Error: Can't subset elements that don't exist. x Location 1 doesn't exist. ℹ There are only 0 elements.

[JAYRJPT]

I am using the updated RNAseqCNV Package. However I am getting the following error RNAseqCNV_wrapper(config = "/media/deepak/Deepak4T/NEW_SAMPLE/SAMPLE_5/RNASEQCNV/RNASEQCNV/config_file" , metadata = "/media/deepak/Deepak4T/NEW_SAMPLE/SAMPLE_5/RNASEQCNV/RNASEQCNV/snv_metadata.csv", snv_format = "vcf") [1] "Analysis initiated" [1] "Normalization for sample: BALL5 completed" [1] "Preparing file with snv information for: BALL5" Reading in vcf file.. Extracting depth.. Extracting reference allele and alternative allele depths.. Needed information from vcf extracted Finished reading vcf Error: Can't subset elements that don't exist. x Location 1 doesn't exist. ℹ There are only 0 elements. Run rlang::last_error() to see where the error occurred. In addition: Warning message: In colnames(count_norm)[2:length(countnorm)] <- paste0("control", : number of items to replace is not a multiple of replacement length

Kindly help in troubleshooting the Issue.

Thanks

[JAYRJPT]

Further I am getting this error in shinny app Problem with filter() input ..1. x i.l is type list which is not supported by data.table join ℹ Input ..1 is |....

[honzee]

Thank you for bringing that up, I will look into it.

Best, Jan

[honzee]

Dear JAYRJPT,

it might have something to do with an incompatible format of the input count data. I have a few questions so we can solve this quickly for you.

1. Could you please run: rlang:last_error() ,so we have more information about the error?

2. Does this happen for all of your files or is this file specific?

3. The fastest way to solve this issue would be to send me the data (in this case the count file would be probably enough) and I would find out what the issue was. However, I understand, that this might not be possible. I will try to help you nonetheless.

Best, Jan

[JAYRJPT]

I have used the same file which I used before for RNAseqCNV analysis. Earlier it worked but now its not. 1. Here is the error > rlang::last_error() <error/dplyr_error> Problem with filter() input ..1. x i.l is type list which is not supported by data.table join ℹ Input ..1 is |.... Backtrace:

1. RNAseqCNV::RNAseqCNV_wrapper(...)
   19. base::.handleSimpleError(...)
   20. dplyr:::h(simpleError(msg, call))
   21. dplyr:::stop_dplyr(...) Run rlang::last_trace() to see the full context.

2. Error is same in all the files. I have generated the vcf using gatk pipeline.

3. How to send you the data? Its not possible to send all the files. Representative files can be sent.

Thanks, Jay

[honzee]

Thank you for the information. Since these are the files, that previously worked, I will try to rewind some of the changes in code that might be behind these issues. If this does not work, we can arrange sending some representative files.

Thanks, Jan

[honzee]

Dear JAY,

I have one more question for you. Have you updated the RNAseqCNV package before it stopped working? This is quite important. If you did, then the current changes (back to the former version) might help you and I would suggest you to install the RNAseqCNV version I uploaded today. On the other hand, if the analysis stopped working without you updating RNAseqCNV, then it might have something to do with versioning of the other packages used and I would need to look for problems there

In any case, you could share the test data through dropbox/google disc or some other storage option. You could send me the link to this email: jan.barinka@lfmotol.cuni.cz

Thank you, Jan

[JAYRJPT]

Dear JAN, Yes I have updated the package before it stopped working. I have once again removed the package and reinstalled it but unfortunately I am getting the same error. I think problem lies with some of its dependencies. I will send you the files sure Thanks, JAY

[honzee]

I agree, that there might be a dependency issue. Some new package version is probably not compatible with RNAseqCNV. Please run:

utils::sessionInfo()

This enables me to explore the differences in our environments and hopefully get to the bottom of the problem. Thanks, Jan

[honzee]

P.S. Your file ran without a problem on my machine.

[JAYRJPT]

R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8 LC_PAPER=en_IN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] RNAseqCNV_1.2

loaded via a namespace (and not attached): [1] colorspace_1.4-1 ggsignif_0.6.0 ellipsis_0.3.1 rio_0.5.16 htmlTable_2.0.1 XVector_0.26.0 GenomicRanges_1.38.0
[8] base64enc_0.1-3 fs_1.5.0 rstudioapi_0.11 ggpubr_0.4.0 bit64_4.0.2 AnnotationDbi_1.48.0 fansi_0.4.1
[15] splines_3.6.3 geneplotter_1.64.0 knitr_1.29 Formula_1.2-3 jsonlite_1.7.0 broom_0.7.0 annotate_1.64.0
[22] cluster_2.1.0 png_0.1-7 shiny_1.5.0 compiler_3.6.3 backports_1.1.8 assertthat_0.2.1 Matrix_1.2-18
[29] fastmap_1.0.1 cli_2.0.2 later_1.1.0.1 htmltools_0.5.0 tools_3.6.3 gtable_0.3.0 glue_1.4.1
[36] GenomeInfoDbData_1.2.2 dplyr_1.0.1 Rcpp_1.0.5 carData_3.0-4 Biobase_2.46.0 cellranger_1.1.0 vctrs_0.3.2
[43] xfun_0.16 stringr_1.4.0 openxlsx_4.1.5 mime_0.9 lifecycle_0.2.0 rstatix_0.6.0 XML_3.99-0.3
[50] zlibbioc_1.32.0 scales_1.1.1 hms_0.5.3 promises_1.1.1 parallel_3.6.3 SummarizedExperiment_1.16.1 RColorBrewer_1.1-2
[57] curl_4.3 memoise_1.1.0 gridExtra_2.3 ggplot2_3.3.2 rpart_4.1-15 latticeExtra_0.6-29 stringi_1.4.6
[64] RSQLite_2.2.0 genefilter_1.68.0 S4Vectors_0.24.4 checkmate_2.0.0 BiocGenerics_0.32.0 zip_2.1.0 BiocParallel_1.20.1
[71] GenomeInfoDb_1.22.1 rlang_0.4.7 pkgconfig_2.0.3 matrixStats_0.56.0 bitops_1.0-6 lattice_0.20-41 purrr_0.3.4
[78] htmlwidgets_1.5.1 bit_4.0.4 tidyselect_1.1.0 magrittr_1.5 DESeq2_1.26.0 R6_2.4.1 IRanges_2.20.2
[85] generics_0.0.2 Hmisc_4.4-1 DelayedArray_0.12.3 DBI_1.1.0 pillar_1.4.6 haven_2.3.1 foreign_0.8-76
[92] survival_3.2-3 abind_1.4-5 RCurl_1.98-1.2 nnet_7.3-14 tibble_3.0.3 crayon_1.3.4 car_3.0-9
[99] shinyFiles_0.8.0 jpeg_0.1-8.1 locfit_1.5-9.4 grid_3.6.3 readxl_1.3.1 data.table_1.13.0 blob_1.2.1
[106] forcats_0.5.0 digest_0.6.25 xtable_1.8-4 tidyr_1.1.1 httpuv_1.5.4 stats4_3.6.3 munsell_0.5.0

[honzee]

Dear Jay,

I have updated a number of packages and I encountered a similar error to the one you have sent. This error was due to updated tidyverse functions. I have updated RNAseqCNV accordingly.

I hope this solves your issue, please let me know.

Best, Jan

[JAYRJPT]

Dear Jan, Thanks for the update. I am now able to run the package. However I like to inform you that in the final figure lower panel of the graph( MAF frequency) is mising. Is this the issue with my file or with the package? I have sent you the same file. Did you also faced the same issue? I have also got the following warning-

Warning messages: 1: In dir.create(path = chr_dir) : '/media/deepak/Deepak4T/NEW_SAMPLE/SAMPLE_5/RNASEQCNV/RNASEQCNV/output_dir/BALL5' already exists 2: Graphs cannot be vertically aligned unless the axis parameter is set. Placing graphs unaligned. 3: In max(peak_max) : no non-missing arguments to max; returning -Inf 4: Position guide is perpendicular to the intended axis. Did you mean to specify a different guide position?

Regards, Jay

[honzee]

Dear Jay,

I am glad that the first issue is solved. If you do not mind, I will address the next topic in a new thread.

Best, Jan

[honzee]

https://github.com/honzee/RNAseqCNV/issues/6#issue-678715910