Unable to reproduce "Full pipeline vignette" about echolocator HOT 6 CLOSED

Hi @alexMarCar, could you please share your session info?
utils::sessionInfo()

Sometimes, if finemap_loci() runs into an error the first time you run it (e.g. misspecified arguments, missing input files) an empty .vcf file is generated. When you go to rerun finemap_loci() after correcting the inputs, it will detect the .vcf file and try to use it (which fails). Here's two solutions you can try:

1. Set force_new_LD = T
2. Delete the empty vcf files and try again

Hope that helps!

Thanks,
Brian

from echolocator.

Thanks for the early reply - It did not work though.
Same error after forcing the LD calculation and remove all the files under results dir.

Here is my session info

r$> utils::sessionInfo()                                                                             
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS/LAPACK: /home/acarrasco/.conda/envs/echoR/lib/libopenblasp-r0.3.12.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] echolocatoR_0.1.2

loaded via a namespace (and not attached):
  [1] colorspace_2.0-0            ellipsis_0.3.1              class_7.3-18               
  [4] biovizBase_1.38.0           htmlTable_2.1.0             XVector_0.30.0             
  [7] GenomicRanges_1.42.0        base64enc_0.1-3             gld_2.6.2                  
 [10] dichromat_2.0-0             rstudioapi_0.13             proxy_0.4-25               
 [13] DT_0.18                     bit64_4.0.5                 AnnotationDbi_1.52.0       
 [16] fansi_0.4.2                 mvtnorm_1.1-1               xml2_1.3.2                 
 [19] R.methodsS3_1.8.1           splines_4.0.3               ggbio_1.38.0               
 [22] cachem_1.0.4                rootSolve_1.8.2.1           knitr_1.33                 
 [25] jsonlite_1.7.2              Formula_1.2-4               Rsamtools_2.6.0            
 [28] dbplyr_2.1.1                cluster_2.1.1               R.oo_1.24.0                
 [31] png_0.1-7                   graph_1.68.0                BiocManager_1.30.12        
 [34] compiler_4.0.3              httr_1.4.2                  backports_1.2.1            
 [37] assertthat_0.2.1            Matrix_1.3-2                fastmap_1.1.0              
 [40] lazyeval_0.2.2              htmltools_0.5.1.1           prettyunits_1.1.1          
 [43] tools_4.0.3                 gtable_0.3.0                glue_1.4.2                 
 [46] lmom_2.8                    GenomeInfoDbData_1.2.4      reshape2_1.4.4             
 [49] dplyr_1.0.5                 rappdirs_0.3.3              Rcpp_1.0.6                 
 [52] Biobase_2.50.0              vctrs_0.3.7                 Biostrings_2.58.0          
 [55] rtracklayer_1.50.0          crosstalk_1.1.1             xfun_0.22                  
 [58] stringr_1.4.0               lifecycle_1.0.0             ensembldb_2.14.1           
 [61] XML_3.99-0.6                zlibbioc_1.36.0             MASS_7.3-53.1              
 [64] scales_1.1.1                BSgenome_1.58.0             VariantAnnotation_1.36.0   
 [67] ProtGenerics_1.22.0         hms_1.0.0                   MatrixGenerics_1.2.1       
 [70] RBGL_1.66.0                 parallel_4.0.3              SummarizedExperiment_1.20.0
 [73] expm_0.999-6                AnnotationFilter_1.14.0     RColorBrewer_1.1-2         
 [76] curl_4.3                    Exact_2.1                   reticulate_1.19            
 [79] memoise_2.0.0               gridExtra_2.3               ggplot2_3.3.3              
 [82] biomaRt_2.46.3              rpart_4.1-15                reshape_0.8.8              
 [85] latticeExtra_0.6-29         stringi_1.5.3               RSQLite_2.2.5              
 [88] S4Vectors_0.28.1            e1071_1.7-6                 checkmate_2.0.0            
 [91] GenomicFeatures_1.42.3      BiocGenerics_0.36.1         boot_1.3-27                
 [94] BiocParallel_1.24.1         GenomeInfoDb_1.26.7         rlang_0.4.10               
 [97] pkgconfig_2.0.3             matrixStats_0.58.0          bitops_1.0-7               
[100] lattice_0.20-41             purrr_0.3.4                 GenomicAlignments_1.26.0   
[103] htmlwidgets_1.5.3           bit_4.0.4                   tidyselect_1.1.0           
[106] GGally_2.1.1                plyr_1.8.6                  magrittr_2.0.1             
[109] R6_2.5.0                    IRanges_2.24.1              DescTools_0.99.41          
[112] generics_0.1.0              Hmisc_4.5-0                 DelayedArray_0.16.3        
[115] DBI_1.1.1                   pillar_1.6.0                foreign_0.8-81             
[118] survival_3.2-11             RCurl_1.98-1.3              nnet_7.3-15                
[121] tibble_3.1.1                crayon_1.4.1                utf8_1.2.1                 
[124] OrganismDbi_1.32.0          BiocFileCache_1.14.0        jpeg_0.1-8.1               
[127] progress_1.2.2              grid_4.0.3                  data.table_1.14.0          
[130] blob_1.2.1                  digest_0.6.27               R.utils_2.10.1             
[133] openssl_1.4.3               stats4_4.0.3                munsell_0.5.0              
[136] askpass_1.1                

Many thanks!,
Alejandro.

from echolocator.

I did not manage to reproduce the full pipeline vignette after trying to install echolocatoR ( and all its deppendencies) directly on my HPC cluster.

I think there is an issue when accessing to the 1000G reference data.

BW,
Alejandro.

from echolocator.

Hi Alejandro,

did you mange to solve the issue on a cluster? I get the same error and issue and am not sure how to solve this?

thanks
saskia

from echolocator.

HI @satzel - No, sorry. I did not look into this further.

from echolocator.

Not sure exactly why this happened, but I agree seems to be related to connecting to the 1KG FTP server on your HPC. I seem to be able to run the pipeline on my local machine. I suppose it's also possible the FTP server was down for a period.

I've made some improvements to the VCF querying functionality in the echoverse branch (soon to become the master branch), via the subpackage echotabix which uses an entirely R-native implementation of tabix querying (rather than relying on the CLI version). Hopefully this will help to avoid these issues in the future.

from echolocator.