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statgen / locuszoom-standalone

Create regional association plots from GWAS or meta-analysis
http://locuszoom.org/
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Error: object 'refFlat' not found #4

Open swvanderlaan opened 6 years ago

swvanderlaan commented 6 years ago

Hi,

I'm getting an error message regarding refFlat which I cannot immediately place. How should I interpret it?

In this case I'd like to plot a region near rs12936587 on 17:16543722-18543722. The gene of interest is RASD1.

Thanks

Sander

**=============================================================================
   INITIALISING LOCUSZOOM PLOTTING FOR rs12936587 LOCUS -- AFTER CLUMPING
=============================================================================
Plotting SUMMARYs for the rs12936587 locus on 17:16543722-18543722.
    * Plotting association SUMMARYs for RASD1 and ILMN_1740426.
    * The rs12936587 tags rs12936587 with r^2 = 1, and permuted p-value = 4.48358e-08 (FDR: 2.6453122e-06).
    Note: the tagging variant can be the same as the index-variant!**

+-----------------------------------------------------------------------------------------+
|                                        LocusZoom 1.3                                    |
|                           (version: 06/20/2014; edit: 2018-02-26)                       |
|                                                                                         |
| Plot regional association results from genome-wide association studies, or regional     |
| genetic analyses.                                                                       |
+-----------------------------------------------------------------------------------------+

Loading settings..
Options in effect are:

+------------+----------------------------------+
|   Option   |              Value               |
+------------+----------------------------------+
| metal      | rs12936587_RASD1_ILMN_1740426.lz |
| chr        | 17                               |
| start      | 16543722                         |
| end        | 18543722                         |
| condsnps   | rs12936587                       |
| build      | hg19                             |
| ld-measure | rsquare                          |
| pop        | EUR                              |
| source     | 1000G_March2012                  |
| snpset     | Illu1M                           |
| gene-table | refFlat                          |
| cache      | ../ld_cache.db                   |
+------------+----------------------------------+

Plotting parameters in effect are:

+-----------------+--------------------------------------------------------+
|      Option     |                         Value                          |
+-----------------+--------------------------------------------------------+
| bigDiamond      | TRUE                                                   |
| hiStart         | 17531791                                               |
| showRefsnpAnnot | TRUE                                                   |
| refsnpLineWidth | 2                                                      |
| axisTextSize    | 1.25                                                   |
| markerCol       | MarkerName                                             |
| title           | rs12936587 tagged by rs12936587 - RASD1 (ILMN_1740426) |
| refsnpTextSize  | 1.0                                                    |
| showAnnot       | TRUE                                                   |
| showRug         | FALSE                                                  |
| theme           | publication                                            |
| geneFontSize    | 1.25                                                   |
| rfrows          | 10                                                     |
| axisSize        | 1.25                                                   |
| clean           | TRUE                                                   |
| drawMarkerNames | FALSE                                                  |
| showRecomb      | TRUE                                                   |
| pvalCol         | P-value                                                |
| ldColors        | "#595A5C,#4C81BF,#1396D8,#C5D220,#F59D10,red,#9A3480"  |
| showGenes       | TRUE                                                   |
| hiEnd           | 17544704                                               |
+-----------------+--------------------------------------------------------+

Using /hpc/local/CentOS7/dhl_ec/software/locuszoom_1.3/bin/locuszoom.normal.R..
Beginning plotting sequence for: chr17_16543722-18543722
Extracting region of interest (chr17:16543722-18543722) from input file..

WARNING: your association results file has both rsID and chr:pos SNP
names. Please make sure you have selected the correct genome build by
using the --build parameter, or by selecting the appropriate build on
the website.

Attempting to find best SNP in region..
Found: 17:17543722
Finding pairwise LD with reference SNP 17:17543722..
Source: 1000G_March2012 | Population: EUR | Build: hg19
Using /hpc/local/CentOS7/dhl_ec/software/plink-1.9-beta3.38.7Jun/plink to compute LD..
Accessing LD cache: ../ld_cache.db
Finding pairwise LD with conditional SNP rs12936587..
Source: 1000G_March2012 | Population: EUR | Build: hg19
Using /hpc/local/CentOS7/dhl_ec/software/plink-1.9-beta3.38.7Jun/plink to compute LD..
Accessing LD cache: ../ld_cache.db
Grabbing annotations from SQLite database..
Creating plot..
No unique match for showRug=FALSE
Error in `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels,  :
  factor level [2] is duplicated
Calls: factor
recover called non-interactively; frames dumped, use debugger() to view
Error: object 'refFlat' not found
recover called non-interactively; frames dumped, use debugger() to view
[1] "recrateRange: "
[1] 100   0
Error in unique(bed_tracks$name) : object 'bed_tracks' not found
Calls: zplot -> unique
recover called non-interactively; frames dumped, use debugger() to view
Error in make.gene.list(refFlat, unit = args[["unit"]]) :
  object 'refFlat' not found
recover called non-interactively; frames dumped, use debugger() to view
Error: object 'geneList' not found
recover called non-interactively; frames dumped, use debugger() to view

Warning message:
In sink() : no sink to remove
Error in save(metal, refFlat, ld, recrate, refSnpPos, args, file = "end.Rdata") :
  object ‘refFlat’ not found
recover called non-interactively; frames dumped, use debugger() to view

Cleaning up.  The following files are begin removed:
Error in RemoveTempFiles(...) : object 'refFlatRaw' not found
Calls: CleanUp -> RemoveTempFiles
recover called non-interactively; frames dumped, use debugger() to view
[1] "Mon Mar  5 21:22:07 2018"
Deleting temporary files..
Time required: 0d:0h:1m:53s
annashcherbina commented 4 years ago

Is there a resolution for this, running into the same issue with locus zoom 1.4. Thanks!

welchr commented 4 years ago

It's unfortunately hard to tell from the error message. My guess is the Error: object 'refFlat' not found message is not the real issue, but rather something triggered later after earlier failures.

It is possible the real error is: 

Error in `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels,  :
  factor level [2] is duplicated
Calls: factor

But unfortunately without a traceback + line numbers it's not obvious to me where that is actually occurring in the code.

If you're able to provide your command line and arguments, that could possibly help. Having the data for the region you're plotting would be helpful as well, but I understand that is usually confidential.