CreateArrowFiles has encountered an error

[jacobHog]

Hello,

I encounter an error when creating the arrowfile. I'm not entirely sure of the cause, but I get this note in my log:
"2022-11-03 10:12:12 : Detected 2 or less cells pass filter (Non-Zero median TSS = 0.92, median Frags = 7256) in file!
Check inputs such as 'filterFrags' or 'filterTSS' to keep cells! Exiting!"

I cannot change the inputs "filterFrags" or "filterTSS", as they are set to null by default. Should I change them to something else?
(Maybe the entire log posted down below gives a better hint of the error, that I do not understand?)
Thanks in advance.

Here is my code

ArrowFiles <- createArrowFiles(
inputFiles = "/data/Grontved/students/JBH/test/GSM4798907_P2003139_fragments.tsv.gz",
sampleNames = "baseq_3139",
addTileMat = TRUE,
addGeneScoreMat = TRUE
)

Here is the process:

And here is my log:

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

Start Time : 2022-11-03 10:09:28

------- ArchR Info

ArchRThreads = 20
ArchRGenome = Mm10

------- System Info

Computer OS = unix
Total Cores = 80

------- Session Info

R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /data/home/spec-jhoeg17/.conda/envs/seurat_environment/lib/libopenblasp-r0.3.18.so

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BSgenome.Mmusculus.UCSC.mm10_1.4.3 BSgenome_1.62.0                   
 [3] rtracklayer_1.54.0                 Biostrings_2.62.0                 
 [5] XVector_0.34.0                     ComplexHeatmap_2.10.0             
 [7] magick_2.7.3                       harmony_1.0                       
 [9] caret_6.0-91                       lattice_0.20-45                   
[11] gplots_3.1.1                       symphony_0.1.0                    
[13] scDblFinder_1.8.0                  SeuratObject_4.0.4                
[15] Seurat_4.1.0                       patchwork_1.1.1                   
[17] dplyr_1.0.9                        pheatmap_1.0.12                   
[19] rhdf5_2.38.1                       SummarizedExperiment_1.24.0       
[21] Biobase_2.54.0                     MatrixGenerics_1.6.0              
[23] Rcpp_1.0.9                         Matrix_1.4-0                      
[25] GenomicRanges_1.46.1               GenomeInfoDb_1.30.1               
[27] IRanges_2.28.0                     S4Vectors_0.32.4                  
[29] BiocGenerics_0.40.0                matrixStats_0.62.0                
[31] data.table_1.14.2                  stringr_1.4.0                     
[33] plyr_1.8.7                         magrittr_2.0.3                    
[35] ggplot2_3.3.6                      gtable_0.3.0                      
[37] gtools_3.9.3                       gridExtra_2.3                     
[39] ArchR_1.0.2                        remotes_2.4.2                     
[41] devtools_2.4.3                     usethis_2.1.5                     
[43] SeuratDisk_0.0.0.9019             

loaded via a namespace (and not attached):
  [1] scattermore_0.8             ModelMetrics_1.2.2.2       
  [3] tidyr_1.2.0                 bit64_4.0.5                
  [5] irlba_2.3.5                 DelayedArray_0.20.0        
  [7] rpart_4.1.16                hardhat_0.2.0              
  [9] RCurl_1.98-1.8              doParallel_1.0.17          
 [11] generics_0.1.3              ScaledMatrix_1.2.0         
 [13] callr_3.7.0                 cowplot_1.1.1              
 [15] RANN_2.6.1                  future_1.24.0              
 [17] bit_4.0.4                   spatstat.data_2.1-2        
 [19] lubridate_1.8.0             httpuv_1.6.5               
 [21] assertthat_0.2.1            viridis_0.6.2              
 [23] gower_1.0.0                 promises_1.2.0.1           
 [25] restfulr_0.0.15             fansi_1.0.3                
 [27] caTools_1.18.2              igraph_1.2.11              
 [29] DBI_1.1.3                   htmlwidgets_1.5.4          
 [31] spatstat.geom_2.3-2         purrr_0.3.4                
 [33] ellipsis_0.3.2              deldir_1.0-6               
 [35] sparseMatrixStats_1.6.0     vctrs_0.4.1                
 [37] SingleCellExperiment_1.16.0 Cairo_1.5-14               
 [39] ROCR_1.0-11                 abind_1.4-5                
 [41] cachem_1.0.6                withr_2.5.0                
 [43] sctransform_0.3.3           GenomicAlignments_1.30.0   
 [45] prettyunits_1.1.1           scran_1.22.1               
 [47] goftest_1.2-3               cluster_2.1.2              
 [49] lazyeval_0.2.2              crayon_1.5.1               
 [51] hdf5r_1.3.5                 edgeR_3.36.0               
 [53] recipes_0.2.0               pkgconfig_2.0.3            
 [55] nlme_3.1-155                vipor_0.4.5                
 [57] pkgload_1.2.4               nnet_7.3-17                
 [59] rlang_1.0.4                 globals_0.14.0             
 [61] lifecycle_1.0.1             miniUI_0.1.1.1             
 [63] rsvd_1.0.5                  ggrastr_1.0.1              
 [65] rprojroot_2.0.2             polyclip_1.10-0            
 [67] lmtest_0.9-39               Rhdf5lib_1.16.0            
 [69] zoo_1.8-9                   beeswarm_0.4.0             
 [71] ggridges_0.5.3              GlobalOptions_0.1.2        
 [73] processx_3.5.2              png_0.1-7                  
 [75] viridisLite_0.4.0           rjson_0.2.21               
 [77] bitops_1.0-7                KernSmooth_2.23-20         
 [79] rhdf5filters_1.6.0          pROC_1.18.0                
 [81] DelayedMatrixStats_1.16.0   shape_1.4.6                
 [83] parallelly_1.30.0           spatstat.random_2.1-0      
 [85] beachmat_2.10.0             scales_1.2.0               
 [87] memoise_2.0.1               ica_1.0-2                  
 [89] zlibbioc_1.40.0             compiler_4.1.2             
 [91] BiocIO_1.4.0                dqrng_0.3.0                
 [93] RColorBrewer_1.1-3          clue_0.3-61                
 [95] fitdistrplus_1.1-8          Rsamtools_2.10.0           
 [97] cli_3.3.0                   listenv_0.8.0              
 [99] pbapply_1.5-0               ps_1.6.0                   
[101] MASS_7.3-55                 mgcv_1.8-39                
[103] tidyselect_1.1.2            stringi_1.7.8              
[105] yaml_2.3.5                  BiocSingular_1.10.0        
[107] locfit_1.5-9.5              ggrepel_0.9.1              
[109] tools_4.1.2                 future.apply_1.8.1         
[111] circlize_0.4.15             bluster_1.4.0              
[113] foreach_1.5.2               metapod_1.2.0              
[115] prodlim_2019.11.13          Rtsne_0.16                 
[117] digest_0.6.29               shiny_1.7.2                
[119] lava_1.6.10                 scuttle_1.4.0              
[121] later_1.3.0                 RcppAnnoy_0.0.19           
[123] httr_1.4.3                  colorspace_2.0-3           
[125] XML_3.99-0.10               brio_1.1.3                 
[127] fs_1.5.2                    tensor_1.5                 
[129] reticulate_1.24             splines_4.1.2              
[131] uwot_0.1.11                 statmod_1.4.36             
[133] spatstat.utils_2.3-0        scater_1.22.0              
[135] xgboost_1.5.2.1             plotly_4.10.0              
[137] sessioninfo_1.2.2           xtable_1.8-4               
[139] jsonlite_1.8.0              timeDate_3043.102          
[141] testthat_3.1.2              ipred_0.9-12               
[143] R6_2.5.1                    pillar_1.8.0               
[145] htmltools_0.5.3             mime_0.12                  
[147] glue_1.6.2                  fastmap_1.1.0              
[149] BiocParallel_1.28.3         BiocNeighbors_1.12.0       
[151] class_7.3-20                codetools_0.2-18           
[153] pkgbuild_1.3.1              utf8_1.2.2                 
[155] spatstat.sparse_2.1-0       tibble_3.1.8               
[157] ggbeeswarm_0.6.0            leiden_0.3.9               
[159] survival_3.3-1              limma_3.50.1               
[161] desc_1.4.1                  munsell_0.5.0              
[163] GetoptLong_1.0.5            GenomeInfoDbData_1.2.7     
[165] iterators_1.0.14            reshape2_1.4.4             
[167] spatstat.core_2.4-0        


------- Log Info


2022-11-03 10:09:28 : createArrowFiles Input-Parameters, Class = list

createArrowFiles Input-Parameters$inputFiles: length = 1
[1] "/data/Grontved/students/JBH/test/GSM4798907_P2003139_fragments.tsv.gz"


createArrowFiles Input-Parameters$sampleNames: length = 1
[1] "baseq_3139"


createArrowFiles Input-Parameters$outputNames: length = 1
[1] "baseq_3139"


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] 20


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-359d975caa10c9-Date-2022-11-03_Time-10-09-28.log"


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


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



2022-11-03 10:09:28 : Cleaning Temporary Files
2022-11-03 10:09:28 : Batch Execution w/ safelapply!, 0 mins elapsed.

###########
2022-11-03 10:09:28 : Creating Arrow File baseq_3139.arrow (baseq_3139 : 1 of 1)
###########


2022-11-03 10:09:28 : validBC, Class = NULL

validBC: length = 0
NULL



2022-11-03 10:09:28 : (baseq_3139 : 1 of 1) Determining Arrow Method to use!
2022-11-03 10:10:08 : (baseq_3139 : 1 of 1) Reading In Fragments from inputFiles (readMethod = tabix), 0.658 mins elapsed.
2022-11-03 10:10:08 : (baseq_3139 : 1 of 1) Tabix Bed To Temporary File, 0.658 mins elapsed.

2022-11-03 10:10:08 : tileChromSizes, Class = GRanges
GRanges object with 105 ranges and 1 metadata column:
        seqnames              ranges strand |     chunkName
           <Rle>           <IRanges>  <Rle> |   <character>
    [1]     chr1          1-39094394      * |   chr1#chunk1
    [2]     chr1   39094395-78188788      * |   chr1#chunk2
    [3]     chr1  78188789-117283182      * |   chr1#chunk3
    [4]     chr1 117283183-156377576      * |   chr1#chunk4
    [5]     chr1 156377577-195471971      * |   chr1#chunk5
    ...      ...                 ...    ... .           ...
  [101]     chrY          1-18348939      * | chrY#chunk101
  [102]     chrY   18348940-36697879      * | chrY#chunk102
  [103]     chrY   36697880-55046818      * | chrY#chunk103
  [104]     chrY   55046819-73395758      * | chrY#chunk104
  [105]     chrY   73395759-91744698      * | chrY#chunk105
  -------
  seqinfo: 21 sequences from an unspecified genome; no seqlengths

2022-11-03 10:10:26 : (baseq_3139 : 1 of 1) Reading TabixFile 39 Percent, 0.969 mins elapsed.

2022-11-03 10:10:29 : (baseq_3139 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 105)-chr1:1-39094394, Class = data.table
 
2022-11-03 10:10:29 : (baseq_3139 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 105)-chr1:1-39094394, Class = data.frame
(baseq_3139 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 105)-chr1:1-39094394: nRows = 2929732, nCols = 3
      V2    V3                 V4
1: 10074 10192 GAGACTTTCTGCTACC-1
2: 10074 10284 ACAGAAATCCCAGCGA-1
3: 10074 10327 GGGACCTTCGGTGATT-1
4: 10086 10284 CGCTGGATCGTCTAGA-1
5: 10103 10309 CAGTATGTCTGTGTCC-1
6: 10137 10279 CCACGTTTCTGTGTCC-1



2022-11-03 10:10:29 : (baseq_3139 : 1 of 1) .tabixToTmp Barcodes-Chunk-(1 of 105)-chr1:1-39094394, Class = character

(baseq_3139 : 1 of 1) .tabixToTmp Barcodes-Chunk-(1 of 105)-chr1:1-39094394: length = 75914
[1] "GAGACTTTCTGCTACC-1" "ACAGAAATCCCAGCGA-1" "GGGACCTTCGGTGATT-1"
[4] "CGCTGGATCGTCTAGA-1" "CAGTATGTCTGTGTCC-1" "CCACGTTTCTGTGTCC-1"


2022-11-03 10:10:45 : (baseq_3139 : 1 of 1) Reading TabixFile 78 Percent, 1.281 mins elapsed.
2022-11-03 10:11:04 : (baseq_3139 : 1 of 1) Parallel Hdf5 Linkage Temporary File, 1.595 mins elapsed.
2022-11-03 10:11:05 : (baseq_3139 : 1 of 1) Successful creation of Temporary File, 1.606 mins elapsed.
2022-11-03 10:11:05 : (baseq_3139 : 1 of 1) Creating ArrowFile From Temporary File, 1.606 mins elapsed.

2022-11-03 10:11:05 : (baseq_3139 : 1 of 1) chunkChrNames, Class = data.frame
(baseq_3139 : 1 of 1) chunkChrNames: nRows = 103, nCols = 1
     chunkNames
1   chr1#chunk1
2   chr1#chunk2
3   chr1#chunk3
4   chr1#chunk4
5   chr1#chunk5
6 chr10#chunk46


2022-11-03 10:11:05 : (baseq_3139 : 1 of 1) Counting Unique Barcodes From Temporary File, 1.609 mins elapsed.

2022-11-03 10:11:22 : (baseq_3139 : 1 of 1) BarcodeFrequencyTable, Class = data.table
 
2022-11-03 10:11:22 : (baseq_3139 : 1 of 1) BarcodeFrequencyTable, Class = data.frame
(baseq_3139 : 1 of 1) BarcodeFrequencyTable: nRows = 367957, nCols = 2
            values.V1     V1
1: GTCCATCTCGTCTAGA-1 500400
2: CAGTGCGGTGTTGGTT-1 343922
3: TATGTGGCACCCTTTG-1 207725
4: TTTGGTTGTGCTTCCT-1 177379
5: TTGCTTAAGAGCTGTG-1 176334
6: TAGCGGCTCGCGCTGA-1 171446



2022-11-03 10:11:22 : (baseq_3139 : 1 of 1) BarcodesMinMaxFrags, Class = data.frame
(baseq_3139 : 1 of 1) BarcodesMinMaxFrags: nRows = 8029, nCols = 1
                  bc
1 TGGGTGCGTCTAACCA-1
2 AGATAGAGTGTGAGGT-1
3 AACGGGAGTCTGATTG-1
4 ACAGCGCCACTACACA-1
5 AACCTGAGTACGCCCA-1
6 CCCTAACTCGTGTGCG-1



2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Unique Chromosomes, Class = data.frame
(baseq_3139 : 1 of 1) Unique Chromosomes: nRows = 21, nCols = 1
   chr
1 chr1
2 chr2
3 chr3
4 chr4
5 chr5
6 chr6


2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 1 of 21, 1.911 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 2 of 21, 1.911 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 3 of 21, 1.912 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 4 of 21, 1.912 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 5 of 21, 1.913 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 6 of 21, 1.913 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 7 of 21, 1.913 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 8 of 21, 1.914 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 9 of 21, 1.914 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 10 of 21, 1.915 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 11 of 21, 1.915 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 12 of 21, 1.916 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 13 of 21, 1.916 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 14 of 21, 1.916 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 15 of 21, 1.917 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 16 of 21, 1.917 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 17 of 21, 1.918 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 18 of 21, 1.918 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 19 of 21, 1.919 mins elapsed.
2022-11-03 10:11:23 : (baseq_3139 : 1 of 1) Adding Chromosome 20 of 21, 1.919 mins elapsed.
2022-11-03 10:11:28 : (baseq_3139 : 1 of 1) Adding Chromosome 21 of 21, 2.002 mins elapsed.

2022-11-03 10:11:34 : (baseq_3139 : 1 of 1) .tmpToArrow Fragments-Chr-(1 of 21)-chr1, Class = IRanges

(baseq_3139 : 1 of 1) .tmpToArrow Fragments-Chr-(1 of 21)-chr1: length = 7579353
IRanges object with 6 ranges and 1 metadata column:
          start       end     width |                 RG
      <integer> <integer> <integer> |              <Rle>
  [1]    778385    778719       335 | TGGGTGCGTCTAACCA-1
  [2]    827552    827632        81 | TGGGTGCGTCTAACCA-1
  [3]    848476    848858       383 | TGGGTGCGTCTAACCA-1
  [4]    869967    870037        71 | TGGGTGCGTCTAACCA-1
  [5]    876861    877309       449 | TGGGTGCGTCTAACCA-1
  [6]    904687    904813       127 | TGGGTGCGTCTAACCA-1



2022-11-03 10:11:34 : (baseq_3139 : 1 of 1) .tmpToArrow Barcodes-Chr-(1 of 21)-chr1, Class = data.frame
(baseq_3139 : 1 of 1) .tmpToArrow Barcodes-Chr-(1 of 21)-chr1: nRows = 8029, nCols = 1
                  bc
1 TGGGTGCGTCTAACCA-1
2 AGATAGAGTGTGAGGT-1
3 AACGGGAGTCTGATTG-1
4 ACAGCGCCACTACACA-1
5 AACCTGAGTACGCCCA-1
6 CCCTAACTCGTGTGCG-1


2022-11-03 10:11:35 : (baseq_3139 : 1 of 1) Parallel Hdf5 Linkage Arrow File, 2.12 mins elapsed.
2022-11-03 10:11:36 : (baseq_3139 : 1 of 1) Successful creation of Arrow File, 2.125 mins elapsed.
2022-11-03 10:11:38 : (baseq_3139 : 1 of 1) Adding Fragment Summary, 2.156 mins elapsed.
2022-11-03 10:11:57 : (baseq_3139 : 1 of 1) Plotting Fragment Size Distribution, 2.483 mins elapsed.
2022-11-03 10:11:59 : (baseq_3139 : 1 of 1) Computing TSS Enrichment Scores, 2.51 mins elapsed.
2022-11-03 10:12:12 : (baseq_3139 : 1 of 1) Computed TSS Scores!, 0.219 mins elapsed.

2022-11-03 10:12:12 : Detected 2 or less cells pass filter (Non-Zero median TSS = 0.92, median Frags = 7256) in file!
       Check inputs such as 'filterFrags' or 'filterTSS' to keep cells! Exiting!

2022-11-03 10:12:12 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..

------- Completed

End Time : 2022-11-03 10:12:12
Elapsed Time Minutes = 2.74173064231873
Elapsed Time Hours = 0.0456956936915716

-------

[rcorces]

It appears that you are using a mouse reference genome to analyze a human dataset