That looks like a hiccup in the file system or something. Did you try again?
Also, if the error remains, please report what traceback() outputs (as
the first command after you get the error).
/Henrik
On Wed, Jul 13, 2016 at 4:19 AM, <thomas.grombac...@merckgroup.com> wrote:
> 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
>
>
>
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
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--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
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