SNPhood 1.13.0
Christian Arnold
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SNPhood |
| Branch: master |
| Last Commit: cd53135 |
| Last Changed Date: 2018-10-30 11:54:35 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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###
### Running command:
###
### chmod a+r SNPhood -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SNPhood
###
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* checking for file 'SNPhood/DESCRIPTION' ... OK
* preparing 'SNPhood':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'IntroductionToSNPhood.Rmd' using rmarkdown
--- finished re-building 'IntroductionToSNPhood.Rmd'
--- re-building 'workflow.Rmd' using rmarkdown
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
rowSums, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
The following objects are masked from 'package:S4Vectors':
first, second
Loading required package: checkmate
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
------------------------------------------------------------------------------------------------------------------
| Welcome to the SNPhood package and thank you for using our software. This is SNPhood version 1.13.0. |
| See the vignettes (type browseVignettes("SNPhood") or the help pages for how to use SNPhood for your analyses. |
| Thank you for using our software. Please do not hesitate to contact us if there are any questions. |
------------------------------------------------------------------------------------------------------------------
Search for files with the pattern '*.bam' in directory C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata (recursive: FALSE, case-sensitive:FALSE)
Found the following files:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam
C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam
C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam
C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam
Total size of all objects: 7.8 Mb
START WITH AUTOMATED PIPELINE
The following arguments have been provided:
SUCCESSFULLY FINISHED PARSING AND CHECKING THE CONFIGURATION FILE. PARSED PARAMETERS:
Parameter "readFlag_isPaired": "TRUE"
Parameter "readFlag_isProperPair": "TRUE"
Parameter "readFlag_isUnmappedQuery": "FALSE"
Parameter "readFlag_hasUnmappedMate": "FALSE"
Parameter "readFlag_isMinusStrand": "NA"
Parameter "readFlag_isMateMinusStrand": "NA"
Parameter "readFlag_isFirstMateRead": "NA"
Parameter "readFlag_isSecondMateRead": "NA"
Parameter "readFlag_isNotPrimaryRead": "FALSE"
Parameter "readFlag_isNotPassingQualityControls": "FALSE"
Parameter "readFlag_isDuplicate": "FALSE"
Parameter "readFlag_reverseComplement": "FALSE"
Parameter "readFlag_simpleCigar": "TRUE"
Parameter "readFlag_minMapQ": "0"
Parameter "path_userRegions": "C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/cisQ.H3K27AC.chr21.txt"
Parameter "zeroBasedCoordinates": "FALSE"
Parameter "regionSize": "500"
Parameter "binSize": "25"
Parameter "readGroupSpecific": "TRUE"
Parameter "strand": "both"
Parameter "startOpen": "FALSE"
Parameter "endOpen": "FALSE"
Parameter "headerLine": "FALSE"
Parameter "linesToParse": "-1"
Parameter "lastBinTreatment": "delete"
Parameter "assemblyVersion": "hg19"
Parameter "effectiveGenomeSizePercentage": "-1"
Parameter "nCores": "1"
Parameter "keepAllReadCounts": "FALSE"
Parameter "normByInput": "FALSE"
Parameter "normAmongEachOther": "TRUE"
Parameter "poolDatasets": "FALSE"
Add strand information for all regions. Assume strand is irrelevant (*)...
Modify chromosome names because they do not start with "chr"
Parse the user regions file
Finished parsing. Number of entries processed: 178
Execution time: 0 secs
Parse BAM header...
Read group specific reporting has been requested. The following read groups have been identified in the BAM header: paternal, maternal, ambiguous
PROCESS INPUT FILE SET NA (1 of 1)
PROCESS INDIVIDUAL 1 from 4: C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam
PROCESS FILE 1 of 1:C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam
Parse BAM header...
Execution time: 0 secs
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam for the full SNP regions (this may take a while)...
Analyze read counts specifically for each read group (this may take a while)...
Read group paternal...
Filtered 18264 reads out of 19740 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Read group maternal...
Filtered 18440 reads out of 19740 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Read group ambiguous...
Filtered 2776 reads out of 19740 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
FINISHED PROCESSING INDIVIDUAL
Execution time: 18.4 secs
PROCESS INDIVIDUAL 2 from 4: C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam
PROCESS FILE 1 of 1:C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam
Parse BAM header...
Execution time: 0 secs
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam for the full SNP regions (this may take a while)...
Analyze read counts specifically for each read group (this may take a while)...
Read group paternal...
Filtered 16404 reads out of 17811 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Read group maternal...
Filtered 16571 reads out of 17811 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Read group ambiguous...
Filtered 2647 reads out of 17811 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
FINISHED PROCESSING INDIVIDUAL
Execution time: 32.5 secs
PROCESS INDIVIDUAL 3 from 4: C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam
PROCESS FILE 1 of 1:C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam
Parse BAM header...
Execution time: 0 secs
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam for the full SNP regions (this may take a while)...
Analyze read counts specifically for each read group (this may take a while)...
Read group paternal...
Filtered 22093 reads out of 24190 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Read group maternal...
Filtered 20942 reads out of 24190 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Read group ambiguous...
Filtered 5345 reads out of 24190 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
FINISHED PROCESSING INDIVIDUAL
Execution time: 24.3 secs
PROCESS INDIVIDUAL 4 from 4: C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam
PROCESS FILE 1 of 1:C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam
Parse BAM header...
Execution time: 0 secs
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam for the full SNP regions (this may take a while)...
Analyze read counts specifically for each read group (this may take a while)...
Read group paternal...
Filtered 23567 reads out of 25759 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Read group maternal...
Filtered 22863 reads out of 25759 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Read group ambiguous...
Filtered 5088 reads out of 25759 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
FINISHED PROCESSING INDIVIDUAL
Execution time: 30 secs
FINISHED PROCESSING INPUT SET NA.
Execution time: 1.8 mins
FINISHED SUCCESSFULLY WITH ALL INPUT FILES.
Execution time: 1.8 mins
Warnings may have occurred, as indicated. Please check them carefully with unique(warnings()).
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/qualityTest-1.png" -trim "workflow_files/figure-html/qualityTest-1.png"' execution failed with error code 4
Total size of all objects: 7.9 Mb
START WITH AUTOMATED PIPELINE
The following arguments have been provided:
SUCCESSFULLY FINISHED PARSING AND CHECKING THE CONFIGURATION FILE. PARSED PARAMETERS:
Parameter "readFlag_isPaired": "TRUE"
Parameter "readFlag_isProperPair": "TRUE"
Parameter "readFlag_isUnmappedQuery": "FALSE"
Parameter "readFlag_hasUnmappedMate": "FALSE"
Parameter "readFlag_isMinusStrand": "NA"
Parameter "readFlag_isMateMinusStrand": "NA"
Parameter "readFlag_isFirstMateRead": "NA"
Parameter "readFlag_isSecondMateRead": "NA"
Parameter "readFlag_isNotPrimaryRead": "FALSE"
Parameter "readFlag_isNotPassingQualityControls": "FALSE"
Parameter "readFlag_isDuplicate": "FALSE"
Parameter "readFlag_reverseComplement": "FALSE"
Parameter "readFlag_simpleCigar": "TRUE"
Parameter "readFlag_minMapQ": "0"
Parameter "path_userRegions": "C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/cisQ.H3K27AC.chr21.txt"
Parameter "zeroBasedCoordinates": "FALSE"
Parameter "regionSize": "500"
Parameter "binSize": "25"
Parameter "readGroupSpecific": "TRUE"
Parameter "strand": "both"
Parameter "startOpen": "FALSE"
Parameter "endOpen": "FALSE"
Parameter "headerLine": "FALSE"
Parameter "linesToParse": "-1"
Parameter "lastBinTreatment": "delete"
Parameter "assemblyVersion": "hg19"
Parameter "effectiveGenomeSizePercentage": "-1"
Parameter "nCores": "1"
Parameter "keepAllReadCounts": "FALSE"
Parameter "normByInput": "FALSE"
Parameter "normAmongEachOther": "TRUE"
Parameter "poolDatasets": "TRUE"
Add strand information for all regions. Assume strand is irrelevant (*)...
Modify chromosome names because they do not start with "chr"
Parse the user regions file
Finished parsing. Number of entries processed: 178
Split regions into bins
The last bin in each region will be deleted as they are shorter than the other bins (1 bp as compared to 25 bp).
Split 174 entries into 6960 bins
Execution time: 0.4 secs
Parse BAM header...
Read group specific reporting has been requested. The following read groups have been identified in the BAM header: paternal, maternal, ambiguous
PROCESS INPUT FILE SET NA (1 of 1)
PROCESS INDIVIDUAL 1 from 2: GM10847
PROCESS FILE 1 of 2:C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam
Parse BAM header...
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam for the SNPs only (this may take a while)...
Determine genotype distribution at original user positions for A, C, G, and T...
Read group paternal
Read group maternal
Read group ambiguous
Execution time: 2.8 secs
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam for the full SNP regions (this may take a while)...
Analyze read counts specifically for each read group (this may take a while)...
Read group paternal...
Filtered 18252 reads out of 19726 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Read group maternal...
Filtered 18426 reads out of 19726 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Read group ambiguous...
Filtered 2774 reads out of 19726 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
PROCESS FILE 2 of 2:C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam
Parse BAM header...
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam for the SNPs only (this may take a while)...
Determine genotype distribution at original user positions for A, C, G, and T...
Read group paternal
Read group maternal
Read group ambiguous
Execution time: 3.5 secs
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam for the full SNP regions (this may take a while)...
Analyze read counts specifically for each read group (this may take a while)...
Read group paternal...
Filtered 16388 reads out of 17792 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Read group maternal...
Filtered 16552 reads out of 17792 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Read group ambiguous...
Filtered 2644 reads out of 17792 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM10847_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Normalize library sizes...
converting counts to integer mode
Number of genes on which library normalization using DeSeq2 is based on out of 174:171
FINISHED PROCESSING INDIVIDUAL
Execution time: 38.5 secs
PROCESS INDIVIDUAL 2 from 2: GM12890
PROCESS FILE 1 of 2:C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam
Parse BAM header...
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam for the SNPs only (this may take a while)...
Determine genotype distribution at original user positions for A, C, G, and T...
Read group paternal
Read group maternal
Read group ambiguous
Execution time: 2.8 secs
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam for the full SNP regions (this may take a while)...
Analyze read counts specifically for each read group (this may take a while)...
Read group paternal...
Filtered 22076 reads out of 24172 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Read group maternal...
Filtered 20929 reads out of 24172 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Read group ambiguous...
Filtered 5339 reads out of 24172 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_1_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
PROCESS FILE 2 of 2:C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam
Parse BAM header...
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam for the SNPs only (this may take a while)...
Determine genotype distribution at original user positions for A, C, G, and T...
Read group paternal
Read group maternal
Read group ambiguous
Execution time: 2.8 secs
Extract data from BAM file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam for the full SNP regions (this may take a while)...
Analyze read counts specifically for each read group (this may take a while)...
Read group paternal...
Filtered 23541 reads out of 25733 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Read group maternal...
Filtered 22839 reads out of 25733 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Read group ambiguous...
Filtered 5086 reads out of 25733 in file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/SNYDER_HG19_GM12890_H3K27AC_2_reconcile.dedup.chr21.bam because of strand and read group
Analyze read counts per bin (this may take a while)...
Normalize library sizes...
converting counts to integer mode
Number of genes on which library normalization using DeSeq2 is based on out of 174:159
FINISHED PROCESSING INDIVIDUAL
Execution time: 34.4 secs
FINISHED PROCESSING INPUT SET NA.
Execution time: 1.2 mins
FINISHED SUCCESSFULLY WITH ALL INPUT FILES.
Execution time: 1.3 mins
Warnings may have occurred, as indicated. Please check them carefully with unique(warnings()).
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/visualizeCounts-1.png" -trim "workflow_files/figure-html/visualizeCounts-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/visualizeCounts-2.png" -trim "workflow_files/figure-html/visualizeCounts-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/visualizeCounts-3.png" -trim "workflow_files/figure-html/visualizeCounts-3.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/visualizeCounts-4.png" -trim "workflow_files/figure-html/visualizeCounts-4.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/visualizeCounts2-1.png" -trim "workflow_files/figure-html/visualizeCounts2-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/allelicBias2-1.png" -trim "workflow_files/figure-html/allelicBias2-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/allelicBias2-2.png" -trim "workflow_files/figure-html/allelicBias2-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/allelicBias3-1.png" -trim "workflow_files/figure-html/allelicBias3-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/clusterCountMatrix-1.png" -trim "workflow_files/figure-html/clusterCountMatrix-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/clusterCountMatrix-2.png" -trim "workflow_files/figure-html/clusterCountMatrix-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/clusterCountMatrix2-1.png" -trim "workflow_files/figure-html/clusterCountMatrix2-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/summarizeClusters-1.png" -trim "workflow_files/figure-html/summarizeClusters-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "workflow_files/figure-html/summarizeClusters-2.png" -trim "workflow_files/figure-html/summarizeClusters-2.png"' execution failed with error code 4
Import genotypes from file C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPhoodData/extdata/genotypes.vcf.gz. This may take a while...
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Quitting from lines 331-336 (workflow.Rmd)
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
--- failed re-building 'workflow.Rmd'
SUMMARY: processing the following file failed:
'workflow.Rmd'
Error: Vignette re-building failed.
Execution halted