When I ran the following code, an error occurred. The Arrow file could not be created successfully. I was able to create it successfully before. My R environment is on a cluster, and I’m not sure if the issue is due to changes in the environment.
addArchRThreads(threads = 1)
geneAnnotation <- readRDS("/ATAC-matrix/geneAnnotation.rds")
geneAnnotation
genomeAnnotation <- readRDS("/ATAC-matrix/genomeAnnotation.rds")
genomeAnnotation
inputFiles = c('/slurm/home/fragments.tsv.gz')
sampleNames = c("EUE1")
install.packages('/slurm/source/ggplot2_3.3.0.tar.gz')
创建 Arrow 文件
ArrowFiles <- createArrowFiles(
inputFiles = inputFiles,
sampleNames = sampleNames,
minTSS = 4, # 替换为 minTSS
minFrags = 1000, # 替换为 minFrags
addTileMat = TRUE,
addGeneScoreMat = TRUE,
geneAnnotation = geneAnnotation,
genomeAnnotation = genomeAnnotation)
The error message is:
2025-02-20 20:56:54 : ERROR Found in .fastTSSCounts for (EUE1 : 1 of 1)
LogFile = ArchRLogs/ArchR-createArrows-464f289d75db-Date-2025-02-20_Time-20-31-39.log
<simpleError in .Call2("C_find_overlaps_NCList", start(query), end(query), start(subject), end(subject), nclist, nclist_is_q, maxgap, minoverlap, type, select, circle.length, PACKAGE = "IRanges"): build_NCList: memory allocation failed>
2025-02-20 20:56:54 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
ArchR logging successful to : ArchRLogs/ArchR-createArrows-464f289d75db-Date-2025-02-20_Time-20-31-39.log
There were 20 warnings (use warnings() to see them)
Below is the work log. I would greatly appreciate it if you could help me resolve the issue.
This is an issue template made by the developers of ArchR. You MUST follow these instructions.
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
Logging With ArchR!
Start Time : 2025-02-20 20:31:39
------- ArchR Info
ArchRThreads = 1
------- System Info
Computer OS = unix
Total Cores = 96
------- Session Info
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /slurm/soft/R/4.2.1/lib64/R/lib/libRblas.so
LAPACK: /slurm/soft/R/4.2.1/lib64/R/lib/libRlapack.so
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
[4] 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
[10] 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
[10] base
other attached packages:
[1] Rsamtools_2.14.0 Biostrings_2.66.0 XVector_0.38.0
[4] rhdf5_2.44.0 SummarizedExperiment_1.28.0 Biobase_2.58.0
[7] MatrixGenerics_1.18.0 Rcpp_1.0.13-1 Matrix_1.6-5
[10] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0
[13] S4Vectors_0.44.0 BiocGenerics_0.52.0 matrixStats_1.4.1
[16] data.table_1.16.2 stringr_1.5.1 plyr_1.8.9
[19] magrittr_2.0.3 ggplot2_3.5.1 gtable_0.3.6
[22] gtools_3.9.5 gridExtra_2.3 ArchR_1.0.2
loaded via a namespace (and not attached):
[1] lattice_0.22-6 circlize_0.4.16 png_0.1-8 digest_0.6.37
[5] foreach_1.5.2 utf8_1.2.4 R6_2.5.1 SparseArray_1.6.1
[9] pillar_1.9.0 GlobalOptions_0.1.2 zlibbioc_1.44.0 rlang_1.1.4
[13] rstudioapi_0.17.1 GetoptLong_1.0.5 labeling_0.4.3 BiocParallel_1.32.6
[17] pheatmap_1.0.12 RCurl_1.98-1.16 munsell_0.5.1 DelayedArray_0.32.0
[21] compiler_4.2.1 pkgconfig_2.0.3 shape_1.4.6.1 tidyselect_1.2.1
[25] tibble_3.2.1 GenomeInfoDbData_1.2.9 codetools_0.2-20 fansi_1.0.6
[29] crayon_1.5.3 dplyr_1.1.4 withr_3.0.2 rhdf5filters_1.12.1
[33] bitops_1.0-9 lifecycle_1.0.4 scales_1.3.0 cli_3.6.3
[37] stringi_1.8.4 farver_2.1.2 doParallel_1.0.17 generics_0.1.3
[41] vctrs_0.6.5 Rhdf5lib_1.20.0 rjson_0.2.23 RColorBrewer_1.1-3
[45] Cairo_1.6-2 iterators_1.0.14 tools_4.2.1 glue_1.8.0
[49] abind_1.4-8 clue_0.3-65 colorspace_2.1-1 cluster_2.1.6
[53] S4Arrays_1.6.0 ComplexHeatmap_2.14.0
------- Log Info
2025-02-20 20:31:39 : createArrowFiles Input-Parameters, Class = list
createArrowFiles Input-Parameters$inputFiles: length = 1
[1] "/slurm/home/yrd/fanlab/mayue/Ovarian_endometriosis_scATAC/ATAC-matrix/EUE1/fragments.tsv.gz"
createArrowFiles Input-Parameters$sampleNames: length = 1
[1] "EUE1"
createArrowFiles Input-Parameters$outputNames: length = 1
[1] "EUE1"
createArrowFiles Input-Parameters$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$threads: length = 1
[1] 1
createArrowFiles Input-Parameters$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-464f289d75db-Date-2025-02-20_Time-20-31-39.log"
createArrowFiles Input-Parameters$filterFrags: length = 1
[1] 1000
createArrowFiles Input-Parameters$filterTSS: length = 1
[1] 4
2025-02-20 20:31:39 : Cleaning Temporary Files
2025-02-20 20:31:39 : Batch Execution w/ safelapply!, 0 mins elapsed.
###########
2025-02-20 20:31:39 : Creating Arrow File EUE1.arrow (EUE1 : 1 of 1)
###########
2025-02-20 20:31:39 : validBC, Class = NULL
validBC: length = 0
NULL
2025-02-20 20:31:39 : (EUE1 : 1 of 1) Determining Arrow Method to use!
2025-02-20 20:31:39 : (EUE1 : 1 of 1) Reading In Fragments from inputFiles (readMethod = tabix), 0 mins elapsed.
2025-02-20 20:31:39 : (EUE1 : 1 of 1) Tabix Bed To Temporary File, 0.001 mins elapsed.
2025-02-20 20:31:39 : tileChromSizes, Class = GRanges
GRanges object with 200 ranges and 1 metadata column:
seqnames ranges strand | chunkName
|
[1] chr1 1-49791284 * | chr1#chunk1
[2] chr1 49791285-99582568 * | chr1#chunk2
[3] chr1 99582569-149373853 * | chr1#chunk3
[4] chr1 149373854-199165137 * | chr1#chunk4
[5] chr1 199165138-248956422 * | chr1#chunk5
... ... ... ... . ...
[196] KI270713.1 1-8149 * | KI270713.1#chunk196
[197] KI270713.1 8150-16298 * | KI270713.1#chunk197
[198] KI270713.1 16299-24447 * | KI270713.1#chunk198
[199] KI270713.1 24448-32596 * | KI270713.1#chunk199
[200] KI270713.1 32597-40745 * | KI270713.1#chunk200
seqinfo: 40 sequences from an unspecified genome; no seqlengths
2025-02-20 20:32:08 : (EUE1 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 200)-chr1:1-49791284, Class = data.table
2025-02-20 20:32:08 : (EUE1 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 200)-chr1:1-49791284, Class = data.frame
(EUE1 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 200)-chr1:1-49791284: nRows = 7932397, nCols = 3
V2 V3 V4
1: 10067 10429 TCACAGAGTGCTTACA-1
2: 10078 10339 TTCATTGGTCACATTG-1
3: 10084 10297 TGGCGCAGTACCCACG-1
4: 10085 10309 CACCTGTTCCGATGCG-1
5: 10091 10338 GCCAGCAAGCCATCAT-1
6: 10097 10273 ACCGCAGTCTGACATG-1
2025-02-20 20:32:08 : (EUE1 : 1 of 1) .tabixToTmp Barcodes-Chunk-(1 of 200)-chr1:1-49791284, Class = character
(EUE1 : 1 of 1) .tabixToTmp Barcodes-Chunk-(1 of 200)-chr1:1-49791284: length = 75135
[1] "TCACAGAGTGCTTACA-1" "TTCATTGGTCACATTG-1" "TGGCGCAGTACCCACG-1" "CACCTGTTCCGATGCG-1"
[5] "GCCAGCAAGCCATCAT-1" "ACCGCAGTCTGACATG-1"
2025-02-20 20:34:12 : (EUE1 : 1 of 1) Reading TabixFile 5 Percent, 2.542 mins elapsed.
2025-02-20 20:36:02 : (EUE1 : 1 of 1) Reading TabixFile 10 Percent, 4.381 mins elapsed.
2025-02-20 20:37:07 : (EUE1 : 1 of 1) Reading TabixFile 15 Percent, 5.468 mins elapsed.
2025-02-20 20:38:19 : (EUE1 : 1 of 1) Reading TabixFile 20 Percent, 6.665 mins elapsed.
2025-02-20 20:39:29 : (EUE1 : 1 of 1) Reading TabixFile 25 Percent, 7.837 mins elapsed.
2025-02-20 20:41:25 : (EUE1 : 1 of 1) Reading TabixFile 30 Percent, 9.755 mins elapsed.
2025-02-20 20:42:24 : (EUE1 : 1 of 1) Reading TabixFile 35 Percent, 10.749 mins elapsed.
2025-02-20 20:43:50 : (EUE1 : 1 of 1) Reading TabixFile 40 Percent, 12.187 mins elapsed.
2025-02-20 20:45:55 : (EUE1 : 1 of 1) Reading TabixFile 45 Percent, 14.26 mins elapsed.
2025-02-20 20:47:52 : (EUE1 : 1 of 1) Reading TabixFile 50 Percent, 16.216 mins elapsed.
2025-02-20 20:49:21 : (EUE1 : 1 of 1) Reading TabixFile 55 Percent, 17.691 mins elapsed.
2025-02-20 20:50:08 : (EUE1 : 1 of 1) Reading TabixFile 60 Percent, 18.47 mins elapsed.
2025-02-20 20:50:21 : (EUE1 : 1 of 1) Reading TabixFile 65 Percent, 18.7 mins elapsed.
2025-02-20 20:50:29 : (EUE1 : 1 of 1) Reading TabixFile 70 Percent, 18.828 mins elapsed.
2025-02-20 20:50:37 : (EUE1 : 1 of 1) Reading TabixFile 75 Percent, 18.958 mins elapsed.
2025-02-20 20:50:45 : (EUE1 : 1 of 1) Reading TabixFile 80 Percent, 19.087 mins elapsed.
2025-02-20 20:50:52 : (EUE1 : 1 of 1) Reading TabixFile 85 Percent, 19.216 mins elapsed.
2025-02-20 20:51:00 : (EUE1 : 1 of 1) Reading TabixFile 90 Percent, 19.344 mins elapsed.
2025-02-20 20:51:07 : (EUE1 : 1 of 1) Reading TabixFile 95 Percent, 19.459 mins elapsed.
2025-02-20 20:51:15 : (EUE1 : 1 of 1) Reading TabixFile 100 Percent, 19.587 mins elapsed.
2025-02-20 20:51:15 : (EUE1 : 1 of 1) Successful creation of Temporary File, 19.6 mins elapsed.
2025-02-20 20:51:15 : (EUE1 : 1 of 1) Creating ArrowFile From Temporary File, 19.6 mins elapsed.
2025-02-20 20:51:15 : (EUE1 : 1 of 1) chunkChrNames, Class = data.frame
(EUE1 : 1 of 1) chunkChrNames: nRows = 192, nCols = 1
chunkNames
1 GL000009.2#chunk136
2 GL000009.2#chunk137
3 GL000009.2#chunk138
4 GL000009.2#chunk139
5 GL000009.2#chunk140
6 GL000194.1#chunk141
2025-02-20 20:51:15 : (EUE1 : 1 of 1) Counting Unique Barcodes From Temporary File, 19.601 mins elapsed.
2025-02-20 20:51:24 : (EUE1 : 1 of 1) BarcodeFrequencyTable, Class = data.table
2025-02-20 20:51:24 : (EUE1 : 1 of 1) BarcodeFrequencyTable, Class = data.frame
(EUE1 : 1 of 1) BarcodeFrequencyTable: nRows = 472168, nCols = 2
values.V1 V1
1: CCTGGGAGTGGCCTTG-1 101731
2: AAACTCGGTCATGAGG-1 90713
3: AGACAAATCCAAGTCA-1 88487
4: GAAGAGCAGGGAGATA-1 88017
5: GTAGGAGGTTGTGACT-1 86641
6: CCGTGAGCATGGTAAA-1 82796
2025-02-20 20:51:24 : (EUE1 : 1 of 1) BarcodesMinMaxFrags, Class = data.frame
(EUE1 : 1 of 1) BarcodesMinMaxFrags: nRows = 13022, nCols = 1
bc
1 AAACTCGGTCATGAGG-1
2 AGACAAATCCAAGTCA-1
3 GAAGAGCAGGGAGATA-1
4 GTAGGAGGTTGTGACT-1
5 CCGTGAGCATGGTAAA-1
6 AAACGAACAAGCAACG-1
2025-02-20 20:51:25 : (EUE1 : 1 of 1) Unique Chromosomes, Class = data.frame
(EUE1 : 1 of 1) Unique Chromosomes: nRows = 40, nCols = 1
chr
1 chr1
2 chr10
3 chr11
4 chr12
5 chr13
6 chr14
2025-02-20 20:51:25 : (EUE1 : 1 of 1) Adding Chromosome 1 of 40, 19.76 mins elapsed.
2025-02-20 20:51:47 : (EUE1 : 1 of 1) .tmpToArrow Fragments-Chr-(1 of 40)-chr1, Class = IRanges
(EUE1 : 1 of 1) .tmpToArrow Fragments-Chr-(1 of 40)-chr1: length = 24388815
IRanges object with 6 ranges and 1 metadata column:
start end width | RG
|
[1] 778368 778617 250 | AAACTCGGTCATGAGG-1
[2] 778593 778637 45 | AAACTCGGTCATGAGG-1
[3] 778863 778909 47 | AAACTCGGTCATGAGG-1
[4] 858101 858173 73 | AAACTCGGTCATGAGG-1
[5] 880812 881133 322 | AAACTCGGTCATGAGG-1
[6] 894998 895156 159 | AAACTCGGTCATGAGG-1
2025-02-20 20:51:47 : (EUE1 : 1 of 1) .tmpToArrow Barcodes-Chr-(1 of 40)-chr1, Class = data.frame
(EUE1 : 1 of 1) .tmpToArrow Barcodes-Chr-(1 of 40)-chr1: nRows = 13022, nCols = 1
bc
1 AAACTCGGTCATGAGG-1
2 AGACAAATCCAAGTCA-1
3 GAAGAGCAGGGAGATA-1
4 GTAGGAGGTTGTGACT-1
5 CCGTGAGCATGGTAAA-1
6 AAACGAACAAGCAACG-1
2025-02-20 20:51:48 : (EUE1 : 1 of 1) Adding Chromosome 2 of 40, 20.145 mins elapsed.
2025-02-20 20:51:58 : (EUE1 : 1 of 1) Adding Chromosome 3 of 40, 20.32 mins elapsed.
2025-02-20 20:52:12 : (EUE1 : 1 of 1) Adding Chromosome 4 of 40, 20.546 mins elapsed.
2025-02-20 20:52:25 : (EUE1 : 1 of 1) Adding Chromosome 5 of 40, 20.765 mins elapsed.
2025-02-20 20:52:32 : (EUE1 : 1 of 1) Adding Chromosome 6 of 40, 20.875 mins elapsed.
2025-02-20 20:52:40 : (EUE1 : 1 of 1) Adding Chromosome 7 of 40, 21.006 mins elapsed.
2025-02-20 20:52:48 : (EUE1 : 1 of 1) Adding Chromosome 8 of 40, 21.151 mins elapsed.
2025-02-20 20:52:59 : (EUE1 : 1 of 1) Adding Chromosome 9 of 40, 21.326 mins elapsed.
2025-02-20 20:53:09 : (EUE1 : 1 of 1) Adding Chromosome 10 of 40, 21.493 mins elapsed.
2025-02-20 20:53:14 : (EUE1 : 1 of 1) Adding Chromosome 11 of 40, 21.582 mins elapsed.
2025-02-20 20:53:23 : (EUE1 : 1 of 1) Adding Chromosome 12 of 40, 21.733 mins elapsed.
2025-02-20 20:53:42 : (EUE1 : 1 of 1) Adding Chromosome 13 of 40, 22.053 mins elapsed.
2025-02-20 20:53:48 : (EUE1 : 1 of 1) Adding Chromosome 14 of 40, 22.153 mins elapsed.
2025-02-20 20:53:52 : (EUE1 : 1 of 1) Adding Chromosome 15 of 40, 22.212 mins elapsed.
2025-02-20 20:53:57 : (EUE1 : 1 of 1) Adding Chromosome 16 of 40, 22.291 mins elapsed.
2025-02-20 20:54:14 : (EUE1 : 1 of 1) Adding Chromosome 17 of 40, 22.57 mins elapsed.
2025-02-20 20:54:27 : (EUE1 : 1 of 1) Adding Chromosome 18 of 40, 22.79 mins elapsed.
2025-02-20 20:54:40 : (EUE1 : 1 of 1) Adding Chromosome 19 of 40, 23.017 mins elapsed.
2025-02-20 20:54:54 : (EUE1 : 1 of 1) Adding Chromosome 20 of 40, 23.252 mins elapsed.
2025-02-20 20:55:08 : (EUE1 : 1 of 1) Adding Chromosome 21 of 40, 23.474 mins elapsed.
2025-02-20 20:55:20 : (EUE1 : 1 of 1) Adding Chromosome 22 of 40, 23.682 mins elapsed.
2025-02-20 20:55:33 : (EUE1 : 1 of 1) Adding Chromosome 23 of 40, 23.891 mins elapsed.
2025-02-20 20:55:33 : (EUE1 : 1 of 1) detected 0 Fragments for chrM
2025-02-20 20:55:33 : (EUE1 : 1 of 1) Adding Chromosome 24 of 40, 23.891 mins elapsed.
2025-02-20 20:55:42 : (EUE1 : 1 of 1) Adding Chromosome 25 of 40, 24.046 mins elapsed.
2025-02-20 20:55:43 : (EUE1 : 1 of 1) Adding Chromosome 26 of 40, 24.066 mins elapsed.
2025-02-20 20:55:45 : (EUE1 : 1 of 1) Adding Chromosome 27 of 40, 24.088 mins elapsed.
2025-02-20 20:55:46 : (EUE1 : 1 of 1) Adding Chromosome 28 of 40, 24.108 mins elapsed.
2025-02-20 20:55:47 : (EUE1 : 1 of 1) Adding Chromosome 29 of 40, 24.129 mins elapsed.
2025-02-20 20:55:48 : (EUE1 : 1 of 1) Adding Chromosome 30 of 40, 24.15 mins elapsed.
2025-02-20 20:55:50 : (EUE1 : 1 of 1) Adding Chromosome 31 of 40, 24.172 mins elapsed.
2025-02-20 20:55:51 : (EUE1 : 1 of 1) Adding Chromosome 32 of 40, 24.192 mins elapsed.
2025-02-20 20:55:52 : (EUE1 : 1 of 1) Adding Chromosome 33 of 40, 24.213 mins elapsed.
2025-02-20 20:55:53 : (EUE1 : 1 of 1) Adding Chromosome 34 of 40, 24.234 mins elapsed.
2025-02-20 20:55:55 : (EUE1 : 1 of 1) Adding Chromosome 35 of 40, 24.254 mins elapsed.
2025-02-20 20:55:56 : (EUE1 : 1 of 1) Adding Chromosome 36 of 40, 24.275 mins elapsed.
2025-02-20 20:55:57 : (EUE1 : 1 of 1) Adding Chromosome 37 of 40, 24.295 mins elapsed.
2025-02-20 20:55:58 : (EUE1 : 1 of 1) Adding Chromosome 38 of 40, 24.315 mins elapsed.
2025-02-20 20:55:59 : (EUE1 : 1 of 1) Adding Chromosome 39 of 40, 24.335 mins elapsed.
2025-02-20 20:56:01 : (EUE1 : 1 of 1) Adding Chromosome 40 of 40, 24.356 mins elapsed.
2025-02-20 20:56:02 : (EUE1 : 1 of 1) Successful creation of Arrow File, 24.377 mins elapsed.
2025-02-20 20:56:03 : (EUE1 : 1 of 1) Adding Fragment Summary, 24.391 mins elapsed.
2025-02-20 20:56:52 : (EUE1 : 1 of 1) Plotting Fragment Size Distribution, 25.216 mins elapsed.
2025-02-20 20:56:52 : Continuing through after error ggplot for Fragment Size Distribution, 25.217 mins elapsed.
2025-02-20 20:56:53 : (EUE1 : 1 of 1) Computing TSS Enrichment Scores, 25.23 mins elapsed.
2025-02-20 20:56:54 : ERROR Found in .fastTSSCounts for (EUE1 : 1 of 1)
LogFile = ArchRLogs/ArchR-createArrows-464f289d75db-Date-2025-02-20_Time-20-31-39.log
<simpleError in .Call2("C_find_overlaps_NCList", start(query), end(query), start(subject), end(subject), nclist, nclist_is_q, maxgap, minoverlap, type, select, circle.length, PACKAGE = "IRanges"): build_NCList: memory allocation failed>
2025-02-20 20:56:54 : errorList, Class = list
errorList$x: length = 1
[1] 1
errorList$chr: length = 1
[1] "GL000009.2"
errorList$fragments: length = 1
[1] "Error with Fragments!"
errorList$features: length = 1
[1] "Error with Features!"
2025-02-20 20:56:54 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
------- Completed
End Time : 2025-02-20 20:56:54
Elapsed Time Minutes = 25.2505369027456
Elapsed Time Hours = 0.420842320985264
When I ran the following code, an error occurred. The Arrow file could not be created successfully. I was able to create it successfully before. My R environment is on a cluster, and I’m not sure if the issue is due to changes in the environment.
addArchRThreads(threads = 1)
geneAnnotation <- readRDS("
/ATAC-matrix/geneAnnotation.rds")/ATAC-matrix/genomeAnnotation.rds")geneAnnotation
genomeAnnotation <- readRDS("
genomeAnnotation
inputFiles = c('/slurm/home/fragments.tsv.gz')
sampleNames = c("EUE1")
install.packages('/slurm/source/ggplot2_3.3.0.tar.gz')
创建 Arrow 文件
ArrowFiles <- createArrowFiles(
inputFiles = inputFiles,
sampleNames = sampleNames,
minTSS = 4, # 替换为 minTSS
minFrags = 1000, # 替换为 minFrags
addTileMat = TRUE,
addGeneScoreMat = TRUE,
geneAnnotation = geneAnnotation,
genomeAnnotation = genomeAnnotation)
The error message is:
2025-02-20 20:56:54 : ERROR Found in .fastTSSCounts for (EUE1 : 1 of 1)
LogFile = ArchRLogs/ArchR-createArrows-464f289d75db-Date-2025-02-20_Time-20-31-39.log
<simpleError in .Call2("C_find_overlaps_NCList", start(query), end(query), start(subject), end(subject), nclist, nclist_is_q, maxgap, minoverlap, type, select, circle.length, PACKAGE = "IRanges"): build_NCList: memory allocation failed>
2025-02-20 20:56:54 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
ArchR logging successful to : ArchRLogs/ArchR-createArrows-464f289d75db-Date-2025-02-20_Time-20-31-39.log
There were 20 warnings (use warnings() to see them)
Below is the work log. I would greatly appreciate it if you could help me resolve the issue.
This is an issue template made by the developers of ArchR. You MUST follow these instructions.
Logging With ArchR!
Start Time : 2025-02-20 20:31:39
------- ArchR Info
ArchRThreads = 1
------- System Info
Computer OS = unix
Total Cores = 96
------- Session Info
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /slurm/soft/R/4.2.1/lib64/R/lib/libRblas.so
LAPACK: /slurm/soft/R/4.2.1/lib64/R/lib/libRlapack.so
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
[4] 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
[10] 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
[10] base
other attached packages:
[1] Rsamtools_2.14.0 Biostrings_2.66.0 XVector_0.38.0
[4] rhdf5_2.44.0 SummarizedExperiment_1.28.0 Biobase_2.58.0
[7] MatrixGenerics_1.18.0 Rcpp_1.0.13-1 Matrix_1.6-5
[10] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0
[13] S4Vectors_0.44.0 BiocGenerics_0.52.0 matrixStats_1.4.1
[16] data.table_1.16.2 stringr_1.5.1 plyr_1.8.9
[19] magrittr_2.0.3 ggplot2_3.5.1 gtable_0.3.6
[22] gtools_3.9.5 gridExtra_2.3 ArchR_1.0.2
loaded via a namespace (and not attached):
[1] lattice_0.22-6 circlize_0.4.16 png_0.1-8 digest_0.6.37
[5] foreach_1.5.2 utf8_1.2.4 R6_2.5.1 SparseArray_1.6.1
[9] pillar_1.9.0 GlobalOptions_0.1.2 zlibbioc_1.44.0 rlang_1.1.4
[13] rstudioapi_0.17.1 GetoptLong_1.0.5 labeling_0.4.3 BiocParallel_1.32.6
[17] pheatmap_1.0.12 RCurl_1.98-1.16 munsell_0.5.1 DelayedArray_0.32.0
[21] compiler_4.2.1 pkgconfig_2.0.3 shape_1.4.6.1 tidyselect_1.2.1
[25] tibble_3.2.1 GenomeInfoDbData_1.2.9 codetools_0.2-20 fansi_1.0.6
[29] crayon_1.5.3 dplyr_1.1.4 withr_3.0.2 rhdf5filters_1.12.1
[33] bitops_1.0-9 lifecycle_1.0.4 scales_1.3.0 cli_3.6.3
[37] stringi_1.8.4 farver_2.1.2 doParallel_1.0.17 generics_0.1.3
[41] vctrs_0.6.5 Rhdf5lib_1.20.0 rjson_0.2.23 RColorBrewer_1.1-3
[45] Cairo_1.6-2 iterators_1.0.14 tools_4.2.1 glue_1.8.0
[49] abind_1.4-8 clue_0.3-65 colorspace_2.1-1 cluster_2.1.6
[53] S4Arrays_1.6.0 ComplexHeatmap_2.14.0
------- Log Info
2025-02-20 20:31:39 : createArrowFiles Input-Parameters, Class = list
createArrowFiles Input-Parameters$inputFiles: length = 1
[1] "/slurm/home/yrd/fanlab/mayue/Ovarian_endometriosis_scATAC/ATAC-matrix/EUE1/fragments.tsv.gz"
createArrowFiles Input-Parameters$sampleNames: length = 1
[1] "EUE1"
createArrowFiles Input-Parameters$outputNames: length = 1
[1] "EUE1"
createArrowFiles Input-Parameters$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$threads: length = 1
[1] 1
createArrowFiles Input-Parameters$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-464f289d75db-Date-2025-02-20_Time-20-31-39.log"
createArrowFiles Input-Parameters$filterFrags: length = 1
[1] 1000
createArrowFiles Input-Parameters$filterTSS: length = 1
[1] 4
2025-02-20 20:31:39 : Cleaning Temporary Files
2025-02-20 20:31:39 : Batch Execution w/ safelapply!, 0 mins elapsed.
###########
2025-02-20 20:31:39 : Creating Arrow File EUE1.arrow (EUE1 : 1 of 1)
###########
2025-02-20 20:31:39 : validBC, Class = NULL
validBC: length = 0
NULL
2025-02-20 20:31:39 : (EUE1 : 1 of 1) Determining Arrow Method to use!
2025-02-20 20:31:39 : (EUE1 : 1 of 1) Reading In Fragments from inputFiles (readMethod = tabix), 0 mins elapsed.
2025-02-20 20:31:39 : (EUE1 : 1 of 1) Tabix Bed To Temporary File, 0.001 mins elapsed.
2025-02-20 20:31:39 : tileChromSizes, Class = GRanges
GRanges object with 200 ranges and 1 metadata column:
seqnames ranges strand | chunkName
|
[1] chr1 1-49791284 * | chr1#chunk1
[2] chr1 49791285-99582568 * | chr1#chunk2
[3] chr1 99582569-149373853 * | chr1#chunk3
[4] chr1 149373854-199165137 * | chr1#chunk4
[5] chr1 199165138-248956422 * | chr1#chunk5
... ... ... ... . ...
[196] KI270713.1 1-8149 * | KI270713.1#chunk196
[197] KI270713.1 8150-16298 * | KI270713.1#chunk197
[198] KI270713.1 16299-24447 * | KI270713.1#chunk198
[199] KI270713.1 24448-32596 * | KI270713.1#chunk199
[200] KI270713.1 32597-40745 * | KI270713.1#chunk200
seqinfo: 40 sequences from an unspecified genome; no seqlengths
2025-02-20 20:32:08 : (EUE1 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 200)-chr1:1-49791284, Class = data.table
2025-02-20 20:32:08 : (EUE1 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 200)-chr1:1-49791284, Class = data.frame
(EUE1 : 1 of 1) .tabixToTmp Fragments-Chunk-(1 of 200)-chr1:1-49791284: nRows = 7932397, nCols = 3
V2 V3 V4
1: 10067 10429 TCACAGAGTGCTTACA-1
2: 10078 10339 TTCATTGGTCACATTG-1
3: 10084 10297 TGGCGCAGTACCCACG-1
4: 10085 10309 CACCTGTTCCGATGCG-1
5: 10091 10338 GCCAGCAAGCCATCAT-1
6: 10097 10273 ACCGCAGTCTGACATG-1
2025-02-20 20:32:08 : (EUE1 : 1 of 1) .tabixToTmp Barcodes-Chunk-(1 of 200)-chr1:1-49791284, Class = character
(EUE1 : 1 of 1) .tabixToTmp Barcodes-Chunk-(1 of 200)-chr1:1-49791284: length = 75135
[1] "TCACAGAGTGCTTACA-1" "TTCATTGGTCACATTG-1" "TGGCGCAGTACCCACG-1" "CACCTGTTCCGATGCG-1"
[5] "GCCAGCAAGCCATCAT-1" "ACCGCAGTCTGACATG-1"
2025-02-20 20:34:12 : (EUE1 : 1 of 1) Reading TabixFile 5 Percent, 2.542 mins elapsed.
2025-02-20 20:36:02 : (EUE1 : 1 of 1) Reading TabixFile 10 Percent, 4.381 mins elapsed.
2025-02-20 20:37:07 : (EUE1 : 1 of 1) Reading TabixFile 15 Percent, 5.468 mins elapsed.
2025-02-20 20:38:19 : (EUE1 : 1 of 1) Reading TabixFile 20 Percent, 6.665 mins elapsed.
2025-02-20 20:39:29 : (EUE1 : 1 of 1) Reading TabixFile 25 Percent, 7.837 mins elapsed.
2025-02-20 20:41:25 : (EUE1 : 1 of 1) Reading TabixFile 30 Percent, 9.755 mins elapsed.
2025-02-20 20:42:24 : (EUE1 : 1 of 1) Reading TabixFile 35 Percent, 10.749 mins elapsed.
2025-02-20 20:43:50 : (EUE1 : 1 of 1) Reading TabixFile 40 Percent, 12.187 mins elapsed.
2025-02-20 20:45:55 : (EUE1 : 1 of 1) Reading TabixFile 45 Percent, 14.26 mins elapsed.
2025-02-20 20:47:52 : (EUE1 : 1 of 1) Reading TabixFile 50 Percent, 16.216 mins elapsed.
2025-02-20 20:49:21 : (EUE1 : 1 of 1) Reading TabixFile 55 Percent, 17.691 mins elapsed.
2025-02-20 20:50:08 : (EUE1 : 1 of 1) Reading TabixFile 60 Percent, 18.47 mins elapsed.
2025-02-20 20:50:21 : (EUE1 : 1 of 1) Reading TabixFile 65 Percent, 18.7 mins elapsed.
2025-02-20 20:50:29 : (EUE1 : 1 of 1) Reading TabixFile 70 Percent, 18.828 mins elapsed.
2025-02-20 20:50:37 : (EUE1 : 1 of 1) Reading TabixFile 75 Percent, 18.958 mins elapsed.
2025-02-20 20:50:45 : (EUE1 : 1 of 1) Reading TabixFile 80 Percent, 19.087 mins elapsed.
2025-02-20 20:50:52 : (EUE1 : 1 of 1) Reading TabixFile 85 Percent, 19.216 mins elapsed.
2025-02-20 20:51:00 : (EUE1 : 1 of 1) Reading TabixFile 90 Percent, 19.344 mins elapsed.
2025-02-20 20:51:07 : (EUE1 : 1 of 1) Reading TabixFile 95 Percent, 19.459 mins elapsed.
2025-02-20 20:51:15 : (EUE1 : 1 of 1) Reading TabixFile 100 Percent, 19.587 mins elapsed.
2025-02-20 20:51:15 : (EUE1 : 1 of 1) Successful creation of Temporary File, 19.6 mins elapsed.
2025-02-20 20:51:15 : (EUE1 : 1 of 1) Creating ArrowFile From Temporary File, 19.6 mins elapsed.
2025-02-20 20:51:15 : (EUE1 : 1 of 1) chunkChrNames, Class = data.frame
(EUE1 : 1 of 1) chunkChrNames: nRows = 192, nCols = 1
chunkNames
1 GL000009.2#chunk136
2 GL000009.2#chunk137
3 GL000009.2#chunk138
4 GL000009.2#chunk139
5 GL000009.2#chunk140
6 GL000194.1#chunk141
2025-02-20 20:51:15 : (EUE1 : 1 of 1) Counting Unique Barcodes From Temporary File, 19.601 mins elapsed.
2025-02-20 20:51:24 : (EUE1 : 1 of 1) BarcodeFrequencyTable, Class = data.table
2025-02-20 20:51:24 : (EUE1 : 1 of 1) BarcodeFrequencyTable, Class = data.frame
(EUE1 : 1 of 1) BarcodeFrequencyTable: nRows = 472168, nCols = 2
values.V1 V1
1: CCTGGGAGTGGCCTTG-1 101731
2: AAACTCGGTCATGAGG-1 90713
3: AGACAAATCCAAGTCA-1 88487
4: GAAGAGCAGGGAGATA-1 88017
5: GTAGGAGGTTGTGACT-1 86641
6: CCGTGAGCATGGTAAA-1 82796
2025-02-20 20:51:24 : (EUE1 : 1 of 1) BarcodesMinMaxFrags, Class = data.frame
(EUE1 : 1 of 1) BarcodesMinMaxFrags: nRows = 13022, nCols = 1
bc
1 AAACTCGGTCATGAGG-1
2 AGACAAATCCAAGTCA-1
3 GAAGAGCAGGGAGATA-1
4 GTAGGAGGTTGTGACT-1
5 CCGTGAGCATGGTAAA-1
6 AAACGAACAAGCAACG-1
2025-02-20 20:51:25 : (EUE1 : 1 of 1) Unique Chromosomes, Class = data.frame
(EUE1 : 1 of 1) Unique Chromosomes: nRows = 40, nCols = 1
chr
1 chr1
2 chr10
3 chr11
4 chr12
5 chr13
6 chr14
2025-02-20 20:51:25 : (EUE1 : 1 of 1) Adding Chromosome 1 of 40, 19.76 mins elapsed.
2025-02-20 20:51:47 : (EUE1 : 1 of 1) .tmpToArrow Fragments-Chr-(1 of 40)-chr1, Class = IRanges
(EUE1 : 1 of 1) .tmpToArrow Fragments-Chr-(1 of 40)-chr1: length = 24388815
IRanges object with 6 ranges and 1 metadata column:
start end width | RG
|
[1] 778368 778617 250 | AAACTCGGTCATGAGG-1
[2] 778593 778637 45 | AAACTCGGTCATGAGG-1
[3] 778863 778909 47 | AAACTCGGTCATGAGG-1
[4] 858101 858173 73 | AAACTCGGTCATGAGG-1
[5] 880812 881133 322 | AAACTCGGTCATGAGG-1
[6] 894998 895156 159 | AAACTCGGTCATGAGG-1
2025-02-20 20:51:47 : (EUE1 : 1 of 1) .tmpToArrow Barcodes-Chr-(1 of 40)-chr1, Class = data.frame
(EUE1 : 1 of 1) .tmpToArrow Barcodes-Chr-(1 of 40)-chr1: nRows = 13022, nCols = 1
bc
1 AAACTCGGTCATGAGG-1
2 AGACAAATCCAAGTCA-1
3 GAAGAGCAGGGAGATA-1
4 GTAGGAGGTTGTGACT-1
5 CCGTGAGCATGGTAAA-1
6 AAACGAACAAGCAACG-1
2025-02-20 20:51:48 : (EUE1 : 1 of 1) Adding Chromosome 2 of 40, 20.145 mins elapsed.
2025-02-20 20:51:58 : (EUE1 : 1 of 1) Adding Chromosome 3 of 40, 20.32 mins elapsed.
2025-02-20 20:52:12 : (EUE1 : 1 of 1) Adding Chromosome 4 of 40, 20.546 mins elapsed.
2025-02-20 20:52:25 : (EUE1 : 1 of 1) Adding Chromosome 5 of 40, 20.765 mins elapsed.
2025-02-20 20:52:32 : (EUE1 : 1 of 1) Adding Chromosome 6 of 40, 20.875 mins elapsed.
2025-02-20 20:52:40 : (EUE1 : 1 of 1) Adding Chromosome 7 of 40, 21.006 mins elapsed.
2025-02-20 20:52:48 : (EUE1 : 1 of 1) Adding Chromosome 8 of 40, 21.151 mins elapsed.
2025-02-20 20:52:59 : (EUE1 : 1 of 1) Adding Chromosome 9 of 40, 21.326 mins elapsed.
2025-02-20 20:53:09 : (EUE1 : 1 of 1) Adding Chromosome 10 of 40, 21.493 mins elapsed.
2025-02-20 20:53:14 : (EUE1 : 1 of 1) Adding Chromosome 11 of 40, 21.582 mins elapsed.
2025-02-20 20:53:23 : (EUE1 : 1 of 1) Adding Chromosome 12 of 40, 21.733 mins elapsed.
2025-02-20 20:53:42 : (EUE1 : 1 of 1) Adding Chromosome 13 of 40, 22.053 mins elapsed.
2025-02-20 20:53:48 : (EUE1 : 1 of 1) Adding Chromosome 14 of 40, 22.153 mins elapsed.
2025-02-20 20:53:52 : (EUE1 : 1 of 1) Adding Chromosome 15 of 40, 22.212 mins elapsed.
2025-02-20 20:53:57 : (EUE1 : 1 of 1) Adding Chromosome 16 of 40, 22.291 mins elapsed.
2025-02-20 20:54:14 : (EUE1 : 1 of 1) Adding Chromosome 17 of 40, 22.57 mins elapsed.
2025-02-20 20:54:27 : (EUE1 : 1 of 1) Adding Chromosome 18 of 40, 22.79 mins elapsed.
2025-02-20 20:54:40 : (EUE1 : 1 of 1) Adding Chromosome 19 of 40, 23.017 mins elapsed.
2025-02-20 20:54:54 : (EUE1 : 1 of 1) Adding Chromosome 20 of 40, 23.252 mins elapsed.
2025-02-20 20:55:08 : (EUE1 : 1 of 1) Adding Chromosome 21 of 40, 23.474 mins elapsed.
2025-02-20 20:55:20 : (EUE1 : 1 of 1) Adding Chromosome 22 of 40, 23.682 mins elapsed.
2025-02-20 20:55:33 : (EUE1 : 1 of 1) Adding Chromosome 23 of 40, 23.891 mins elapsed.
2025-02-20 20:55:33 : (EUE1 : 1 of 1) detected 0 Fragments for chrM
2025-02-20 20:55:33 : (EUE1 : 1 of 1) Adding Chromosome 24 of 40, 23.891 mins elapsed.
2025-02-20 20:55:42 : (EUE1 : 1 of 1) Adding Chromosome 25 of 40, 24.046 mins elapsed.
2025-02-20 20:55:43 : (EUE1 : 1 of 1) Adding Chromosome 26 of 40, 24.066 mins elapsed.
2025-02-20 20:55:45 : (EUE1 : 1 of 1) Adding Chromosome 27 of 40, 24.088 mins elapsed.
2025-02-20 20:55:46 : (EUE1 : 1 of 1) Adding Chromosome 28 of 40, 24.108 mins elapsed.
2025-02-20 20:55:47 : (EUE1 : 1 of 1) Adding Chromosome 29 of 40, 24.129 mins elapsed.
2025-02-20 20:55:48 : (EUE1 : 1 of 1) Adding Chromosome 30 of 40, 24.15 mins elapsed.
2025-02-20 20:55:50 : (EUE1 : 1 of 1) Adding Chromosome 31 of 40, 24.172 mins elapsed.
2025-02-20 20:55:51 : (EUE1 : 1 of 1) Adding Chromosome 32 of 40, 24.192 mins elapsed.
2025-02-20 20:55:52 : (EUE1 : 1 of 1) Adding Chromosome 33 of 40, 24.213 mins elapsed.
2025-02-20 20:55:53 : (EUE1 : 1 of 1) Adding Chromosome 34 of 40, 24.234 mins elapsed.
2025-02-20 20:55:55 : (EUE1 : 1 of 1) Adding Chromosome 35 of 40, 24.254 mins elapsed.
2025-02-20 20:55:56 : (EUE1 : 1 of 1) Adding Chromosome 36 of 40, 24.275 mins elapsed.
2025-02-20 20:55:57 : (EUE1 : 1 of 1) Adding Chromosome 37 of 40, 24.295 mins elapsed.
2025-02-20 20:55:58 : (EUE1 : 1 of 1) Adding Chromosome 38 of 40, 24.315 mins elapsed.
2025-02-20 20:55:59 : (EUE1 : 1 of 1) Adding Chromosome 39 of 40, 24.335 mins elapsed.
2025-02-20 20:56:01 : (EUE1 : 1 of 1) Adding Chromosome 40 of 40, 24.356 mins elapsed.
2025-02-20 20:56:02 : (EUE1 : 1 of 1) Successful creation of Arrow File, 24.377 mins elapsed.
2025-02-20 20:56:03 : (EUE1 : 1 of 1) Adding Fragment Summary, 24.391 mins elapsed.
2025-02-20 20:56:52 : (EUE1 : 1 of 1) Plotting Fragment Size Distribution, 25.216 mins elapsed.
2025-02-20 20:56:52 : Continuing through after error ggplot for Fragment Size Distribution, 25.217 mins elapsed.
2025-02-20 20:56:53 : (EUE1 : 1 of 1) Computing TSS Enrichment Scores, 25.23 mins elapsed.
2025-02-20 20:56:54 : ERROR Found in .fastTSSCounts for (EUE1 : 1 of 1)
LogFile = ArchRLogs/ArchR-createArrows-464f289d75db-Date-2025-02-20_Time-20-31-39.log
<simpleError in .Call2("C_find_overlaps_NCList", start(query), end(query), start(subject), end(subject), nclist, nclist_is_q, maxgap, minoverlap, type, select, circle.length, PACKAGE = "IRanges"): build_NCList: memory allocation failed>
2025-02-20 20:56:54 : errorList, Class = list
errorList$x: length = 1
[1] 1
errorList$chr: length = 1
[1] "GL000009.2"
errorList$fragments: length = 1
[1] "Error with Fragments!"
errorList$features: length = 1
[1] "Error with Features!"
2025-02-20 20:56:54 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
------- Completed
End Time : 2025-02-20 20:56:54
Elapsed Time Minutes = 25.2505369027456
Elapsed Time Hours = 0.420842320985264