createArrowFiles has encountered an error #1778

wz0527 · 2022-12-20T13:59:02Z

wz0527
Dec 20, 2022

Hello,
I encounter an error "createArrowFiles has encountered an error, checking if any ArrowFiles completed" when I used the function createArrowFiles, and the returned object was empty. I don't know what the exact issue is about this error and how to fix it. By the way, my datasets were generated from Zebrafish. Thanks!

My code is below:

>addArchRThreads(threads = 16)
>genomeAnnotation = createGenomeAnnotation(genome = BSgenome.Drerio.UCSC.danRer10)
>levels(genomeAnnotation@listData$chromSizes@seqnames) = c(1:25)

>geneAnnotation <- createGeneAnnotation(TxDb = TxDb.Drerio.UCSC.danRer10.refGene, 
                                       OrgDb = org.Dr.eg.db)
>levels(geneAnnotation@listData$genes@seqnames)[1:26] = c(1:25,'MT')
>levels(geneAnnotation@listData$exons@seqnames)[1:26] = c(1:25,'MT')
>levels(geneAnnotation@listData$TSS@seqnames)[1:26] = c(1:25,'MT')

>zf_frag = c("ZF_Het_Comb" = './Het/outs/fragments.tsv.gz',
            "ZF_WT_Comb" = './Wt/outs/fragments.tsv.gz')

>zf_comb <- createArrowFiles(
  inputFiles = zf_frag,
  sampleNames = names(zf_frag),
  minTSS = 4, #Dont set this too high because you can always increase later
  minFrags = 1000, 
  addTileMat = TRUE,
  addGeneScoreMat = TRUE,
  genomeAnnotation = genomeAnnotation ,
  geneAnnotation = geneAnnotation
)

After encountered the error

> traceback()
8: FUN(X[[i]], ...)
7: lapply(X = X, FUN = FUN, ...)
6: sapply(pkgDesc, function(x) !is.null(x$Priority) && x$Priority == 
       "base")
5: sessionInfo()
4: withVisible(...elt(i))
3: utils::capture.output(sessionInfo(), file = logFile, append = TRUE)
2: .startLogging(logFile = logFile)
1: createArrowFiles(inputFiles = zf_frag, sampleNames = names(zf_frag), 
       minTSS = 4, minFrags = 1000, addTileMat = TRUE, addGeneScoreMat = TRUE, 
       genomeAnnotation = genomeAnnotation, geneAnnotation = geneAnnotation)

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] Rsamtools_2.10.0                        future_1.30.0                           patchwork_1.1.2                        
 [4] org.Dr.eg.db_3.14.0                     TxDb.Drerio.UCSC.danRer10.refGene_3.4.6 GenomicFeatures_1.46.5                 
 [7] AnnotationDbi_1.56.2                    BSgenome.Drerio.UCSC.danRer10_1.4.2     BSgenome_1.62.0                        
[10] rtracklayer_1.54.0                      Biostrings_2.62.0                       XVector_0.34.0                         
[13] rhdf5_2.38.1                            SummarizedExperiment_1.24.0             Biobase_2.54.0                         
[16] MatrixGenerics_1.6.0                    Rcpp_1.0.9                              Matrix_1.5-3                           
[19] GenomicRanges_1.46.1                    GenomeInfoDb_1.30.1                     IRanges_2.28.0                         
[22] S4Vectors_0.32.4                        BiocGenerics_0.40.0                     matrixStats_0.63.0                     
[25] data.table_1.14.6                       stringr_1.5.0                           plyr_1.8.8                             
[28] magrittr_2.0.3                          ggplot2_3.3.6                           gtable_0.3.1                           
[31] gtools_3.9.4                            gridExtra_2.3                           ArchR_1.0.2                            
[34] Signac_1.9.0                            SeuratObject_4.1.3                      Seurat_4.3.0                           

loaded via a namespace (and not attached):
  [1] utf8_1.2.2               spatstat.explore_3.0-5   reticulate_1.26          tidyselect_1.2.0        
  [5] RSQLite_2.2.19           htmlwidgets_1.5.4        BiocParallel_1.28.3      Rtsne_0.16              
  [9] munsell_0.5.0            codetools_0.2-18         ica_1.0-3                miniUI_0.1.1.1          
 [13] withr_2.5.0              spatstat.random_3.0-1    colorspace_2.0-3         progressr_0.12.0        
 [17] filelock_1.0.2           rstudioapi_0.14          ROCR_1.0-11              tensor_1.5              
 [21] listenv_0.9.0            labeling_0.4.2           GenomeInfoDbData_1.2.7   polyclip_1.10-4         
 [25] bit64_4.0.5              farver_2.1.1             parallelly_1.33.0        vctrs_0.5.1             
 [29] generics_0.1.3           BiocFileCache_2.2.1      R6_2.5.1                 bitops_1.0-7            
 [33] rhdf5filters_1.6.0       spatstat.utils_3.0-1     cachem_1.0.6             DelayedArray_0.20.0     
 [37] assertthat_0.2.1         promises_1.2.0.1         BiocIO_1.4.0             scales_1.2.1            
 [41] Cairo_1.6-0              globals_0.16.2           goftest_1.2-3            rlang_1.0.6             
 [45] RcppRoll_0.3.0           splines_4.1.0            lazyeval_0.2.2           spatstat.geom_3.0-3     
 [49] yaml_2.3.6               reshape2_1.4.4           abind_1.4-5              httpuv_1.6.7            
 [53] tools_4.1.0              ellipsis_0.3.2           RColorBrewer_1.1-3       ggridges_0.5.4          
 [57] progress_1.2.2           zlibbioc_1.40.0          purrr_0.3.5              RCurl_1.98-1.9          
 [61] prettyunits_1.1.1        deldir_1.0-6             pbapply_1.6-0            cowplot_1.1.1           
 [65] zoo_1.8-11               ggrepel_0.9.1            cluster_2.1.4            scattermore_0.8         
 [69] lmtest_0.9-40            RANN_2.6.1               fitdistrplus_1.1-8       hms_1.1.2               
 [73] mime_0.12                xtable_1.8-4             XML_3.99-0.13            compiler_4.1.0          
 [77] biomaRt_2.50.3           tibble_3.1.8             KernSmooth_2.23-20       crayon_1.5.2            
 [81] htmltools_0.5.4          later_1.3.0              tidyr_1.2.1              DBI_1.1.3               
 [85] dbplyr_2.2.1             MASS_7.3-58.1            rappdirs_0.3.3           cli_3.4.1               
 [89] igraph_1.3.5             pkgconfig_2.0.3          GenomicAlignments_1.30.0 sp_1.5-1                
 [93] plotly_4.10.0            spatstat.sparse_3.0-0    xml2_1.3.3               digest_0.6.31           
 [97] sctransform_0.3.5        RcppAnnoy_0.0.20         spatstat.data_3.0-0      leiden_0.4.3            
[101] fastmatch_1.1-3          uwot_0.1.14              restfulr_0.0.15          curl_4.3.3              
[105] shiny_1.7.2              rjson_0.2.21             lifecycle_1.0.3          nlme_3.1-161            
[109] jsonlite_1.8.4           Rhdf5lib_1.16.0          viridisLite_0.4.1        fansi_1.0.3             
[113] pillar_1.8.1             lattice_0.20-45          KEGGREST_1.34.0          fastmap_1.1.0           
[117] httr_1.4.4               survival_3.4-0           glue_1.6.2               png_0.1-8               
[121] bit_4.0.5                stringi_1.7.8            blob_1.2.3               memoise_2.0.1           
[125] dplyr_1.0.10             irlba_2.3.5.1            future.apply_1.9.1

My log file is below:

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
Logging With ArchR!

Start Time : 2022-12-20 13:47:13

------- ArchR Info

ArchRThreads = 16

------- System Info

Computer OS = unix
Total Cores = 32

------- Session Info

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] Rsamtools_2.10.0                        future_1.30.0                           patchwork_1.1.2                        
 [4] org.Dr.eg.db_3.14.0                     TxDb.Drerio.UCSC.danRer10.refGene_3.4.6 GenomicFeatures_1.46.5                 
 [7] AnnotationDbi_1.56.2                    BSgenome.Drerio.UCSC.danRer10_1.4.2     BSgenome_1.62.0                        
[10] rtracklayer_1.54.0                      Biostrings_2.62.0                       XVector_0.34.0                         
[13] rhdf5_2.38.1                            SummarizedExperiment_1.24.0             Biobase_2.54.0                         
[16] MatrixGenerics_1.6.0                    Rcpp_1.0.9                              Matrix_1.5-3                           
[19] GenomicRanges_1.46.1                    GenomeInfoDb_1.30.1                     IRanges_2.28.0                         
[22] S4Vectors_0.32.4                        BiocGenerics_0.40.0                     matrixStats_0.63.0                     
[25] data.table_1.14.6                       stringr_1.4.1                           plyr_1.8.8                             
[28] magrittr_2.0.3                          ggplot2_3.3.6                           gtable_0.3.1                           
[31] gtools_3.9.4                            gridExtra_2.3                           ArchR_1.0.2                            
[34] Signac_1.9.0                            SeuratObject_4.1.3                      Seurat_4.3.0                           

loaded via a namespace (and not attached):
  [1] utf8_1.2.2               spatstat.explore_3.0-5   reticulate_1.26          tidyselect_1.1.2        
  [5] RSQLite_2.2.19           htmlwidgets_1.5.4        BiocParallel_1.28.3      Rtsne_0.16              
  [9] munsell_0.5.0            codetools_0.2-18         ica_1.0-3                miniUI_0.1.1.1          
 [13] withr_2.5.0              spatstat.random_3.0-1    colorspace_2.0-3         progressr_0.12.0        
 [17] filelock_1.0.2           rstudioapi_0.14          ROCR_1.0-11              tensor_1.5              
 [21] listenv_0.9.0            labeling_0.4.2           GenomeInfoDbData_1.2.7   polyclip_1.10-4         
 [25] bit64_4.0.5              farver_2.1.1             parallelly_1.33.0        vctrs_0.5.1             
 [29] generics_0.1.3           BiocFileCache_2.2.1      R6_2.5.1                 bitops_1.0-7            
 [33] rhdf5filters_1.6.0       spatstat.utils_3.0-1     cachem_1.0.6             DelayedArray_0.20.0     
 [37] assertthat_0.2.1         promises_1.2.0.1         BiocIO_1.4.0             scales_1.2.1            
 [41] Cairo_1.6-0              globals_0.16.2           goftest_1.2-3            rlang_1.0.6             
 [45] RcppRoll_0.3.0           splines_4.1.0            lazyeval_0.2.2           spatstat.geom_3.0-3     
 [49] yaml_2.3.6               reshape2_1.4.4           abind_1.4-5              httpuv_1.6.7            
 [53] tools_4.1.0              ellipsis_0.3.2           RColorBrewer_1.1-3       ggridges_0.5.4          
 [57] progress_1.2.2           zlibbioc_1.40.0          purrr_0.3.5              RCurl_1.98-1.9          
 [61] prettyunits_1.1.1        deldir_1.0-6             pbapply_1.6-0            cowplot_1.1.1           
 [65] zoo_1.8-11               ggrepel_0.9.1            cluster_2.1.4            scattermore_0.8         
 [69] lmtest_0.9-40            RANN_2.6.1               fitdistrplus_1.1-8       hms_1.1.2               
 [73] mime_0.12                xtable_1.8-4             XML_3.99-0.13            compiler_4.1.0          
 [77] biomaRt_2.50.3           tibble_3.1.8             KernSmooth_2.23-20       crayon_1.5.2            
 [81] htmltools_0.5.4          later_1.3.0              tidyr_1.2.1              DBI_1.1.3               
 [85] dbplyr_2.2.1             MASS_7.3-58.1            rappdirs_0.3.3           cli_3.4.1               
 [89] igraph_1.3.5             pkgconfig_2.0.3          GenomicAlignments_1.30.0 sp_1.5-1                
 [93] plotly_4.10.0            spatstat.sparse_3.0-0    xml2_1.3.3               digest_0.6.31           
 [97] sctransform_0.3.5        RcppAnnoy_0.0.20         spatstat.data_3.0-0      leiden_0.4.3            
[101] fastmatch_1.1-3          uwot_0.1.14              restfulr_0.0.15          curl_4.3.3              
[105] shiny_1.7.2              rjson_0.2.21             lifecycle_1.0.3          nlme_3.1-161            
[109] jsonlite_1.8.4           Rhdf5lib_1.16.0          viridisLite_0.4.1        fansi_1.0.3             
[113] pillar_1.8.1             lattice_0.20-45          KEGGREST_1.34.0          fastmap_1.1.0           
[117] httr_1.4.4               survival_3.4-0           glue_1.6.2               png_0.1-8               
[121] bit_4.0.5                stringi_1.7.8            blob_1.2.3               memoise_2.0.1           
[125] dplyr_1.0.10             irlba_2.3.5.1            future.apply_1.9.1      


------- Log Info


2022-12-20 13:47:13 : createArrowFiles Input-Parameters, Class = list

createArrowFiles Input-Parameters$inputFiles: length = 2
                                                                    ZF_Het_Comb 
"/data/depater_group/wzhang/atac_seq/EdP_Het_ZF_combined/outs/fragments.tsv.gz" 
                                                                     ZF_WT_Comb 
  "/data/depater_group/wzhang/atac_seq/EdP_WT_ZFcombined/outs/fragments.tsv.gz" 


createArrowFiles Input-Parameters$sampleNames: length = 2
[1] "ZF_Het_Comb" "ZF_WT_Comb" 


createArrowFiles Input-Parameters$outputNames: length = 2
[1] "ZF_Het_Comb" "ZF_WT_Comb" 


createArrowFiles Input-Parameters$validBarcodes: length = 0
NULL


createArrowFiles Input-Parameters$minTSS: length = 1
[1] 4


createArrowFiles Input-Parameters$minFrags: length = 1
[1] 1000


createArrowFiles Input-Parameters$maxFrags: length = 1
[1] 1e+05


createArrowFiles Input-Parameters$minFragSize: length = 1
[1] 10


createArrowFiles Input-Parameters$maxFragSize: length = 1
[1] 2000


createArrowFiles Input-Parameters$QCDir: length = 1
[1] "QualityControl"


createArrowFiles Input-Parameters$nucLength: length = 1
[1] 147


createArrowFiles Input-Parameters$promoterRegion: length = 2
[1] 2000  100


createArrowFiles Input-Parameters$excludeChr: length = 2
[1] "chrM" "chrY"


createArrowFiles Input-Parameters$nChunk: length = 1
[1] 5


createArrowFiles Input-Parameters$bcTag: length = 1
[1] "qname"


createArrowFiles Input-Parameters$gsubExpression: length = 0
NULL


createArrowFiles Input-Parameters$bamFlag: length = 0
NULL


createArrowFiles Input-Parameters$offsetPlus: length = 1
[1] 4


createArrowFiles Input-Parameters$offsetMinus: length = 1
[1] -5


createArrowFiles Input-Parameters$addTileMat: length = 1
[1] TRUE


createArrowFiles Input-Parameters$addGeneScoreMat: length = 1
[1] TRUE


createArrowFiles Input-Parameters$force: length = 1
[1] FALSE


createArrowFiles Input-Parameters$threads: length = 1
[1] 16


createArrowFiles Input-Parameters$parallelParam: length = 0
NULL


createArrowFiles Input-Parameters$subThreading: length = 1
[1] TRUE


createArrowFiles Input-Parameters$verbose: length = 1
[1] TRUE


createArrowFiles Input-Parameters$cleanTmp: length = 1
[1] TRUE


createArrowFiles Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-createArrows-1839f448420825-Date-2022-12-20_Time-13-47-13.log"


createArrowFiles Input-Parameters$filterFrags: length = 1
[1] 1000


createArrowFiles Input-Parameters$filterTSS: length = 1
[1] 4



2022-12-20 13:47:15 : Cleaning Temporary Files
2022-12-20 13:47:17 : Batch Execution w/ safelapply!, 0 mins elapsed.

###########
2022-12-20 13:47:17 : Creating Arrow File ZF_Het_Comb.arrow (ZF_Het_Comb : 1 of 2)
###########


2022-12-20 13:47:17 : validBC, Class = NULL

validBC: length = 0
NULL



###########
2022-12-20 13:47:17 : Creating Arrow File ZF_WT_Comb.arrow (ZF_WT_Comb : 2 of 2)
###########


2022-12-20 13:47:17 : validBC, Class = NULL

validBC: length = 0

2022-12-20 13:47:17 : (ZF_Het_Comb : 1 of 2) Determining Arrow Method to use!
NULL

2022-12-20 13:47:18 : (ZF_Het_Comb : 1 of 2) Reading In Fragments from inputFiles (readMethod = tabix), 0.005 mins elapsed.

2022-12-20 13:47:18 : (ZF_Het_Comb : 1 of 2) Tabix Bed To Temporary File, 0.005 mins elapsed.

2022-12-20 13:47:18 : (ZF_WT_Comb : 2 of 2) Determining Arrow Method to use!
2022-12-20 13:47:18 : (ZF_WT_Comb : 2 of 2) Reading In Fragments from inputFiles (readMethod = tabix), 0.006 mins elapsed.
2022-12-20 13:47:18 : (ZF_WT_Comb : 2 of 2) Tabix Bed To Temporary File, 0.007 mins elapsed.

2022-12-20 13:47:18 : tileChromSizes, Class = GRanges
GRanges object with 125 ranges and 1 metadata column:
        seqnames            ranges strand |   chunkName
           <Rle>         <IRanges>  <Rle> | <character>
    [1]        1        1-11774383      * |    1#chunk1
    [2]        1 11774384-23548766      * |    1#chunk2
    [3]        1 23548767-35323150      * |    1#chunk3
    [4]        1 35323151-47097533      * |    1#chunk4
    [5]        1 47097534-58871917      * |    1#chunk5
    ...      ...               ...    ... .         ...
  [121]       25         1-7379752      * | 25#chunk121
  [122]       25  7379753-14759504      * | 25#chunk122
  [123]       25 14759505-22139256      * | 25#chunk123
  [124]       25 22139257-29519008      * | 25#chunk124
  [125]       25 29519009-36898761      * | 25#chunk125
  -------
  seqinfo: 25 sequences from an unspecified genome; no seqlengths


2022-12-20 13:47:18 : tileChromSizes, Class = GRanges
GRanges object with 125 ranges and 1 metadata column:
        seqnames            ranges strand |   chunkName
           <Rle>         <IRanges>  <Rle> | <character>
    [1]        1        1-11774383      * |    1#chunk1
    [2]        1 11774384-23548766      * |    1#chunk2
    [3]        1 23548767-35323150      * |    1#chunk3
    [4]        1 35323151-47097533      * |    1#chunk4
    [5]        1 47097534-58871917      * |    1#chunk5
    ...      ...               ...    ... .         ...
  [121]       25         1-7379752      * | 25#chunk121
  [122]       25  7379753-14759504      * | 25#chunk122
  [123]       25 14759505-22139256      * | 25#chunk123
  [124]       25 22139257-29519008      * | 25#chunk124
  [125]       25 29519009-36898761      * | 25#chunk125
  -------
  seqinfo: 25 sequences from an unspecified genome; no seqlengths


2022-12-20 13:47:21 : (ZF_WT_Comb : 2 of 2) .tabixToTmp Fragments-Chunk-(1 of 125)-1:1-11774383, Class = data.table
 
2022-12-20 13:47:21 : (ZF_WT_Comb : 2 of 2) .tabixToTmp Fragments-Chunk-(1 of 125)-1:1-11774383, Class = data.frame
(ZF_WT_Comb : 2 of 2) .tabixToTmp Fragments-Chunk-(1 of 125)-1:1-11774383: nRows = 617594, nCols = 3
   V2  V3                 V4
1:  5 188 TCACCACAGTATGGGC-1
2: 19 186 GTGACATCAAAGAAGG-1
3: 41 249 TGATGCAAGTGTCCCG-1
4: 47 239 ACGTTAGAGCAATAAC-1
5: 66 103 ACTACGAGTAACCGAG-1
6: 66 262 TTACTTGTCCACACCT-1



2022-12-20 13:47:21 : (ZF_WT_Comb : 2 of 2) .tabixToTmp Barcodes-Chunk-(1 of 125)-1:1-11774383, Class = character

(ZF_WT_Comb : 2 of 2) .tabixToTmp Barcodes-Chunk-(1 of 125)-1:1-11774383: length = 67811
[1] "TCACCACAGTATGGGC-1" "GTGACATCAAAGAAGG-1" "TGATGCAAGTGTCCCG-1" "ACGTTAGAGCAATAAC-1" "ACTACGAGTAACCGAG-1"
[6] "TTACTTGTCCACACCT-1"



2022-12-20 13:47:23 : (ZF_Het_Comb : 1 of 2) .tabixToTmp Fragments-Chunk-(1 of 125)-1:1-11774383, Class = data.table
 
2022-12-20 13:47:23 : (ZF_Het_Comb : 1 of 2) .tabixToTmp Fragments-Chunk-(1 of 125)-1:1-11774383, Class = data.frame
(ZF_Het_Comb : 1 of 2) .tabixToTmp Fragments-Chunk-(1 of 125)-1:1-11774383: nRows = 1156135, nCols = 3
   V2  V3                 V4
1:  6 176 GCTCCTATCATGTTCT-1
2: 16 239 GCGGAAAGTCACCGCA-1
3: 16 249 ATGTTTCGTATCACAC-1
4: 18 226 TGTAAGCCACGAACGA-1
5: 26 229 CATTCCGGTCCGTCGA-1
6: 40 249 TAGCACACATTCTCGC-1



2022-12-20 13:47:23 : (ZF_Het_Comb : 1 of 2) .tabixToTmp Barcodes-Chunk-(1 of 125)-1:1-11774383, Class = character

(ZF_Het_Comb : 1 of 2) .tabixToTmp Barcodes-Chunk-(1 of 125)-1:1-11774383: length = 77257
[1] "GCTCCTATCATGTTCT-1" "GCGGAAAGTCACCGCA-1" "ATGTTTCGTATCACAC-1" "TGTAAGCCACGAACGA-1" "CATTCCGGTCCGTCGA-1"
[6] "TAGCACACATTCTCGC-1"


2022-12-20 13:47:32 : (ZF_WT_Comb : 2 of 2) Reading TabixFile 14 Percent, 0.241 mins elapsed.
2022-12-20 13:47:36 : (ZF_Het_Comb : 1 of 2) Reading TabixFile 14 Percent, 0.314 mins elapsed.
2022-12-20 13:47:43 : (ZF_WT_Comb : 2 of 2) Reading TabixFile 27 Percent, 0.428 mins elapsed.
2022-12-20 13:47:53 : (ZF_Het_Comb : 1 of 2) Reading TabixFile 27 Percent, 0.601 mins elapsed.
2022-12-20 13:47:58 : (ZF_WT_Comb : 2 of 2) Reading TabixFile 41 Percent, 0.686 mins elapsed.
2022-12-20 13:48:13 : (ZF_WT_Comb : 2 of 2) Reading TabixFile 54 Percent, 0.922 mins elapsed.
2022-12-20 13:48:17 : (ZF_Het_Comb : 1 of 2) Reading TabixFile 41 Percent, 0.989 mins elapsed.
2022-12-20 13:48:27 : (ZF_WT_Comb : 2 of 2) Reading TabixFile 68 Percent, 1.157 mins elapsed.
2022-12-20 13:48:34 : (ZF_Het_Comb : 1 of 2) Reading TabixFile 54 Percent, 1.278 mins elapsed.
2022-12-20 13:48:40 : (ZF_WT_Comb : 2 of 2) Reading TabixFile 82 Percent, 1.371 mins elapsed.
2022-12-20 13:48:52 : (ZF_WT_Comb : 2 of 2) Reading TabixFile 95 Percent, 1.581 mins elapsed.
2022-12-20 13:48:52 : (ZF_Het_Comb : 1 of 2) Reading TabixFile 68 Percent, 1.587 mins elapsed.
2022-12-20 13:49:00 : (ZF_WT_Comb : 2 of 2) Parallel Hdf5 Linkage Temporary File, 1.713 mins elapsed.
2022-12-20 13:49:02 : (ZF_WT_Comb : 2 of 2) Successful creation of Temporary File, 1.74 mins elapsed.
2022-12-20 13:49:02 : (ZF_WT_Comb : 2 of 2) Creating ArrowFile From Temporary File, 1.74 mins elapsed.

2022-12-20 13:49:03 : (ZF_WT_Comb : 2 of 2) chunkChrNames, Class = data.frame
(ZF_WT_Comb : 2 of 2) chunkChrNames: nRows = 125, nCols = 1
  chunkNames
1   1#chunk1
2   1#chunk2
3   1#chunk3
4   1#chunk4
5   1#chunk5
6 10#chunk46


2022-12-20 13:49:03 : (ZF_WT_Comb : 2 of 2) Counting Unique Barcodes From Temporary File, 1.759 mins elapsed.
2022-12-20 13:49:09 : (ZF_Het_Comb : 1 of 2) Reading TabixFile 82 Percent, 1.867 mins elapsed.

2022-12-20 13:49:26 : (ZF_WT_Comb : 2 of 2) BarcodeFrequencyTable, Class = data.table
 
2022-12-20 13:49:26 : (ZF_WT_Comb : 2 of 2) BarcodeFrequencyTable, Class = data.frame
(ZF_WT_Comb : 2 of 2) BarcodeFrequencyTable: nRows = 383670, nCols = 2
            values.V1     V1
1: GGAATCTTCGGTAGGA-1 108637
2: GGTGAAGGTTAGGAAT-1 103106
3: GCGAGAAAGTCTGGGA-1 100268
4: GTCACAACACGAACGA-1  97041
5: ACCGCAGGTTGGAGGT-1  86553
6: GTGATCATCCACGGCA-1  78191



2022-12-20 13:49:26 : (ZF_WT_Comb : 2 of 2) BarcodesMinMaxFrags, Class = data.frame
(ZF_WT_Comb : 2 of 2) BarcodesMinMaxFrags: nRows = 15544, nCols = 1
                  bc
1 GTCACAACACGAACGA-1
2 ACCGCAGGTTGGAGGT-1
3 GTGATCATCCACGGCA-1
4 TTGGTCCTCGTGAACT-1
5 ACGTTAGAGAGGTACC-1
6 ATGTCTTGTGAGGTCA-1


2022-12-20 13:49:26 : (ZF_Het_Comb : 1 of 2) Reading TabixFile 95 Percent, 2.153 mins elapsed.

2022-12-20 13:49:28 : (ZF_WT_Comb : 2 of 2) Unique Chromosomes, Class = data.frame
(ZF_WT_Comb : 2 of 2) Unique Chromosomes: nRows = 25, nCols = 1
  chr
1   1
2   2
3   3
4   4
5   5
6   6


2022-12-20 13:49:29 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 1 of 25, 2.19 mins elapsed.
2022-12-20 13:49:29 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 2 of 25, 2.192 mins elapsed.
2022-12-20 13:49:29 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 3 of 25, 2.193 mins elapsed.
2022-12-20 13:49:29 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 4 of 25, 2.195 mins elapsed.
2022-12-20 13:49:29 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 5 of 25, 2.196 mins elapsed.
2022-12-20 13:49:29 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 6 of 25, 2.198 mins elapsed.
2022-12-20 13:49:29 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 7 of 25, 2.199 mins elapsed.
2022-12-20 13:49:29 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 8 of 25, 2.201 mins elapsed.

2022-12-20 13:49:35 : (ZF_WT_Comb : 2 of 2) .tmpToArrow Fragments-Chr-(1 of 25)-1, Class = IRanges

(ZF_WT_Comb : 2 of 2) .tmpToArrow Fragments-Chr-(1 of 25)-1: length = 1901641
IRanges object with 6 ranges and 1 metadata column:
          start       end     width |                 RG
      <integer> <integer> <integer> |              <Rle>
  [1]      9665      9719        55 | GTCACAACACGAACGA-1
  [2]     11559     11776       218 | GTCACAACACGAACGA-1
  [3]     14063     14094        32 | GTCACAACACGAACGA-1
  [4]     16702     16937       236 | GTCACAACACGAACGA-1
  [5]     18612     18657        46 | GTCACAACACGAACGA-1
  [6]     27214     27545       332 | GTCACAACACGAACGA-1



2022-12-20 13:49:35 : (ZF_WT_Comb : 2 of 2) .tmpToArrow Barcodes-Chr-(1 of 25)-1, Class = data.frame
(ZF_WT_Comb : 2 of 2) .tmpToArrow Barcodes-Chr-(1 of 25)-1: nRows = 15544, nCols = 1
                  bc
1 GTCACAACACGAACGA-1
2 ACCGCAGGTTGGAGGT-1
3 GTGATCATCCACGGCA-1
4 TTGGTCCTCGTGAACT-1
5 ACGTTAGAGAGGTACC-1
6 ATGTCTTGTGAGGTCA-1


2022-12-20 13:49:37 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 9 of 25, 2.324 mins elapsed.
2022-12-20 13:49:37 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 10 of 25, 2.335 mins elapsed.
2022-12-20 13:49:38 : (ZF_Het_Comb : 1 of 2) Parallel Hdf5 Linkage Temporary File, 2.342 mins elapsed.
2022-12-20 13:49:38 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 11 of 25, 2.344 mins elapsed.
2022-12-20 13:49:38 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 12 of 25, 2.346 mins elapsed.
2022-12-20 13:49:39 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 13 of 25, 2.355 mins elapsed.
2022-12-20 13:49:39 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 14 of 25, 2.358 mins elapsed.
2022-12-20 13:49:39 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 15 of 25, 2.362 mins elapsed.
2022-12-20 13:49:39 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 16 of 25, 2.364 mins elapsed.
2022-12-20 13:49:39 : (ZF_Het_Comb : 1 of 2) Successful creation of Temporary File, 2.37 mins elapsed.
2022-12-20 13:49:39 : (ZF_Het_Comb : 1 of 2) Creating ArrowFile From Temporary File, 2.37 mins elapsed.

2022-12-20 13:49:40 : (ZF_Het_Comb : 1 of 2) chunkChrNames, Class = data.frame
(ZF_Het_Comb : 1 of 2) chunkChrNames: nRows = 125, nCols = 1
  chunkNames
1   1#chunk1
2   1#chunk2
3   1#chunk3
4   1#chunk4
5   1#chunk5
6 10#chunk46


2022-12-20 13:49:40 : (ZF_Het_Comb : 1 of 2) Counting Unique Barcodes From Temporary File, 2.386 mins elapsed.
2022-12-20 13:49:45 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 17 of 25, 2.463 mins elapsed.
2022-12-20 13:49:45 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 18 of 25, 2.465 mins elapsed.
2022-12-20 13:49:45 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 19 of 25, 2.469 mins elapsed.
2022-12-20 13:49:46 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 20 of 25, 2.475 mins elapsed.
2022-12-20 13:49:47 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 21 of 25, 2.491 mins elapsed.
2022-12-20 13:49:48 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 22 of 25, 2.508 mins elapsed.
2022-12-20 13:49:48 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 23 of 25, 2.511 mins elapsed.
2022-12-20 13:49:48 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 24 of 25, 2.517 mins elapsed.
2022-12-20 13:49:53 : (ZF_WT_Comb : 2 of 2) Adding Chromosome 25 of 25, 2.597 mins elapsed.
2022-12-20 13:50:00 : (ZF_WT_Comb : 2 of 2) Parallel Hdf5 Linkage Arrow File, 2.716 mins elapsed.
2022-12-20 13:50:01 : (ZF_WT_Comb : 2 of 2) Successful creation of Arrow File, 2.723 mins elapsed.
2022-12-20 13:50:03 : (ZF_WT_Comb : 2 of 2) Adding Fragment Summary, 2.756 mins elapsed.

2022-12-20 13:50:08 : (ZF_Het_Comb : 1 of 2) BarcodeFrequencyTable, Class = data.table
 
2022-12-20 13:50:08 : (ZF_Het_Comb : 1 of 2) BarcodeFrequencyTable, Class = data.frame
(ZF_Het_Comb : 1 of 2) BarcodeFrequencyTable: nRows = 454268, nCols = 2
            values.V1    V1
1: TCAAGCATCGATAGCT-1 68894
2: GCATTCCTCGGACGAA-1 61462
3: TTTGCGCAGGGCTCTC-1 60932
4: TCGGGACAGTCAGCCC-1 55703
5: ACAAGCTGTCCAACCG-1 54249
6: GTGCACGCAAAGGCCA-1 53015



2022-12-20 13:50:08 : (ZF_Het_Comb : 1 of 2) BarcodesMinMaxFrags, Class = data.frame
(ZF_Het_Comb : 1 of 2) BarcodesMinMaxFrags: nRows = 52341, nCols = 1
                  bc
1 TCAAGCATCGATAGCT-1
2 GCATTCCTCGGACGAA-1
3 TTTGCGCAGGGCTCTC-1
4 TCGGGACAGTCAGCCC-1
5 ACAAGCTGTCCAACCG-1
6 GTGCACGCAAAGGCCA-1



2022-12-20 13:50:09 : (ZF_Het_Comb : 1 of 2) Unique Chromosomes, Class = data.frame
(ZF_Het_Comb : 1 of 2) Unique Chromosomes: nRows = 25, nCols = 1
  chr
1   1
2   2
3   3
4   4
5   5
6   6


2022-12-20 13:50:10 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 1 of 25, 2.876 mins elapsed.
2022-12-20 13:50:10 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 2 of 25, 2.878 mins elapsed.
2022-12-20 13:50:10 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 3 of 25, 2.879 mins elapsed.
2022-12-20 13:50:10 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 4 of 25, 2.881 mins elapsed.
2022-12-20 13:50:10 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 5 of 25, 2.882 mins elapsed.
2022-12-20 13:50:10 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 6 of 25, 2.884 mins elapsed.
2022-12-20 13:50:10 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 7 of 25, 2.885 mins elapsed.
2022-12-20 13:50:10 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 8 of 25, 2.887 mins elapsed.
2022-12-20 13:50:13 : (ZF_WT_Comb : 2 of 2) Plotting Fragment Size Distribution, 2.929 mins elapsed.
2022-12-20 13:50:14 : (ZF_WT_Comb : 2 of 2) Computing TSS Enrichment Scores, 2.953 mins elapsed.

2022-12-20 13:50:18 : (ZF_Het_Comb : 1 of 2) .tmpToArrow Fragments-Chr-(1 of 25)-1, Class = IRanges

(ZF_Het_Comb : 1 of 2) .tmpToArrow Fragments-Chr-(1 of 25)-1: length = 5513469
IRanges object with 6 ranges and 1 metadata column:
          start       end     width |                 RG
      <integer> <integer> <integer> |              <Rle>
  [1]     25387     25577       191 | TCAAGCATCGATAGCT-1
  [2]     25578     25606        29 | TCAAGCATCGATAGCT-1
  [3]     29804     29845        42 | TCAAGCATCGATAGCT-1
  [4]     39076     39304       229 | TCAAGCATCGATAGCT-1
  [5]     53409     53593       185 | TCAAGCATCGATAGCT-1
  [6]     53810     53987       178 | TCAAGCATCGATAGCT-1



2022-12-20 13:50:18 : (ZF_Het_Comb : 1 of 2) .tmpToArrow Barcodes-Chr-(1 of 25)-1, Class = data.frame
(ZF_Het_Comb : 1 of 2) .tmpToArrow Barcodes-Chr-(1 of 25)-1: nRows = 52341, nCols = 1
                  bc
1 TCAAGCATCGATAGCT-1
2 GCATTCCTCGGACGAA-1
3 TTTGCGCAGGGCTCTC-1
4 TCGGGACAGTCAGCCC-1
5 ACAAGCTGTCCAACCG-1
6 GTGCACGCAAAGGCCA-1


2022-12-20 13:50:21 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 9 of 25, 3.061 mins elapsed.
2022-12-20 13:50:21 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 10 of 25, 3.066 mins elapsed.
2022-12-20 13:50:21 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 11 of 25, 3.067 mins elapsed.
2022-12-20 13:50:22 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 12 of 25, 3.074 mins elapsed.
2022-12-20 13:50:22 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 13 of 25, 3.085 mins elapsed.
2022-12-20 13:50:22 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 14 of 25, 3.087 mins elapsed.
2022-12-20 13:50:23 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 15 of 25, 3.103 mins elapsed.
2022-12-20 13:50:24 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 16 of 25, 3.105 mins elapsed.
2022-12-20 13:50:31 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 17 of 25, 3.233 mins elapsed.
2022-12-20 13:50:33 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 18 of 25, 3.257 mins elapsed.
2022-12-20 13:50:33 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 19 of 25, 3.259 mins elapsed.
2022-12-20 13:50:33 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 20 of 25, 3.266 mins elapsed.
2022-12-20 13:50:33 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 21 of 25, 3.268 mins elapsed.
2022-12-20 13:50:33 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 22 of 25, 3.27 mins elapsed.
2022-12-20 13:50:34 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 23 of 25, 3.276 mins elapsed.
2022-12-20 13:50:35 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 24 of 25, 3.299 mins elapsed.
2022-12-20 13:50:43 : (ZF_Het_Comb : 1 of 2) Adding Chromosome 25 of 25, 3.422 mins elapsed.
2022-12-20 13:50:53 : (ZF_Het_Comb : 1 of 2) Parallel Hdf5 Linkage Arrow File, 3.598 mins elapsed.
2022-12-20 13:50:54 : (ZF_Het_Comb : 1 of 2) Successful creation of Arrow File, 3.607 mins elapsed.
2022-12-20 13:50:55 : (ZF_Het_Comb : 1 of 2) Adding Fragment Summary, 3.631 mins elapsed.
2022-12-20 13:51:21 : (ZF_Het_Comb : 1 of 2) Plotting Fragment Size Distribution, 4.06 mins elapsed.
2022-12-20 13:51:22 : (ZF_Het_Comb : 1 of 2) Computing TSS Enrichment Scores, 4.082 mins elapsed.

2022-12-20 13:51:22 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..

------- Completed

End Time : 2022-12-20 13:51:22
Elapsed Time Minutes = 4.16247562964757
Elapsed Time Hours = 0.0693747172090742

-------

rcorces · 2022-12-22T02:06:31Z

rcorces
Dec 22, 2022
Maintainer

In the future, errors should be posted to Issues.
Presumably you have already done addArchRChrPrefix(chrPrefix = FALSE) or else you wouldnt have gotten this far right?
To me, this looks like it could be a problem related to the genome or gene annotation or both. Looking at the Dr TxDB object, it has a ton of chrUn chromosomes. I would remove those from your gene annotation using keepStandardChromosomes() and your genome annotation using the filterChr option. Like so:

> gA <- createGeneAnnotation(TxDb = keepStandardChromosomes(TxDb.Drerio.UCSC.danRer10.refGene), OrgDb = org.Dr.eg.db)
Getting Genes..
  25 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one
  reference sequence, so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use suppressMessages() to suppress this
  message.
Determined Annotation Style = ENTREZID
Getting Exons..
Getting TSS..
> levels(gA@listData$TSS@seqnames)
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17"
[18] "chr18" "chr19" "chr20" "chr21" "chr22" "chr23" "chr24" "chr25" "chrM"

> filterChr <- seqlevels(BSgenome.Drerio.UCSC.danRer10)[-(1:26)]
> genomeAnnotation <- createGenomeAnnotation(genome = BSgenome.Drerio.UCSC.danRer10, filterChr = filterChr, filter = TRUE)
Getting genome..
Attempting to infer chromSizes..
Attempting to infer blacklist..
Blacklist not downloaded! Continuing without, be careful for downstream biases..
> genomeAnnotation
List of length 3
names(3): genome chromSizes blacklist
> genomeAnnotation$chromSizes
GRanges object with 26 ranges and 0 metadata columns:
       seqnames     ranges strand
          <Rle>  <IRanges>  <Rle>
   [1]     chr1 1-58871917      *
   [2]     chr2 1-59543403      *
   [3]     chr3 1-62385949      *
   [4]     chr4 1-76625712      *
   [5]     chr5 1-71715914      *
   ...      ...        ...    ...
  [22]    chr22 1-39226288      *
  [23]    chr23 1-46272358      *
  [24]    chr24 1-42251103      *
  [25]    chr25 1-36898761      *
  [26]     chrM    1-16596      *
  -------
  seqinfo: 26 sequences from an unspecified genome

You may also need to filter these nonstandard chromosomes from your fragments files. Despite being one of the developers, I've never used these non-standard species.

6 replies

rcorces Dec 22, 2022
Maintainer

Its very hard for me to know as I really have zero experience working with this type of genome. The full log might be helpful but I imagine I still wont know what the problem is.

wz0527 Dec 23, 2022
Author

Hope this log file could be helpful. Thanks!
ArchR-createArrows-1860ab5d167d8c-Date-2022-12-22_Time-10-40-24.log

rcorces Dec 29, 2022
Maintainer

Thanks for providing the log file. I think your issue is related to a bug that has been fixed on the dev branch as discussed here #1527

You should install the dev branch and try again and let me know if it works.

devtools::install_github("GreenleafLab/ArchR", ref="dev_matchID", repos = BiocManager::repositories())
detach("package:ArchR", unload=TRUE)
library(ArchR)

wz0527 Jan 2, 2023
Author

Hi @rcorces,
Thanks for your help, the error mentioned before was fixed after reinstalled the package. Unfortunately, I encountered another error, the full log file is below:
ArchR-createArrows-1946253acb62cc-Date-2023-01-02_Time-12-47-09.log

Happy new year!

rcorces Jan 2, 2023
Maintainer

I cant be certain why that is happening but presumably you have some problematic gene regions. I've added a more thorough error report into the dev branch. Can you re-install the dev branch using the instructions I provided previously and try again? Hopefully it will tell you which of the gene regions is causing problems. From the log file, i think they should be on chr16

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