Hello,
I have used the standard pipeline for SNP6 CEL files described in the
CRMAv2 vignette. I did run the pipeline before several times, without any
issue.
Now, the fragment length normalization step failed with an error:
Error in gzfile(file, mode) : cannot open the connection
I am not clear where this error comes from.
Any support or idea is welcome.
Best regards,
Thomas
*My sessionInfo:*
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.light_3.0.0 aroma.affymetrix_3.0.0 aroma.core_3.0.0
[4] R.devices_2.14.0 R.filesets_2.10.0 R.utils_2.3.0
[7] R.oo_1.20.0 affxparser_1.42.0 R.methodsS3_1.7.1
loaded via a namespace (and not attached):
[1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_0.14.0
[5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.2.1
[9] R.cache_0.12.0 parallel_3.2.1 base64enc_0.1-3 aroma.apd_0.6.0
[13] R.rsp_0.30.0 globals_0.6.1 DNAcopy_1.44.0
*The full output of the process(fln, verbose=verbose) function:*
> cesN <- process(fln, verbose=verbose)
20160713 12:50:05|Normalizing set for PCR fragment-length effects...
20160713 12:51:07| Identifying SNP and CN units...
types
1 2 5
621 934968 945826
20160713 12:51:09| subsetToUpdate:
int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
20160713 12:51:09| Identifying SNP and CN units...done
20160713 12:51:09| Retrieving SNP information annotations...
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na33,hg19,dbSNP137,HB20140118
Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl
File size: 7.18 MiB (7526422 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
20160713 12:51:10| Retrieving SNP information annotations...done
20160713 12:51:10| Identifying the subset used to fit normalization
function(s)...
20160713 12:51:10| Identifying units that are SNP and CN probes...
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na33,hg19,dbSNP137,HB20140118
Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl
File size: 7.18 MiB (7526422 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
20160713 12:51:10| Identifying SNPs and CN probes...
types
1 2 5
621 934968 945826
20160713 12:51:11| units:
int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
20160713 12:51:11| Identifying SNPs and CN probes...done
20160713 12:51:11| Identify subset of units from genome information...
20160713 12:51:11| subsetToFit: -XY
UgpGenomeInformation:
Name: GenomeWideSNP_6
Tags: Full,na33,hg19,dbSNP137,HB20140118
Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ugp
File size: 8.97 MiB (9407882 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
20160713 12:51:18| Units to exclude:
int [1:96544] 61101 61102 61103 61104 61105 61106 61107 61108 61109 61110
...
20160713 12:51:19| Units to include:
int [1:1784871] 1 2 3 4 5 6 7 8 9 10 ...
20160713 12:51:19| Identify subset of units from genome information...done
20160713 12:51:19| Reading fragment lengths...
20160713 12:51:19| Reading and filtering fragment lengths...
20160713 12:51:19| Reading fragment lengths...
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na33,hg19,dbSNP137,HB20140118
Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl
File size: 7.18 MiB (7526422 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
20160713 12:51:26| Summary of non-filtered fragment lengths:
int [1:1880794, 1:2] 395 4056 633 831 970 1508 4025 4557 3779 420 ...
V1 V2
Min. : 7.0 Min. : 7
1st Qu.: 430.0 1st Qu.: 628
Median : 676.0 Median : 1078
Mean : 915.2 Mean : 1410
3rd Qu.: 970.0 3rd Qu.: 1730
Max. :32767.0 Max. :32767
NA's :2279 NA's :447301
20160713 12:51:27| Reading fragment lengths...done
20160713 12:51:27| Filtering fragment lengths...
20160713 12:51:27| Filtering fragment lengths...done
20160713 12:51:27| Reading and filtering fragment lengths...done
20160713 12:51:27| Reading fragment lengths...done
20160713 12:51:28| Identifying units that are SNP and CN probes...done
int [1:1784250] 622 623 624 625 626 627 628 629 630 631 ...
20160713 12:51:28| Identifying the subset used to fit normalization
function(s)...done
20160713 12:51:28| Shift: 0
20160713 12:51:28| onMissing: median
20160713 12:51:28| Array #1 of 1213
('ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002')...
20160713 12:51:28| Reading and filtering fragment lengths...
20160713 12:51:28| Reading fragment lengths...
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na33,hg19,dbSNP137,HB20140118
Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl
File size: 7.18 MiB (7526422 bytes)
RAM: 14.36 MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
20160713 12:51:33| Summary of non-filtered fragment lengths:
int [1:1880794, 1:2] 395 4056 633 831 970 1508 4025 4557 3779 420 ...
V1 V2
Min. : 7.0 Min. : 7
1st Qu.: 430.0 1st Qu.: 628
Median : 676.0 Median : 1078
Mean : 915.2 Mean : 1410
3rd Qu.: 970.0 3rd Qu.: 1730
Max. :32767.0 Max. :32767
NA's :2279 NA's :447301
20160713 12:51:37| Reading fragment lengths...done
20160713 12:51:37| Filtering fragment lengths...
20160713 12:51:37| Filtering fragment lengths...done
20160713 12:51:37| Reading and filtering fragment lengths...done
V1 V2
Min. : 7.0 Min. : 7
1st Qu.: 430.0 1st Qu.: 628
Median : 676.0 Median : 1078
Mean : 915.2 Mean : 1410
3rd Qu.: 970.0 3rd Qu.: 1730
Max. :32767.0 Max. :32767
NA's :2279 NA's :447301
int [1:1784250] 1 2 3 4 5 6 7 8 9 10 ...
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na33,hg19,dbSNP137,HB20140118
Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
Pathname:
annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl
File size: 7.18 MiB (7526422 bytes)
RAM: 14.36 MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
20160713 12:51:40| Setting up predefined target functions...
20160713 12:51:40| Target type: zero
20160713 12:51:40| Setting up predefined target functions...done
20160713 12:51:40| Getting cell matrix map...
'UnitGroupCellMatrixMap' int [1:1880794, 1:2] 622 624 626 628 630 632 634
636 638 640 ...
20160713 12:51:44| Getting cell matrix map...done
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file
'/scratch/tmp/RtmpwSx59C/libloc_178_ccc298d560fce69b.rds', probable reason
'No such file or directory'
20160713 12:51:45| Array #1 of 1213
('ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002')...done
20160713 12:51:45|Normalizing set for PCR fragment-length effects...done
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