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Some IDAT files are not present in the supplied base directory #54

Closed jennyujin22 closed 2 months ago

jennyujin22 commented 2 months ago

Dear Michael,

Even I already specify the barcode (SentrixID_SentrixPosition) and check if IDAT prefix is corresponding to barcode, there is an error "Some IDAT files are not present in the supplied base directory". (also I checked scientific notations).

here is my sessionInfo()

R version 4.4.0 (2024-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=Korean_Korea.utf8 LC_CTYPE=Korean_Korea.utf8 LC_MONETARY=Korean_Korea.utf8 LC_NUMERIC=C
[5] LC_TIME=Korean_Korea.utf8

time zone: Asia/Seoul tzcode source: internal

attached base packages: [1] parallel grid stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] RnBeads.hg19_1.36.0 RnBeads_2.22.0 plyr_1.8.9
[4] methylumi_2.50.0 minfi_1.50.0 bumphunter_1.46.0
[7] locfit_1.5-9.9 iterators_1.0.14 foreach_1.5.2
[10] Biostrings_2.72.0 XVector_0.44.0 SummarizedExperiment_1.34.0
[13] MatrixGenerics_1.16.0 FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.19.1
[16] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.56.0 AnnotationDbi_1.66.0
[19] reshape2_1.4.4 scales_1.3.0 Biobase_2.64.0
[22] illuminaio_0.46.0 matrixStats_1.3.0 limma_3.60.0
[25] gridExtra_2.3 gplots_3.1.3.1 ggplot2_3.5.1
[28] fields_15.2 viridisLite_0.4.2 spam_2.10-0
[31] ff_4.0.12 bit_4.0.5 cluster_2.1.6
[34] MASS_7.3-60.2 GenomicRanges_1.56.0 GenomeInfoDb_1.40.0
[37] IRanges_2.38.0 S4Vectors_0.41.6 sesame_1.22.0
[40] sesameData_1.22.0 ExperimentHub_2.12.0 AnnotationHub_3.12.0
[43] BiocFileCache_2.11.2 dbplyr_2.5.0 BiocGenerics_0.49.1

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 magrittr_2.0.3 BiocIO_1.14.0
[6] zlibbioc_1.50.0 vctrs_0.6.5 multtest_2.60.0 memoise_2.0.1 Rsamtools_2.20.0
[11] DelayedMatrixStats_1.26.0 RCurl_1.98-1.14 askpass_1.2.0 S4Arrays_1.4.0 curl_5.2.1
[16] Rhdf5lib_1.26.0 rhdf5_2.48.0 SparseArray_1.4.0 nor1mix_1.3-3 KernSmooth_2.23-22
[21] cachem_1.0.8 GenomicAlignments_1.40.0 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-0
[26] R6_2.5.1 fastmap_1.1.1 GenomeInfoDbData_1.2.12 digest_0.6.35 siggenes_1.78.0
[31] reshape_0.8.9 colorspace_2.1-0 RSQLite_2.3.6 base64_2.0.1 filelock_1.0.3
[36] fansi_1.0.6 beanplot_1.3.1 httr_1.4.7 abind_1.4-5 compiler_4.4.0
[41] rngtools_1.5.2 bit64_4.0.5 withr_3.0.0 BiocParallel_1.38.0 DBI_1.2.2
[46] HDF5Array_1.32.0 maps_3.4.2 openssl_2.1.2 rappdirs_0.3.3 DelayedArray_0.30.0
[51] rjson_0.2.21 gtools_3.9.5 caTools_1.18.2 tools_4.4.0 quadprog_1.5-8
[56] glue_1.7.0 restfulr_0.0.15 nlme_3.1-164 rhdf5filters_1.16.0 generics_0.1.3
[61] gtable_0.3.5 tzdb_0.4.0 preprocessCore_1.66.0 tidyr_1.3.1 data.table_1.15.4
[66] hms_1.1.3 xml2_1.3.6 utf8_1.2.4 BiocVersion_3.19.1 pillar_1.9.0
[71] stringr_1.5.1 genefilter_1.86.0 splines_4.4.0 dplyr_1.1.4 lattice_0.22-6
[76] survival_3.5-8 rtracklayer_1.64.0 GEOquery_2.72.0 annotate_1.82.0 tidyselect_1.2.1
[81] wheatmap_0.2.0 scrime_1.3.5 statmod_1.5.0 stringi_1.8.3 UCSC.utils_1.0.0
[86] yaml_2.3.8 codetools_0.2-20 tibble_3.2.1 BiocManager_1.30.23 cli_3.6.2
[91] xtable_1.8-4 munsell_0.5.1 Rcpp_1.0.12 png_0.1-8 XML_3.99-0.16.1
[96] readr_2.1.5 blob_1.2.4 mclust_6.1.1 dotCall64_1.1-1 doRNG_1.8.6
[101] sparseMatrixStats_1.16.0 bitops_1.0-7 purrr_1.0.2 crayon_1.5.2 rlang_1.1.3
[106] KEGGREST_1.44.0

Thanks a lot.

Best,

Yujin

Originally posted by @jennyujin22 in https://github.com/epigen/RnBeads/issues/38#issuecomment-2102102765

schmic05 commented 2 months ago

Dear Yujin,

Can you share your sample annotation sheet and the output of ls in your idat directory? Also please show me the command that you use to start RnBeads. You can send this by email to michael.scherer at dkfz.de

Best,

Michael

jennyujin22 @.***> schrieb am Do., 9. Mai 2024, 09:22:

Dear Michael,

Even I already specify the barcode (SentrixID_SentrixPosition) and check if IDAT prefix is corresponding to barcode, there is an error "Some IDAT files are not present in the supplied base directory". (also I checked scientific notations).

here is my sessionInfo()

R version 4.4.0 (2024-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=Korean_Korea.utf8 LC_CTYPE=Korean_Korea.utf8 LC_MONETARY=Korean_Korea.utf8 LC_NUMERIC=C [5] LC_TIME=Korean_Korea.utf8

time zone: Asia/Seoul tzcode source: internal

attached base packages: [1] parallel grid stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] RnBeads.hg19_1.36.0 RnBeads_2.22.0 plyr_1.8.9 [4] methylumi_2.50.0 minfi_1.50.0 bumphunter_1.46.0 [7] locfit_1.5-9.9 iterators_1.0.14 foreach_1.5.2 [10] Biostrings_2.72.0 XVector_0.44.0 SummarizedExperiment_1.34.0 [13] MatrixGenerics_1.16.0 FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.19.1 [16] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.56.0 AnnotationDbi_1.66.0 [19] reshape2_1.4.4 scales_1.3.0 Biobase_2.64.0 [22] illuminaio_0.46.0 matrixStats_1.3.0 limma_3.60.0 [25] gridExtra_2.3 gplots_3.1.3.1 ggplot2_3.5.1 [28] fields_15.2 viridisLite_0.4.2 spam_2.10-0 [31] ff_4.0.12 bit_4.0.5 cluster_2.1.6 [34] MASS_7.3-60.2 GenomicRanges_1.56.0 GenomeInfoDb_1.40.0 [37] IRanges_2.38.0 S4Vectors_0.41.6 sesame_1.22.0 [40] sesameData_1.22.0 ExperimentHub_2.12.0 AnnotationHub_3.12.0 [43] BiocFileCache_2.11.2 dbplyr_2.5.0 BiocGenerics_0.49.1

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 magrittr_2.0.3 BiocIO_1.14.0 [6] zlibbioc_1.50.0 vctrs_0.6.5 multtest_2.60.0 memoise_2.0.1 Rsamtools_2.20.0 [11] DelayedMatrixStats_1.26.0 RCurl_1.98-1.14 askpass_1.2.0 S4Arrays_1.4.0 curl_5.2.1 [16] Rhdf5lib_1.26.0 rhdf5_2.48.0 SparseArray_1.4.0 nor1mix_1.3-3 KernSmooth_2.23-22 [21] cachem_1.0.8 GenomicAlignments_1.40.0 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-0 [26] R6_2.5.1 fastmap_1.1.1 GenomeInfoDbData_1.2.12 digest_0.6.35 siggenes_1.78.0 [31] reshape_0.8.9 colorspace_2.1-0 RSQLite_2.3.6 base64_2.0.1 filelock_1.0.3 [36] fansi_1.0.6 beanplot_1.3.1 httr_1.4.7 abind_1.4-5 compiler_4.4.0 [41] rngtools_1.5.2 bit64_4.0.5 withr_3.0.0 BiocParallel_1.38.0 DBI_1.2.2 [46] HDF5Array_1.32.0 maps_3.4.2 openssl_2.1.2 rappdirs_0.3.3 DelayedArray_0.30.0 [51] rjson_0.2.21 gtools_3.9.5 caTools_1.18.2 tools_4.4.0 quadprog_1.5-8 [56] glue_1.7.0 restfulr_0.0.15 nlme_3.1-164 rhdf5filters_1.16.0 generics_0.1.3 [61] gtable_0.3.5 tzdb_0.4.0 preprocessCore_1.66.0 tidyr_1.3.1 data.table_1.15.4 [66] hms_1.1.3 xml2_1.3.6 utf8_1.2.4 BiocVersion_3.19.1 pillar_1.9.0 [71] stringr_1.5.1 genefilter_1.86.0 splines_4.4.0 dplyr_1.1.4 lattice_0.22-6 [76] survival_3.5-8 rtracklayer_1.64.0 GEOquery_2.72.0 annotate_1.82.0 tidyselect_1.2.1 [81] wheatmap_0.2.0 scrime_1.3.5 statmod_1.5.0 stringi_1.8.3 UCSC.utils_1.0.0 [86] yaml_2.3.8 codetools_0.2-20 tibble_3.2.1 BiocManager_1.30.23 cli_3.6.2 [91] xtable_1.8-4 munsell_0.5.1 Rcpp_1.0.12 png_0.1-8 XML_3.99-0.16.1 [96] readr_2.1.5 blob_1.2.4 mclust_6.1.1 dotCall64_1.1-1 doRNG_1.8.6 [101] sparseMatrixStats_1.16.0 bitops_1.0-7 purrr_1.0.2 crayon_1.5.2 rlang_1.1.3 [106] KEGGREST_1.44.0

Thanks a lot.

Best,

Yujin

Originally posted by @jennyujin22 https://github.com/jennyujin22 in #38 (comment) https://github.com/epigen/RnBeads/issues/38#issuecomment-2102102765

— Reply to this email directly, view it on GitHub https://github.com/epigen/RnBeads/issues/54, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADYQQ6CXHQNHA2PIQUUIVBTZBMP4XAVCNFSM6AAAAABHOKAWUKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4DOMBWHAZDGMA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

jennyujin22 commented 2 months ago

I sent it by email :)

Thanks a lot!