Closed csijcs closed 2 years ago
Thanks for raising the issue separately. Have you tried to visualize the chromosome 4 normalized PC scores using "viz" command? If not, please try the following -
Rscript dchicf.r --file 40kb_input.txt --pcatype viz --diffdir all_samples_40Kb --genome hg38 --pcgroup pcQnm
This will help me to debug the issue.
When I run:
Rscript ~/dcHiC/dchicf.r --file 40kb_input.txt --pcatype viz --diffdir all_samples_40kb --genome hg38
I get the following:
Warning messages:
1: In dir.create(paste0(diffdir, "/viz")) :
cannot create dir 'DifferentialResult/all_samples_40kb/viz', reason 'No such file or directory'
2: In dir.create(paste0(diffdir, "/viz/files")) :
cannot create dir 'DifferentialResult/all_samples_40kb/viz/files', reason 'No such file or directory'
But it appears to be an error and not just a warning because the viz folder is not created
Did you successfully execute this step? Do you see the DifferentialResult/all_samples_40kb/fdr_result
directory?
Rscript ~/dcHiC/dchicf.r --file 40kb_input.txt --pcatype analyze --dirovwt T --diffdir all_samples_40Kb
Because the previous error says it didn't find the DifferentialResult/all_samples_40kb
directory. The analyze step should create the DifferentialResult/all_samples_40kb
directory and the viz step expects it.
I did successfully execute that step and the folders DifferentialResult/all_samples_40kb
and DifferentialResult/all_samples_40kb/fdr_result
do exist.
Do you mind sharing the directory architecture of DifferentialResult/all_samples_40kb?
Something like a tree command will be sufficient, I just want to look at the generated files.
Till now, I am not exactly sure what actually caused this error (Never seen this error before).
Sorry for all the inconvenience.
It contains 10 *_data
folders for the 10 samples, which each contain and *_intra_chr.pc.bedgraph
for each chromosome and repliacte, as well as an intra_chr_combined.pcOri.bedgraph
and intra_chr_combined.pcQnm.bedgraph
for each chromosome.
It also contains pcOri and pcQnm folders with intra_sample_chr_combined.*.begraph
for each chromosome.
The DifferentialResult/all_samples_40Kb/fdr_result
folder contains the following files:
differential.intra_compartmentLoops.bedpe differential.intra_sample_chr16_combined.pcQnm.bedGraph differential.intra_sample_chr2_combined.pcQnm.bedGraph differential.intra_sample_chrX_combined.pcQnm.bedGraph
differential.intra_compartmentLoops.txt differential.intra_sample_chr17_combined.pcQnm.bedGraph differential.intra_sample_chr3_combined.pcQnm.bedGraph differential.intra_sample_combined.Filtered.pcQnm.bedGraph
differential.intra_sample_chr10_combined.pcQnm.bedGraph differential.intra_sample_chr18_combined.pcQnm.bedGraph differential.intra_sample_chr4_combined.pcQnm.bedGraph differential.intra_sample_combined.pcQnm.bedGraph
differential.intra_sample_chr11_combined.pcQnm.bedGraph differential.intra_sample_chr19_combined.pcQnm.bedGraph differential.intra_sample_chr5_combined.pcQnm.bedGraph differential.intra_sample_group.Filtered.pcOri.bedGraph
differential.intra_sample_chr12_combined.pcQnm.bedGraph differential.intra_sample_chr1_combined.pcQnm.bedGraph differential.intra_sample_chr6_combined.pcQnm.bedGraph differential.intra_sample_group.Filtered.pcQnm.bedGraph
differential.intra_sample_chr13_combined.pcQnm.bedGraph differential.intra_sample_chr20_combined.pcQnm.bedGraph differential.intra_sample_chr7_combined.pcQnm.bedGraph differential.intra_sample_group.pcOri.bedGraph
differential.intra_sample_chr14_combined.pcQnm.bedGraph differential.intra_sample_chr21_combined.pcQnm.bedGraph differential.intra_sample_chr8_combined.pcQnm.bedGraph differential.intra_sample_group.pcQnm.bedGraph
differential.intra_sample_chr15_combined.pcQnm.bedGraph differential.intra_sample_chr22_combined.pcQnm.bedGraph differential.intra_sample_chr9_combined.pcQnm.bedGraph
Hi,
So, I just noticed that there is a difference in the name of diffdir between two of yours previous dcHiC commands -
Rscript ~/dcHiC/dchicf.r --file 40kb_input.txt --pcatype analyze --dirovwt T --diffdir all_samples_40Kb
&
Rscript ~/dcHiC/dchicf.r --file 40kb_input.txt --pcatype viz --diffdir all_samples_40kb --genome hg38
The first one is 40KB and the second one is 40kb and probably this is the reason you're getting an error during the viz step. Try this -
Rscript ~/dcHiC/dchicf.r --file 40kb_input.txt --pcatype viz --diffdir all_samples_40Kb --genome hg38
It is strange to me that the "viz" step is failing. This step only requires one of the differential.intra_sample_group.*.bedGraph files, which is successfully generated. If the new command still fails, can you please send me the differential.intra_sample_group.pcOri.bedGraph and differential.intra_sample_group.pcQnm.bedGraph files to abhijit@lji.org? I like to replicate the error and give you some meaningful comments.
Wow, I'm embarrassed. Indeed it was 40Kb instead of 40kb. Really sorry to take up your time over a typo. Thanks very much for your help
No issues! happy to help you out. If you still facing the subcompartment issue, please let me know.
I am having an issue with subcompartment analysis step of the dchicf.r script. When I run:
Rscript ~/dcHiC/dchicf.r --file 40kb_input.txt --pcatype subcomp --dirovwt T --diffdir all_samples_40Kb
I get the error:
The subcompartment analysis runs for many chromosomes and samples, but then fails when it starts chr4 for the first sample in the input.txt
Prior to this I successfully ran:
I have also successfully run the subcompartment analysis on subsets of these samples, including for chr4 on the first sample in the input.txt, but I get this error when running all samples together.