Open HaixJiang opened 9 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.
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
have you solved this problem? I met the same error
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.
Describe the bug, threads = 16
ArchR-createArrows-162e37760c4f2-Date-2024-01-13_Time-21-45-08.689397.log
I modified the threads = 1
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