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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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ERROR:Found in .fastTSSCounts for/ERROR:ArrowFiles completed./ERROR:double free or corruption #2097

Open HaixJiang opened 10 months ago

HaixJiang commented 10 months ago

Hi,Dear software creator, I encountered two types of errors while using createArrowFiles.But,I used the tutorial dataset, and everything worked fine.And than, I have searched some similar issue discussions, but none of them have resolved my problem.Eg:createArrowFiles has encountered an error, checking if any ArrowFiles completed #1275 so on.

ArrowFiles <- createArrowFiles(
 inputFiles = inputFiles,
 sampleNames = "jhxscATAC",
 geneAnnotation = geneAnnotation,
  genomeAnnotation = genomeAnnotation,
 minTSS = 4, #Dont set this too high because you can always increase later
 minFrags = 1000,
 filterTSS = 0.5,
 filterFrags = 100, 
 addTileMat = TRUE,
 force = TRUE,
 addGeneScoreMat = TRUE,
 nChunk = 2,
 subThreading = TRUE,
 cleanTmp = TRUE,
 threads = 1
)

Describe the bug, threads = 16

ERROR Found in .fastTSSCounts for 
createArrowFiles has encountered an error, checking if any ArrowFiles completed..

ArchR-createArrows-162e37760c4f2-Date-2024-01-13_Time-21-45-08.689397.log

I modified the threads = 1

2024-01-13 23:54:20.706903 : (jhxscATAC : 1 of 1) Reading TabixFile 16 Percent,                                                                                                                              86.588 mins elapsed.
*** Error in `/home/JHX68/anaconda3/envs/R4/lib/R/bin/exec/R': double free or co                                                                                                                             rruption (!prev): 0x0000562139e9a790 ***

Attach your log file ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag and drop it here. ArchR-createArrows-162e312890945-Date-2024-01-13_Time-22-27-42.934857.log ArchR-createArrows-20c9c6039b4b5-Date-2024-01-13_Time-09-17-40.620121.log

rcorces commented 10 months ago

Hi @HaixJiang! 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.
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, 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.

HaixJiang commented 10 months ago

I checked the genome file and the annotation file, and there seems to be no problem.

>seqinfo(BSgenome.Gallus)
Seqinfo object with 42 sequences (1 circular) from galGal7b genome:
  seqnames seqlengths isCircular   genome
  chr1      196449156      FALSE galGal
  chr10      20453248      FALSE galGal
  chr11      19638187      FALSE galGal
  chr12      20119077      FALSE galGal
  chr13      17905061      FALSE galGal
  ...             ...        ...      ...
  chr8       29578256      FALSE galGal
  chr9       23733309      FALSE galGal
  MT            16784       TRUE galGal
  W           9109940      FALSE galGal
  Z          86044486      FALSE galGal
>
> seqinfo(txdb)
Seqinfo object with 42 sequences (1 circular) from an unspecified genome:
  seqnames seqlengths isCircular genome
  chr1      196449156       <NA>   <NA>
  chr2      149539284       <NA>   <NA>
  chr3      110642502       <NA>   <NA>
  chr4       90861225       <NA>   <NA>
  chr5       59506338       <NA>   <NA>
  ...             ...        ...    ...
  chr38        667312       <NA>   <NA>
  chr39        177356       <NA>   <NA>
  W           9109940       <NA>   <NA>
  Z          86044486       <NA>   <NA>
  MT            16784       TRUE   <NA>

I tried to rebuild the arrow file, but it still failed.

2024-01-14 03:50:09.386262 : ERROR Found in .addTileMat for 11scATAC
LogFile = ArchRLogs/ArchR-createArrows-14e015870b1b6-Date-2024-01-14_Time-03-03-38.860738.log
<simpleError in validObject(r): invalid class “dgTMatrix” object: 'i' and 'j' slots do not have equal length>
<simpleError in .logError(e, fn = ".addTileMat", info = sampleName, errorList = errorList,     logFile = logFile): Exiting See Error Above>
2024-01-14 03:50:09.396916 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..

ArchR-createArrows-14e015870b1b6-Date-2024-01-14_Time-03-03-38.860738.log

YaoyJiang commented 6 months ago

have you solved this problem? I met the same error