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20 hours ago •
GreenleafLab
GreenleafLab
ERROR createArrowFiles : core dumped
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I am performing analysis on a non-model species, and I encounter a "core dumped" when creating an arrowfile. I'm not sure what could be causing this, and I haven't found any error information in the log files.could you help me?Thank you so much!
ArrowFiles <- createArrowFiles(minFrags = 1000,minTSS = 2,subThreading = F,threads = 1,#minFrags = 1000,minTSS = 1
geneAnnotation = geneAnnotation,
genomeAnnotation = genomeAnnotation,
inputFiles = TB_brain,
sampleNames = "TB_brain",
addTileMat = TRUE,
addGeneScoreMat = F,
force = T
)
ArchR logging to : ArchRLogs/ArchR-createArrows-24409dfc0b13f-Date-2023-05-16_Time-15-20-33.log
If there is an issue, please report to github with logFile!
2023-05-16 15:20:33 : Batch Execution w/ safelapply!, 0 mins elapsed.
2023-05-16 15:20:33 : (TB_brain : 1 of 1) Reading In Fragments from inputFiles (readMethod = tabix), 0.002 mins elapsed.
2023-05-16 15:20:33 : (TB_brain : 1 of 1) Tabix Bed To Temporary File, 0.002 mins elapsed.
2023-05-16 15:20:45 : (TB_brain : 1 of 1) Reading TabixFile 0 Percent, 0.199 mins elapsed.
2023-05-16 15:20:55 : (TB_brain : 1 of 1) Reading TabixFile 1 Percent, 0.362 mins elapsed.
2023-05-16 15:21:04 : (TB_brain : 1 of 1) Reading TabixFile 1 Percent, 0.517 mins elapsed.
2023-05-16 15:21:13 : (TB_brain : 1 of 1) Reading TabixFile 1 Percent, 0.663 mins elapsed.
2023-05-16 15:21:22 : (TB_brain : 1 of 1) Reading TabixFile 1 Percent, 0.813 mins elapsed.
2023-05-16 15:21:33 : (TB_brain : 1 of 1) Reading TabixFile 2 Percent, 0.997 mins elapsed.
2023-05-16 15:21:40 : (TB_brain : 1 of 1) Reading TabixFile 2 Percent, 1.122 mins elapsed.
2023-05-16 15:21:49 : (TB_brain : 1 of 1) Reading TabixFile 2 Percent, 1.272 mins elapsed.
2023-05-16 15:21:58 : (TB_brain : 1 of 1) Reading TabixFile 2 Percent, 1.41 mins elapsed.
2023-05-16 15:22:07 : (TB_brain : 1 of 1) Reading TabixFile 3 Percent, 1.561 mins elapsed.
2023-05-16 15:22:16 : (TB_brain : 1 of 1) Reading TabixFile 3 Percent, 1.707 mins elapsed.
2023-05-16 15:22:24 : (TB_brain : 1 of 1) Reading TabixFile 3 Percent, 1.84 mins elapsed.
2023-05-16 15:22:32 : (TB_brain : 1 of 1) Reading TabixFile 3 Percent, 1.987 mins elapsed.
2023-05-16 15:22:42 : (TB_brain : 1 of 1) Reading TabixFile 4 Percent, 2.146 mins elapsed.
2023-05-16 15:22:58 : (TB_brain : 1 of 1) Reading TabixFile 4 Percent, 2.409 mins elapsed.
2023-05-16 15:23:12 : (TB_brain : 1 of 1) Reading TabixFile 4 Percent, 2.655 mins elapsed.
2023-05-16 15:23:28 : (TB_brain : 1 of 1) Reading TabixFile 5 Percent, 2.917 mins elapsed.
2023-05-16 15:23:40 : (TB_brain : 1 of 1) Reading TabixFile 5 Percent, 3.12 mins elapsed.
2023-05-16 15:23:49 : (TB_brain : 1 of 1) Reading TabixFile 5 Percent, 3.273 mins elapsed.
2023-05-16 15:24:01 : (TB_brain : 1 of 1) Reading TabixFile 5 Percent, 3.468 mins elapsed.
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2023-05-16 15:24:37 : (TB_brain : 1 of 1) Reading TabixFile 6 Percent, 4.07 mins elapsed.
2023-05-16 15:24:51 : (TB_brain : 1 of 1) Reading TabixFile 6 Percent, 4.304 mins elapsed.
2023-05-16 15:25:07 : (TB_brain : 1 of 1) Reading TabixFile 7 Percent, 4.56 mins elapsed.
2023-05-16 15:25:22 : (TB_brain : 1 of 1) Reading TabixFile 7 Percent, 4.819 mins elapsed.
2023-05-16 15:25:39 : (TB_brain : 1 of 1) Reading TabixFile 7 Percent, 5.097 mins elapsed.
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2023-05-16 15:26:10 : (TB_brain : 1 of 1) Reading TabixFile 8 Percent, 5.608 mins elapsed.
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2023-05-16 15:26:42 : (TB_brain : 1 of 1) Reading TabixFile 8 Percent, 6.142 mins elapsed.
2023-05-16 15:26:57 : (TB_brain : 1 of 1) Reading TabixFile 9 Percent, 6.394 mins elapsed.
2023-05-16 15:27:13 : (TB_brain : 1 of 1) Reading TabixFile 9 Percent, 6.659 mins elapsed.
2023-05-16 15:27:28 : (TB_brain : 1 of 1) Reading TabixFile 9 Percent, 6.907 mins elapsed.
2023-05-16 15:27:43 : (TB_brain : 1 of 1) Reading TabixFile 9 Percent, 7.161 mins elapsed.
2023-05-16 15:28:01 : (TB_brain : 1 of 1) Reading TabixFile 10 Percent, 7.457 mins elapsed.
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2023-05-16 15:28:18 : (TB_brain : 1 of 1) Reading TabixFile 10 Percent, 7.748 mins elapsed.
2023-05-16 15:28:27 : (TB_brain : 1 of 1) Reading TabixFile 10 Percent, 7.892 mins elapsed.
2023-05-16 15:28:35 : (TB_brain : 1 of 1) Reading TabixFile 11 Percent, 8.023 mins elapsed.
2023-05-16 15:28:42 : (TB_brain : 1 of 1) Reading TabixFile 11 Percent, 8.15 mins elapsed.
2023-05-16 15:28:50 : (TB_brain : 1 of 1) Reading TabixFile 11 Percent, 8.285 mins elapsed.
2023-05-16 15:28:58 : (TB_brain : 1 of 1) Reading TabixFile 11 Percent, 8.42 mins elapsed.
2023-05-16 15:29:07 : (TB_brain : 1 of 1) Reading TabixFile 12 Percent, 8.566 mins elapsed.
2023-05-16 15:29:18 : (TB_brain : 1 of 1) Reading TabixFile 12 Percent, 8.752 mins elapsed.
2023-05-16 15:29:27 : (TB_brain : 1 of 1) Reading TabixFile 12 Percent, 8.891 mins elapsed.
2023-05-16 15:29:35 : (TB_brain : 1 of 1) Reading TabixFile 13 Percent, 9.029 mins elapsed.
2023-05-16 15:29:43 : (TB_brain : 1 of 1) Reading TabixFile 13 Percent, 9.162 mins elapsed.
2023-05-16 15:29:53 : (TB_brain : 1 of 1) Reading TabixFile 13 Percent, 9.334 mins elapsed.
2023-05-16 15:30:03 : (TB_brain : 1 of 1) Reading TabixFile 13 Percent, 9.494 mins elapsed.
2023-05-16 15:30:11 : (TB_brain : 1 of 1) Reading TabixFile 14 Percent, 9.634 mins elapsed.
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2023-05-16 15:30:28 : (TB_brain : 1 of 1) Reading TabixFile 14 Percent, 9.908 mins elapsed.
2023-05-16 15:30:36 : (TB_brain : 1 of 1) Reading TabixFile 14 Percent, 10.047 mins elapsed.
2023-05-16 15:30:45 : (TB_brain : 1 of 1) Reading TabixFile 15 Percent, 10.191 mins elapsed.
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2023-05-16 15:31:02 : (TB_brain : 1 of 1) Reading TabixFile 15 Percent, 10.48 mins elapsed.
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2023-05-16 15:31:24 : (TB_brain : 1 of 1) Reading TabixFile 16 Percent, 10.841 mins elapsed.
2023-05-16 15:31:33 : (TB_brain : 1 of 1) Reading TabixFile 16 Percent, 10.997 mins elapsed.
2023-05-16 15:31:41 : (TB_brain : 1 of 1) Reading TabixFile 16 Percent, 11.136 mins elapsed.
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2023-05-16 15:36:12 : (TB_brain : 1 of 1) Reading TabixFile 24 Percent, 15.647 mins elapsed.
free(): invalid next size (normal)
Aborted (core dumped)
ArchR-createArrows-24409dfc0b13f-Date-2023-05-16_Time-15-20-33.log
sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /home/minghao/miniconda3/envs/Rnew/lib/libopenblasp-r0.3.21.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] rhdf5_2.42.0 SummarizedExperiment_1.28.0
[3] Biobase_2.58.0 MatrixGenerics_1.10.0
[5] Rcpp_1.0.10 Matrix_1.5-3
[7] matrixStats_0.63.0 data.table_1.14.8
[9] stringr_1.5.0 plyr_1.8.8
[11] magrittr_2.0.3 ggplot2_3.4.1
[13] gtable_0.3.1 gtools_3.9.4
[15] gridExtra_2.3 ArchR_1.0.2
[17] BSgenome.Antarctic.customize.TB_1.4.4 BSgenome_1.66.3
[19] rtracklayer_1.58.0 Biostrings_2.66.0
[21] XVector_0.38.0 GenomicRanges_1.50.1
[23] GenomeInfoDb_1.34.9 IRanges_2.32.0
[25] S4Vectors_0.36.0 BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] lattice_0.20-45 Rsamtools_2.14.0 digest_0.6.31
[4] utf8_1.2.3 IRdisplay_1.1 R6_2.5.1
[7] repr_1.1.6 evaluate_0.20 pillar_1.8.1
[10] zlibbioc_1.44.0 rlang_1.0.6 uuid_1.1-0
[13] BiocParallel_1.32.0 RCurl_1.98-1.12 munsell_0.5.0
[16] DelayedArray_0.24.0 compiler_4.2.3 pkgconfig_2.0.3
[19] base64enc_0.1-3 htmltools_0.5.4 tidyselect_1.2.0
[22] tibble_3.1.8 GenomeInfoDbData_1.2.9 codetools_0.2-19
[25] XML_3.99-0.13 fansi_1.0.4 withr_2.5.0
[28] crayon_1.5.2 dplyr_1.1.0 rhdf5filters_1.10.0
[31] GenomicAlignments_1.34.0 bitops_1.0-7 jsonlite_1.8.4
[34] lifecycle_1.0.3 scales_1.2.1 stringi_1.7.12
[37] cli_3.6.0 vctrs_0.5.2 generics_0.1.3
[40] IRkernel_1.3 Rhdf5lib_1.20.0 rjson_0.2.21
[43] restfulr_0.0.15 tools_4.2.3 glue_1.6.2
[46] parallel_4.2.3 fastmap_1.1.1 yaml_2.3.7
[49] colorspace_2.1-0 pbdZMQ_0.3-9 BiocIO_1.8.0
Thank you so much!
Hi @minghao622! Thanks for using ArchR! I am currently on vacation and will not be responding to any issues or discussion threads until 5/5.
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.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably 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, how will we 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.
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example.
3. Did you post your log file? If not, add it now.
4. 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.
