Closed sdontsay closed 1 year ago
Hi,
Thanks for trying out the package. It seems like you don't have the 'parallel' R package. If not, then please install it from here https://cran.r-project.org/web/packages/parallelly/index.html or type install.packages('parallel') within the R environment. I hope this will resolve the first issue.
Regarding the second issue, please install the 'bedtools' package from here https://bedtools.readthedocs.io/en/latest/ and please make sure the tool is in your $PATH. This is a must package to have for dchic.
I hope the rest of the issues will be resolved once you follow the above instructions.
Hi Ay,
Thanks for your reply! I actually have the parallel package installed in R, and I asked for help from the HPC staff of our university for installing bedtools. It is now installed, and I can load it, and call it, but the error message is still there. Do you have any other advice?
Thanks!
Hi,
You can try out two options - first, you can run with '--cthread 1 --pthread 1' option, so that you will avoid using the clusterApply part. The second option is to log into your HPC system in interactive mode and run dchic with '--cthread 2 --pthread 2' option. Let's try to resolve this issue, I can then help you to resolve the next.
Thank you, Ay. I tried the first option, and I got a new error, "Performing Z transformation : complete!
Performing block wise correlation calculation Error in functionsdchic::oe2cor(mat, (start - 1), (end - 1), 1, 0) :
upper value must be greater than lower value
Calls: lapply -> FUN -> lapply -> FUN ->
Thanks for trying out the option. It seems like an issue either with the file format or the presence of a non-conventional chromosome with very few counts. Do you mind sending me the input bed file and a slice of the matrix files to abhijit@lji.org?
Thank you, Ay, for this kind suggestion! However, because this is unpublished data yet, we may need some time to think about it.
An alternative option is to run the PCA calculation separately (using HOMER/juicer) and use dcHiC to call the differential compartments. Please check the "Using Existing PC values with dcHiC" option under the utility folder.
Hi Ay,
I'm trying to run dcHiC on a Human genome dataset, unfortunately, I got several errors and couldn't get what I want.
I have an error message when running the first step, saying that "Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: Two levels of parallelism are used. See
?assert_cores
. Calls: lapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted " I guess this might be due to the occurrence of chromosomes of Y, M, Z in my data (I do have these chromosomes), but I still wanna ask your opinion on it.In the second step, which selects the best pc, I have an error saying that "Error: Executable for bedtools not found! Please make sure that the software is correctly installed and, if necessary, path variables are set." I'm not familiar with this tool, and I did not see you mention it as a prerequisite for this analysis, so I searched for it and tried installing it on the HPC I am using. However, because I don't have the administration authorization, I still cannot call it when running the program, thus the error is still there. Do you have any suggestions?
Although I have 12 .matrix and .bed files in the data folder, I only have the output of the first one listed in the input file (named NT1_20kb_pca), do you have any idea why was that?
I guess the other errors I encountered in the subsequent steps are the consequences of step 2.
Moreover, the content of my input file is as follows, NT1_20000.matrix NT1_20000_abs.bed NT1_20Kb NT NT2_20000.matrix NT2_20000_abs.bed NT2_20Kb NT PT1_20000.matrix PT1_20000_abs.bed PT1_20Kb PT PT2_20000.matrix PT2_20000_abs.bed PT2_20Kb PT PT3_20000.matrix PT3_20000_abs.bed PT3_20Kb PT PT4_20000.matrix PT4_20000_abs.bed PT4_20Kb PT PT5_20000.matrix PT5_20000_abs.bed PT5_20Kb PT RT1_20000.matrix RT1_20000_abs.bed RT1_20Kb RT RT2_20000.matrix RT2_20000_abs.bed RT2_20Kb RT RT3_20000.matrix RT3_20000_abs.bed RT3_20Kb RT RT4_20000.matrix RT4_20000_abs.bed RT4_20Kb RT RT5_20000.matrix RT5_20000_abs.bed RT5_20Kb RT
Thanks!