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createArrowFiles has encountered an error

Open Tc940417 opened this issue 8 months ago • 1 comments

I have a trouble about createArrowFiles ,there is my code and log. thanks!

Attach your log file

ArchR-createArrows-16c816882c00-Date-2025-03-31_Time-12-16-09.425782.log

Describe the bug createArrowFiles has encountered an error, checking if any ArrowFiles completed..

Screenshots

library(parallel) library(ArchR) library(org.At.tair.db) library(GenomicRanges) library(TxDb.Athaliana.TAIR.10) library(BSgenome.Athaliana.TAIR.10) TxDb <- TxDb.Athaliana.TAIR.10 OrgDb <- org.At.tair.db

addArchRChrPrefix(chrPrefix = FALSE) ArchR is now disabling the requirement of chromosome prefix = 'chr' geneAnno <- createGeneAnnotation(TxDb=TxDb, OrgDb=OrgDb, annoStyle = "TAIR") Getting Genes.. Determined Annotation Style = TAIR Getting Exons.. Getting TSS.. genomeAnno <- createGenomeAnnotation(genome = BSgenome.Athaliana.TAIR.10) Getting genome.. Attempting to infer chromSizes.. Attempting to infer blacklist.. Blacklist not downloaded! Continuing without, be careful for downstream biases..

input.file.list <- c("D:/sn-CUT&TAG/2_fragments/ara.frag/ara9/Ara9.fragments.tsv.gz",

  •                  "D:/sn-CUT&TAG/2_fragments/ara.frag/ara10/Ara10.fragments.tsv.gz",

  •                  "D:/sn-CUT&TAG/2_fragments/ara.frag/ara11/Ara11.fragments.tsv.gz",

  •                  "D:/sn-CUT&TAG/2_fragments/ara.frag/ara12/Ara12.fragments.tsv.gz")

AraNames <- c("Ara9","Ara10","Ara11","Ara12")

ArrowFiles <- createArrowFiles(inputFiles = input.file.list,

  •                            sampleNames = AraNames,

  •                            minTSS = 1 ,

  •                            minFrags = 1000 ,

  •                            geneAnnotation = geneAnno,

  •                            genomeAnnotation = genomeAnno,

  •                            addTileMat = TRUE ,

  •                            TileMatParams = list(tileSize = 500, blacklist = NULL),

  •                            addGeneScoreMat = TRUE ,

  •                            GeneScoreMatParams = list(blacklist = NULL)
  • ) Found Gene Seqnames not in GenomeAnnotation chromSizes, Removing : 1,2,3,4,5,Mt,Pt Found Exon Seqnames not in GenomeAnnotation chromSizes, Removing : 1,2,3,4,5,Mt,Pt Found TSS Seqnames not in GenomeAnnotation chromSizes, Removing : 1,2,3,4,5,Mt,Pt ArchR logging to : ArchRLogs\ArchR-createArrows-16c816882c00-Date-2025-03-31_Time-12-16-09.425782.log If there is an issue, please report to github with logFile! subThreading Enabled since ArchRLocking is FALSE see addArchRLocking 2025-03-31 12:16:09.815 : Batch Execution w/ safelapply!, 0 mins elapsed. 2025-03-31 12:16:09.823817 : (Ara10 : 1 of 4) Reading In Fragments from inputFiles (readMethod = tabix), 0 mins elapsed. 2025-03-31 12:16:09.826849 : (Ara10 : 1 of 4) Tabix Bed To Temporary File, 0 mins elapsed. 2025-03-31 12:19:16.903321 : (Ara10 : 1 of 4) Reading TabixFile 29 Percent, 3.118 mins elapsed. 2025-03-31 12:22:19.778873 : (Ara10 : 1 of 4) Reading TabixFile 57 Percent, 6.166 mins elapsed. 2025-03-31 12:24:46.916849 : (Ara10 : 1 of 4) Reading TabixFile 86 Percent, 8.618 mins elapsed. 2025-03-31 12:24:47.610472 : (Ara10 : 1 of 4) Successful creation of Temporary File, 8.63 mins elapsed. 2025-03-31 12:24:47.611335 : (Ara10 : 1 of 4) Creating ArrowFile From Temporary File, 8.63 mins elapsed. 2025-03-31 12:26:31.167081 : (Ara10 : 1 of 4) Successful creation of Arrow File, 10.356 mins elapsed. 2025-03-31 12:26:35.024639 : createArrowFiles has encountered an error, checking if any ArrowFiles completed.. ArchR logging successful to : ArchRLogs\ArchR-createArrows-16c816882c00-Date-2025-03-31_Time-12-16-09.425782.log

Tc940417 avatar Mar 31 '25 04:03 Tc940417

Hi @Tc940417! 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 avatar Mar 31 '25 04:03 immanuelazn