ParseCNV example problems
Guo Xinru
Dear Joseph Glessner:
I'm sorry to bother you.
I downloaded ParseCNV21.tar and installed it. I tried to run the example command:
perl ParseCNV.pl ExampleFiles/Cases.rawcnv ExampleFiles/Controls.rawcnv ExampleFiles/Cases.fam ExampleFiles/ChrSnp0Pos.map
but got th following erro:
/usr/bin/bash
/home/ubuntu/software/R/R-4.2.1/bin/R
/home/ubuntu/software/plink/plink-1.07-x86_64/plink
NOTICE: --build set to hg18 by default. Please check you are clear and consistent with which build you are using and if not hg18, download build specific files to GeneRef folder as specified in README.txt under "GeneRef Folder download latest versions unix commands", then run ParseCNV again specifying --build option.
Running Command: perl ParseCNV.pl ExampleFiles/Cases.rawcnv ExampleFiles/Controls.rawcnv ExampleFiles/Cases.fam ExampleFiles/ChrSnp0Pos.map
My Path ./
Unable to connect to web to check latest version
Run Started 04:16:35 PM on Mar 24 2023
Chromosomes found: chr1
Average Inter Probe Distance: 1.000
Number of Probes:10
Done Initialization
Progress:100%
Results
-------
Cases: 5
Unaffected: 0
Controls: 4
Count Significant Deletion Probes Case Enrich: 1
Count Significant Duplication Probes Case Enrich: 1
Count Significant Deletion Probes Control Enrich: 0
Count Significant Duplication Probes Control Enrich: 0
GIFDel:0.378
GIFDup:0.134
scan_range2
-----------
CountCNVRsDel: 1
CountCNVRsDup: 1
CountCNVRsDel: 0
CountCNVRsDup: 0
scan_region
-----------
running Gene annotation deletions
running Gene annotation duplications
scan_DescPathway
----------------
Genes annotated with text description and pathway.
Genes annotated with text description and pathway.
Genes annotated with text description and pathway.
Genes annotated with text description and pathway.
scan_rangeJustPos2
------------------
CountCNVRsDel: 1
CountCNVRsDup: 1
CountCNVRsDel: 1
CountCNVRsDup: 1
vlookup SNP to Region ID
------------------------
del
dup
del
dup
countBarcodeOCCURENCE_V2
------------------------
del
dup
del
dup
vlookup Count Sig Regions
-------------------------
del
dup
del
dup
Sort by pvalue
--------------
running Sort deletion p
running Sort duplication p
running Sort deletion p
running Sort duplication p
Data-filter-advanced-unique records only
----------------------------------------
del
dup
del
dup
Create UCSC Custom Track For Review
-----------------------------------
case
state1,cn=0 4
state2,cn=1 1
state5,cn=3 5
state6,cn=4 1
control
state1,cn=0 1
state2,cn=1 1
state5,cn=3 1
state6,cn=4 1
NUMLines
--------
case
control
PercentSamples-AverageNumsnpLenComponentCalls
---------------------------------------------
caseDel
caseDup
controlDel
controlDup
caseDel
caseDup
controlDel
controlDup
SpecificBafLrrAccessMany
------------------------
If BafLrr files available, try --idToPath <file.txt> command line argument.
Automated Quality Review of Association Signals Comments
--------------------------------------------------------
running Segmental Duplication annotation
running Database of Genomic Variants annotation
Telomere Centromere commenting
running GC Base Content annotation
running Inflated Sample annotation
Checking for same inflated sample driving multiple CNV associations
Final CNVR Counts:
------------------
CountCNVRsDel: 1
CountCNVRsDup: 1
CountCNVRsDelControlEnriched: 0
CountCNVRsDupControlEnriched: 0
running Cytoband annotation
running Somatic Rearrangement annotation
running Exon annotation
Now Count Number of Red Flags for Association Results
CNVR Quality Fail Frequency: 1
High fail frequency but some associations may still be reliable
Error: cannot execute system command R CMD BATCH OutputFiles/.AllRes.R
Would you help me solve this?
Thank you very much!
Regards,
Xinru Guo