zip
donor_97_08.zip
mild_69_141.zip
mild_70_142.zip
mild_72_144.zip
severe_51_148.zip
severe_52_149.zip
severe_53_152.zip

severe_74_146.zip

[jumphone]

I’ve checked your code. After getting DATA and BATCH, please save them two. You can use “saveRDS” to directly save them. Then, re-open R (in order to release the memory). And load those two files. And you can send me those two RDS files by using email.

[yueli8]

Hello Zhang Feng, Thank you so much for your patience and kindly help! The DATA file is 372MB. Thank you in advance for your great help and really appreciated! Best, Yue At 2020-05-28 12:58:41, "Zhang, Feng" <[email protected]> wrote: I’ve checked your code. After get DATA and BATCH, please save them two. You can use “saveRDS” to directly save them two. Then, re-open R (in order to release the memory). And load those two files. And you can send me those two RDS files by using email. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. 从网易126邮箱发来的云附件 BATCH_donor_8_patients_9.rds (2.37K, 2020年6月27日 3:20 到期) 下载 DATA_donor_8_patients_9.rds (354.71M, 2020年6月27日 3:21 到期) 下载

[jumphone]

I cannot download those two files. Please send them two to my 163 email.

[email protected]

[yueli8]

Hello jumphone,

Thank you so much for your response! I already figured it out!

Thank you again!

Best,

Yue

[rpghjs]

Can you share the solution

[jumphone]

Please try "https://gitee.com/jumphone/BEER/raw/master/BEER_large.R". By the way, how many cells are you processing? We have tested BEER using around 500,000 cells. On 10/28/2021 ***@***.***> wrote： Can you share the solution — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.