createArrowFiles has encountered an error, checking if any ArrowFiles completed

[yym0825]

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

---

[immanuelazn]

Hi @yym0825! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.

In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Did you post your log file? If not, add it now.
3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[immanuelazn]

Seems like you're running out of memory. Any way you can run htop on your node?

[yym0825]

"This is the command I entered after running top."
10403 mayue 20 0 168820 4896 1656 R 1.6 0.0 0:00.36 top

Sometimes this error occurs, even though I am just creating an arrow file from a single file.
2025-02-20 21:20:18 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
ArchR logging successful to : ArchRLogs/ArchR-createArrows-464f6ae6cce6-Date-2025-02-20_Time-21-11-54.log
Warning message:
In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) :
39 function calls resulted in an error
Session restored from your saved work on 2025-Feb-20 17:16:08 UTC (7 hours ago)

gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 8843646 472.4 16243172 867.5 16243172 867.5
Vcells 23170750 176.8 40296576 307.5 33513807 255.7
My memory should be sufficient; I don't know if something in the environment has changed.

[immanuelazn]

Cool, not entirely sure what is the issue but maybe we can try updating your ArchR to 1.0.3 first. If there's still an issue, maybe try sharing an rds to my email ([email protected]) so I can try diagnosing

[yym0825]

I have already sent you an email. Please kindly check your inbox. Thank you very much for your reply.