createArrowFiles. <simpleError: No fragments found! >

[zahramesri]

Hi. @rcorces ,

When I run:
ArrowFiles <- createArrowFiles(
inputFiles = inputFiles,
minFrags = 1000,
filterFrags = 1000,
filterTSS = 4
)

I receive the following error and my ArrowFile is empty.

2022-04-26 11:39:13 : ERROR Found in .tabixToTmp for (scATAC : 1 of 1)
LogFile = ArchRLogs/ArchR-createArrows-12c042da2425-Date-2022-04-26_Time-11-38-45.log

<simpleError: No fragments found!>

I have attached the logFile here as well. Please let me know if anyone can help
ArchR-createArrows-12c042da2425-Date-2022-04-26_Time-11-38-45.log

This issue also occurs on the example given in the tutorial.
.

[rcorces]

1. please show the first 10 lines of your fragment file.
2. Make sure that your fragment file is bgzipped, not gzipped

[zahramesri]

I tried on the tutorial example. I still get an error and I have attached the log file.

ArrowFiles <- createArrowFiles(
inputFiles = inputFiles,
sampleNames = names(inputFiles),
filterTSS = 4, #Dont set this too high because you can always increase later
filterFrags = 1000,
addTileMat = TRUE,
addGeneScoreMat = TRUE,
threads = 1
)

ERROR:

filterFrags is no longer a valid input. Please use minFrags! Setting filterFrags value to minFrags!
filterTSS is no longer a valid input. Please use minTSS! Setting filterTSS value to minTSS!
Using GeneAnnotation set by addArchRGenome(Hg19)!
Using GeneAnnotation set by addArchRGenome(Hg19)!
ArchR logging to : ArchRLogs/ArchR-createArrows-10d96779089e2-Date-2022-04-27_Time-16-21-09.log
If there is an issue, please report to github with logFile!
2022-04-27 16:21:09 : Batch Execution w/ safelapply!, 0 mins elapsed.
Attempting to index HemeFragments/scATAC_BMMC_R1.fragments.tsv.gz as tabix..
2022-04-27 16:21:09 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
ArchR logging successful to : ArchRLogs/ArchR-createArrows-10d96779089e2-Date-2022-04-27_Time-16-21-09.log
ArchR-createArrows-10d96779089e2-Date-2022-04-27_Time-16-21-09.log

[rcorces]

If you're getting an error on the tutorial data then that is a dead giveaway that something is likely wrong with your environment. Its going to be challenging for me to help troubleshoot that.
The only thing that might provide hints would be the output of traceback() after you receive this error on the tutorial data set.

[zahramesri]

Thank you so much Ryan for your help.

I have tried and there is no luck there.

traceback()
No traceback available

[rcorces]

I'm sorry but without more information, there is no way for me to help you. You'll have to try to figure this out on your own.

[zahramesri]

Please let me know if there is any other information that I can share. Thank you again and I will try on my own.