Error in RnBeads whole genome bisulfite sequencing data analysis

Question

[pawanupadhyay70]

Hi Folks,

I am trying to run RnBeads for WGBS data analysis. Though all the steps in the analysis run successfully but at the end I got the following error:

#################################
2020-03-20 20:53:14    16.7  STATUS                     COMPLETED Running LOLA
2020-03-20 20:53:14    16.7  STATUS                 COMPLETED Region Type: cpgislands
2020-03-20 20:53:14    16.7  STATUS             COMPLETED Differential Methylation LOLA Enrichment Analysis
2020-03-20 20:53:36    16.7  STATUS         COMPLETED Analysis
2020-03-20 20:53:36    16.7  STATUS         STARTED Saving temp objects for debugging
2020-03-20 20:57:51    16.7  STATUS         COMPLETED Saving temp objects for debugging
2020-03-20 20:57:51    16.7  STATUS         STARTED Report Generation
2020-03-20 20:57:51    16.7  STATUS             Added introductory section
2020-03-20 20:57:51    16.7  STATUS             STARTED Adding Site Level Information
2020-03-20 20:57:51    16.7  STATUS                 STARTED Selection of rank cutoffs
opening ff /tmp/131078.tmpdir/RtmpQkhcqo/diffMethTables_74c7771ec/sites_cmp1.ff
2020-03-20 20:58:13    25.0  STATUS                 COMPLETED Selection of rank cutoffs
2020-03-20 20:58:13    25.0  STATUS                 STARTED Adding scatterplots
2020-03-20 21:13:58    20.1  STATUS                 COMPLETED Adding scatterplots
2020-03-20 21:13:58    20.1  STATUS                 STARTED Adding volcano plots
2020-03-20 22:43:55    21.9  STATUS                 COMPLETED Adding volcano plots
2020-03-20 22:43:55    21.9  STATUS                 STARTED Adding tables
2020-03-20 22:59:53    24.0  STATUS                 COMPLETED Adding tables
2020-03-20 22:59:54    24.0  STATUS             COMPLETED Adding Site Level Information
2020-03-20 22:59:54    24.0  STATUS             STARTED Adding Region Level Information
2020-03-20 22:59:54    24.0  STATUS                 STARTED Selection of rank cutoffs
opening ff /tmp/131078.tmpdir/RtmpQkhcqo/diffMethTables_74c7771ec/regions_reg1_cmp1.ff
opening ff /tmp/131078.tmpdir/RtmpQkhcqo/diffMethTables_74c7771ec/regions_reg2_cmp1.ff
opening ff /tmp/131078.tmpdir/RtmpQkhcqo/diffMethTables_74c7771ec/regions_reg3_cmp1.ff
opening ff /tmp/131078.tmpdir/RtmpQkhcqo/diffMethTables_74c7771ec/regions_reg4_cmp1.ff
2020-03-20 22:59:54    24.0  STATUS                 COMPLETED Selection of rank cutoffs
2020-03-20 22:59:54    24.0  STATUS                 STARTED Adding scatterplots
2020-03-20 23:02:16    17.1  STATUS                 COMPLETED Adding scatterplots
2020-03-20 23:02:16    17.1  STATUS                 STARTED Adding volcano plots
2020-03-20 23:05:13    17.1  STATUS                 COMPLETED Adding volcano plots
2020-03-20 23:05:13    17.1  STATUS                 STARTED Adding tables
**Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 54850, 8226**
Calls: rnb.run.analysis ... eval -> eval -> eval -> cbind -> cbind -> data.frame
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
------------------------------------------------------------
#######################

I have got this error multiple times so not sure whether rerunning will resolve the issue as suggested in one discussion thread here.

I am running this tool on HPC and using the docker image. The RAM memory requires to run the tool is using 2 paired samples is about 80GB which is very high. I tried to use all the options recommended to enforce memory management but no help. Also, when I am checking the index HTML files, there are no tables linked with the differential methylations module. I have the following questions:

1. How can we resolve this error?
2. How can I reduce memory usages?
3. Since the analysis created .RData files for each comparison (like GO and LOLA), is it OK to use these .RData files to extract the data for further analysis?

Looking forward to your advice.

Thank you
Pawan

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Secondly, this post is a Question type post, not a Tool type post. You have a question to ask, not a tool to showcase. Please read the how-to posts for more information.