segmentation fault (core dumped) running eQTL.Catalogue.query()

[AMCalejandro]

HI,

I am having this issue running eQTL.Catalogue.query. I thought It could be somehow related with tabix, so I updated the yaml file. I removed tabix, and added htslib to solve the environment again. The output did not change

r$> gwas.qtl_paths <- eQTL_Catalogue.query(sumstats_paths = sumstats_paths,   
                                           qtl_search = c("myeloid","Alasoo_2018"), 
                                           output_dir = "./catalogueR_queries",  
                                           split_files = T,   
                                           merge_with_gwas = T, 
                                           force_new_subset = T, 
                                           nThread=4)                                                                                                                                                      
[1] "++ R package `pbmcapply` not installed. Turning off `progress_bar`."
[1] "+ Optimizing multi-threading..."
[1] "++ Multi-threading across QTL datasets."
[1] "eQTL_Catalogue:: Querying 4 QTL datasets x 1 GWAS loci (4 total)"
Alasoo_2018.macrophage_naive
Alasoo_2018.macrophage_IFNg
Alasoo_2018.macrophage_Salmonella
Alasoo_2018.macrophage_IFNg+Salmonella
[1][1] "++ Extracting locus name from `sumstats_paths` names." "++ Extracting locus name from `sumstats_paths` names."

[1] "++ Extracting locus name from `sumstats_paths` names."
_+_+_+_+_+_+_+_+_--- Locus: BST1 ---_+_+_+_+_+_+_+_+_
_+_+_+_+_+_+_+_+_--- Locus: BST1 ---_+_+_+_+_+_+_+_+_
_+_+_+_+_+_+_+_+_--- Locus: BST1 ---_+_+_+_+_+_+_+_+_
[1] "++ Extracting locus name from `sumstats_paths` names."
_+_+_+_+_+_+_+_+_--- Locus: BST1 ---_+_+_+_+_+_+_+_+_
Start at 2022-02-02 14:39:32

Start at 2022-02-02 14:39:33

Start at 2022-02-02 14:39:33

Start at 2022-02-02 14:39:33


End at 2022-02-02 14:39:38
Runtime in total is: 6 secs

[1] "++ Inferring coordinates from gwas_data"

End at 2022-02-02 14:39:39
Runtime in total is: 6 secs

[1] "+ CONDA:: Identified tabix executable in echoR env."
[1] "/home/acarrasco/.conda/envs/echoR/bin/tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_IFNg+Salmonella.all.tsv.gz 4:14735725-16735661"
Segmentation fault (core dumped)
[1] "Data dimensions: 0 x 0"
[1] "++ Merging GWAS data and QTL query results."
[1] "Data dimensions: 0 x 0"
[1] "Data dimensions:  x "
[1] "+ Returning list of split query results files."
[1] "++ Inferring coordinates from gwas_data"

End at 2022-02-02 14:39:40
Runtime in total is: 7 secs

[1] "+ CONDA:: Identified tabix executable in echoR env."
[1] "/home/acarrasco/.conda/envs/echoR/bin/tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_naive.all.tsv.gz 4:14735725-16735661"
Segmentation fault (core dumped)
[1] "Data dimensions: 0 x 0"
[1] "++ Merging GWAS data and QTL query results."
[1] "Data dimensions: 0 x 0"
[1] "Data dimensions:  x "
[1] "+ Returning list of split query results files."
[1] "++ Inferring coordinates from gwas_data"
[1] "+ CONDA:: Identified tabix executable in echoR env."
[1] "/home/acarrasco/.conda/envs/echoR/bin/tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_IFNg.all.tsv.gz 4:14735725-16735661"
Segmentation fault (core dumped)
[1] "Data dimensions: 0 x 0"
[1] "++ Merging GWAS data and QTL query results."
[1] "Data dimensions: 0 x 0"
[1] "Data dimensions:  x "
[1] "+ Returning list of split query results files."
[1] "++ Returning list of split files paths."
[1] "Data dimensions:  x "
Time difference of 13.5 secs
Warning message:
In lapply_func(qtl_datasets, function(qtl_id, .sumstats_paths = sumstats_paths,  :
  scheduled core 3 encountered error in user code, all values of the job will be affected

r$> sumstats_paths                                                                                                                                                                                         
                                                                                                                               BST1 
"/home/acarrasco/.conda/envs/catalogueR_V2/lib/R/library/catalogueR/extdata/Nalls23andMe_2019/BST1_Nalls23andMe_2019_subset.tsv.gz" 

r$> sessionInfo()                                                                                                                                                                                          
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS/LAPACK: /home/acarrasco/.conda/envs/catalogueR_V2/lib/libopenblasp-r0.3.18.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               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] reticulate_1.24   R.utils_2.11.0    R.oo_1.24.0       R.methodsS3_1.8.1 catalogueR_0.1.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8        pillar_1.7.0      compiler_4.1.2    prettyunits_1.1.1 remotes_2.4.2     tools_4.1.2       pkgbuild_1.3.1    jsonlite_1.7.3    lattice_0.20-45   lifecycle_1.0.1   tibble_3.1.6     
[12] gtable_0.3.0      png_0.1-7         pkgconfig_2.0.3   rlang_1.0.0       Matrix_1.4-0      cli_3.1.1         DBI_1.1.2         parallel_4.1.2    curl_4.3.2        withr_2.4.3       dplyr_1.0.7      
[23] generics_0.1.2    vctrs_0.3.8       rprojroot_2.0.2   grid_4.1.2        tidyselect_1.1.1  glue_1.6.1        data.table_1.14.2 R6_2.5.1          processx_3.5.2    fansi_1.0.2       callr_3.7.0      
[34] purrr_0.3.4       ggplot2_3.3.5     magrittr_2.0.2    scales_1.1.1      ps_1.6.0          ellipsis_0.3.2    assertthat_0.2.1  colorspace_2.0-2  utf8_1.2.2        munsell_0.5.0     crayon_1.4.2     

Update

I read #6, and thought it could make sense to try an install catalogueR directly on the echolocatoR conda env It did not work

Also, I read the README and made sure, I have data.table >1.14. Same error arised

r$> gwas.qtl_paths <- eQTL_Catalogue.query(sumstats_paths = sumstats_paths[1],   
                                           qtl_search = c("myeloid","Alasoo_2018"), 
                                           output_dir = "./catalogueR_queries",  
                                           split_files = T,   
                                           merge_with_gwas = T, 
                                           force_new_subset = T, 
                                           nThread=4)                                                                                                                                                      
[1] "++ R package `pbmcapply` not installed. Turning off `progress_bar`."
[1] "+ Optimizing multi-threading..."
[1] "++ Multi-threading across QTL datasets."
[1] "eQTL_Catalogue:: Querying 4 QTL datasets x 1 GWAS loci (4 total)"
Alasoo_2018.macrophage_naive
Alasoo_2018.macrophage_IFNg
Alasoo_2018.macrophage_Salmonella
Alasoo_2018.macrophage_IFNg+Salmonella
[1][1] "++ Extracting locus name from `sumstats_paths` names." "++ Extracting locus name from `sumstats_paths` names."

_+_+_+_+_+_+_+_+_--- Locus: BST1 ---_+_+_+_+_+_+_+_+_
_+_+_+_+_+_+_+_+_--- Locus: BST1 ---_+_+_+_+_+_+_+_+_
[1] "++ Extracting locus name from `sumstats_paths` names."
_+_+_+_+_+_+_+_+_--- Locus: BST1 ---_+_+_+_+_+_+_+_+_
[1] "++ Extracting locus name from `sumstats_paths` names."
_+_+_+_+_+_+_+_+_--- Locus: BST1 ---_+_+_+_+_+_+_+_+_
Start at 2022-02-03 14:30:21

Start at 2022-02-03 14:30:21

Start at 2022-02-03 14:30:21

Start at 2022-02-03 14:30:21


End at 2022-02-03 14:30:27
Runtime in total is: 6 secs


End at 2022-02-03 14:30:27
Runtime in total is: 6 secs


End at 2022-02-03 14:30:27
Runtime in total is: 6 secs

[1] "++ Inferring coordinates from gwas_data"
[1] "++ Inferring coordinates from gwas_data"
[1] "++ Inferring coordinates from gwas_data"

End at 2022-02-03 14:30:27
Runtime in total is: 6 secs

[1] "++ Inferring coordinates from gwas_data"
[1] "+ CONDA:: Identified tabix executable in echoR env."
[1] "/home/acarrasco/.conda/envs/echoR/bin/tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_IFNg+Salmonella.all.tsv.gz 4:14735725-16735661"
[1] "+ CONDA:: Identified tabix executable in echoR env."
[1] "/home/acarrasco/.conda/envs/echoR/bin/tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_Salmonella.all.tsv.gz 4:14735725-16735661"
[1] "+ CONDA:: Identified tabix executable in echoR env."
[1] "/home/acarrasco/.conda/envs/echoR/bin/tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_naive.all.tsv.gz 4:14735725-16735661"
[1] "+ CONDA:: Identified tabix executable in echoR env."
[1] "/home/acarrasco/.conda/envs/echoR/bin/tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_IFNg.all.tsv.gz 4:14735725-16735661"
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
Segmentation fault (core dumped)
[1] "Data dimensions: 0 x 0"
[1] "++ Merging GWAS data and QTL query results."
[1] "Data dimensions: 0 x 0"
[1] "Data dimensions:  x "
[1] "+ Returning list of split query results files."
[1] "Data dimensions: 0 x 0"
[1] "++ Merging GWAS data and QTL query results."
[1] "Data dimensions: 0 x 0"
[1] "Data dimensions:  x "
[1] "+ Returning list of split query results files."
[1] "Data dimensions: 0 x 0"
[1] "++ Merging GWAS data and QTL query results."
[1] "Data dimensions: 0 x 0"
[1] "Data dimensions:  x "
[1] "+ Returning list of split query results files."
[1] "Data dimensions: 0 x 0"
[1] "++ Merging GWAS data and QTL query results."
[1] "Data dimensions: 0 x 0"
[1] "Data dimensions:  x "
[1] "+ Returning list of split query results files."
[1] "++ Returning list of split files paths."
[1] "Data dimensions:  x "
Time difference of 10.6 secs
Warning message:
In lapply_func(qtl_datasets, function(qtl_id, .sumstats_paths = sumstats_paths,  :
  scheduled core 3 encountered error in user code, all values of the job will be affected

r$> sessionInfo()                                                                                                                                                                                          
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS/LAPACK: /home/acarrasco/.conda/envs/catalogue_V3/lib/libopenblasp-r0.3.18.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               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] R.utils_2.11.0    R.oo_1.24.0       R.methodsS3_1.8.1 reticulate_1.24   data.table_1.13.6 catalogueR_0.1.0 

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.1  remotes_2.4.2     purrr_0.3.4       haven_2.4.3       lattice_0.20-45   colorspace_2.0-2  vctrs_0.3.8       generics_0.1.2    utf8_1.2.2        rlang_1.0.1       pkgbuild_1.3.1   
[12] pillar_1.7.0      glue_1.6.1        withr_2.4.3       DBI_1.1.2         dbplyr_2.1.1      modelr_0.1.8      lifecycle_1.0.1   munsell_0.5.0     gtable_0.3.0      forcats_0.5.1     callr_3.7.0      
[23] tzdb_0.2.0        ps_1.6.0          curl_4.3.2        parallel_4.0.5    fansi_1.0.2       broom_0.7.12      Rcpp_1.0.8        readr_2.1.2       scales_1.1.1      backports_1.4.1   jsonlite_1.7.3   
[34] ggplot2_3.3.5     hms_1.1.1         png_0.1-7         processx_3.5.2    dplyr_1.0.7       grid_4.0.5        rprojroot_2.0.2   cli_3.1.1         tools_4.0.5       magrittr_2.0.2    tibble_3.1.6     
[45] crayon_1.4.2      tidyr_1.2.0       pkgconfig_2.0.3   ellipsis_0.3.2    Matrix_1.4-0      prettyunits_1.1.1 lubridate_1.8.0   assertthat_0.2.1  httr_1.4.2        R6_2.5.1          compiler_4.0.5 

sessionInfo

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

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

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

other attached packages:
 [1] catalogueR_1.0.0                         snpStats_1.47.1                          Matrix_1.4-1                             survival_3.3-1                          
 [5] echolocatoR_2.0.1                        remotes_2.4.2                            ewceData_1.5.0                           ExperimentHub_2.5.0                     
 [9] AnnotationHub_3.5.0                      BiocFileCache_2.5.0                      dbplyr_2.2.1                             MAGMA.Celltyping_2.0.7                  
[13] SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20 BSgenome_1.65.2                          rtracklayer_1.57.0                       Biostrings_2.65.3                       
[17] XVector_0.37.1                           GenomicRanges_1.49.1                     GenomeInfoDb_1.33.5                      IRanges_2.31.2                          
[21] S4Vectors_0.35.3                         BiocGenerics_0.43.1                      here_1.0.1                               forcats_0.5.2                           
[25] stringr_1.4.1                            dplyr_1.0.10                             purrr_0.3.4                              readr_2.1.2                             
[29] tidyr_1.2.0                              tibble_3.1.8                             ggplot2_3.3.6                            tidyverse_1.3.2                         
[33] data.table_1.14.2                       

loaded via a namespace (and not attached):
  [1] Hmisc_4.7-1                   class_7.3-20                  ps_1.7.1                      Rsamtools_2.13.4              rprojroot_2.0.3              
  [6] echotabix_0.99.8              crayon_1.5.1                  MASS_7.3-58.1                 nlme_3.1-159                  backports_1.4.1              
 [11] reprex_2.0.2                  basilisk_1.9.2                rlang_1.0.5                   readxl_1.4.1                  irlba_2.3.5                  
 [16] nloptr_2.0.3                  callr_3.7.2                   limma_3.53.6                  filelock_1.0.2                BiocParallel_1.31.12         
 [21] rjson_0.2.21                  bit64_4.0.5                   glue_1.6.2                    mixsqp_0.3-43                 parallel_4.2.0               
 [26] processx_3.7.0                AnnotationDbi_1.59.1          HGNChelper_0.8.1              haven_2.5.1                   tidyselect_1.1.2             
 [31] SummarizedExperiment_1.27.2   coloc_5.1.0                   XML_3.99-0.10                 ggpubr_0.4.0                  GenomicAlignments_1.33.1     
 [36] echoplot_0.99.5               xtable_1.8-4                  ggnetwork_0.5.10              magrittr_2.0.3                cli_3.3.0                    
 [41] zlibbioc_1.43.0               rstudioapi_0.14               rpart_4.1.16                  echoannot_0.99.7              ensembldb_2.21.4             
 [46] treeio_1.21.2                 shiny_1.7.2                   xfun_0.32                     pkgbuild_1.3.1                cluster_2.1.3                
 [51] echoconda_0.99.7              KEGGREST_1.37.3               interactiveDisplayBase_1.35.0 expm_0.999-6                  ggrepel_0.9.1                
 [56] biovizBase_1.45.0             ape_5.6-2                     echodata_0.99.12              png_0.1-7                     reshape_0.8.9                
 [61] withr_2.5.0                   bitops_1.0-7                  RBGL_1.73.0                   plyr_1.8.7                    cellranger_1.1.0             
 [66] AnnotationFilter_1.21.0       e1071_1.7-11                  pillar_1.8.1                  cachem_1.0.6                  GenomicFeatures_1.49.6       
 [71] fs_1.5.2                      googleAuthR_2.0.0             echoLD_0.99.7                 osfr_0.2.8                    vctrs_0.4.1                  
 [76] ellipsis_0.3.2                generics_0.1.3                gh_1.3.0                      tools_4.2.0                   foreign_0.8-82               
 [81] munsell_0.5.0                 susieR_0.12.27                proxy_0.4-27                  DelayedArray_0.23.1           fastmap_1.1.0                
 [86] compiler_4.2.0                abind_1.4-5                   httpuv_1.6.5                  DescTools_0.99.46             plotly_4.10.0                
 [91] GenomeInfoDbData_1.2.8        gridExtra_2.3                 lattice_0.20-45               dir.expiry_1.5.0              deldir_1.0-6                 
 [96] gitcreds_0.1.1                utf8_1.2.2                    later_1.3.0                   jsonlite_1.8.0                GGally_2.1.2                 
[101] scales_1.2.1                  gld_2.6.5                     graph_1.75.0                  tidytree_0.4.0                carData_3.0-5                
[106] lazyeval_0.2.2                promises_1.2.0.1              car_3.1-0                     RCircos_1.2.2                 latticeExtra_0.6-30          
[111] R.utils_2.12.0                reticulate_1.26               checkmate_2.1.0               openxlsx_4.2.5                textshaping_0.3.6            
[116] dichromat_2.0-0.1             Biobase_2.57.1                igraph_1.3.4                  yaml_2.3.5                    systemfonts_1.0.4            
[121] htmltools_0.5.3               memoise_2.0.1                 VariantAnnotation_1.43.3      BiocIO_1.7.1                  supraHex_1.35.0              
[126] viridisLite_0.4.1             digest_0.6.29                 assertthat_0.2.1              mime_0.12                     piggyback_0.1.3              
[131] rappdirs_0.3.3                dnet_1.1.7                    downloadR_0.99.4              RSQLite_2.2.16                yulab.utils_0.0.5            
[136] Exact_3.1                     orthogene_1.3.2               blob_1.2.3                    R.oo_1.25.0                   ragg_1.2.2                   
[141] splines_4.2.0                 Formula_1.2-4                 labeling_0.4.2                googledrive_2.0.0             OrganismDbi_1.39.1           
[146] ProtGenerics_1.29.0           RCurl_1.98-1.8                broom_1.0.1                   hms_1.1.2                     modelr_0.1.9                 
[151] gprofiler2_0.2.1              colorspace_2.0-3              base64enc_0.1-3               BiocManager_1.30.18           echofinemap_0.99.3           
[156] aplot_0.1.6                   nnet_7.3-17                   Rcpp_1.0.9                    mvtnorm_1.1-3                 fansi_1.0.3                  
[161] tzdb_0.3.0                    R6_2.5.1                      grid_4.2.0                    crul_1.2.0                    lifecycle_1.0.1              
[166] rootSolve_1.8.2.3             zip_2.2.0                     MungeSumstats_1.5.13          curl_4.3.2                    ggsignif_0.6.3               
[171] googlesheets4_1.0.1           minqa_1.2.4                   XGR_1.1.8                     ggbio_1.45.0                  RColorBrewer_1.1-3           
[176] htmlwidgets_1.5.4             biomaRt_2.53.2                gridGraphics_0.5-1            rvest_1.0.3                   lmom_2.9                     
[181] htmlTable_2.4.1               patchwork_1.1.2               codetools_0.2-18              EnsDb.Hsapiens.v75_2.99.0     matrixStats_0.62.0           
[186] lubridate_1.8.0               EWCE_1.5.7                    prettyunits_1.1.1             SingleCellExperiment_1.19.0   basilisk.utils_1.9.2         
[191] R.methodsS3_1.8.2             gtable_0.3.1                  DBI_1.1.3                     ggfun_0.0.7                   httr_1.4.4                   
[196] stringi_1.7.8                 progress_1.2.2                reshape2_1.4.4                farver_2.1.1                  viridis_0.6.2                
[201] hexbin_1.28.2                 Rgraphviz_2.41.1              ggtree_3.5.3                  DT_0.24                       xml2_1.3.3                   
[206] ggdendro_0.1.23               boot_1.3-28                   lme4_1.1-30                   restfulr_0.0.15               RNOmni_1.0.1                 
[211] interp_1.1-3                  ggplotify_0.1.0               homologene_1.4.68.19.3.27     BiocVersion_3.16.0            bit_4.0.4                    
[216] jpeg_0.1-9                    MatrixGenerics_1.9.1          pkgconfig_2.0.3               babelgene_22.3                gargle_1.2.0                 
[221] rstatix_0.7.0                 knitr_1.40                    httpcode_0.3.0       

[bschilder]

Hi @AMCalejandro, I've just finished a major overhaul of catalogueR to make it compatible with the echoverse, and fix a number of issues with the original version.

Could you try reinstalling catalogueR from the master branch and running this example?

sumstats_paths <- echodata::get_Nalls2019_loci(limit_snps = 10)
GWAS.QTL <- catalogueR::eQTLcatalogue_query(
    sumstats_paths = sumstats_paths$BST1,
    qtl_search = "Alasoo_2018.macrophage_naive")

[bschilder]

@AMCalejandro — catalogueR was completely overhauled for echoverse compatibility. The old eQTL_Catalogue.query() function was replaced with eQTLcatalogue_query(). The segfault was likely related to tabix/htslib issues in the conda environment. The new version defaults to the REST API method which avoids tabix entirely. Please reinstall from master and use the updated function names.