problem in creating Arrow Files from Bam file

[zara03]

Hi
I am very new to ArchR . I have downloaded a public dataset and i indexed the fastq with hg19 as they mentioned in paper.This created sam file, which i converted into bam and then indexed the bam.the indexing created 2 files SRR7784432_aligned.bam and SRR7784432_aligned.bam.bai.

Code:
bowtie2 -x hg19_index -U /home/saz22/snATAC_GSE119453_hg19_Data/SRR7784432.fastq -S SRR7784432_aligned.sam

samtools view -bS SRR7784432_aligned.sam | samtools sort -o SRR7784432_aligned.bam

samtools index SRR7784432_aligned.bam

No i am trying to read SRR7784432_aligned.bam as input to create arrow file and it gives me error first it was input is not indexed and now this is error i am facing.

ArrowFiles <- createArrowFiles( inputFiles = "/home/zs/SRR7784432_aligned.bam",
sampleNames = "Sample_SRR7784432",
geneAnnotation = getGeneAnnotation("hg19"),
genomeAnnotation = getGenomeAnnotation("hg19"),
minTSS = 4,
minFrags = 1000,
addTileMat = TRUE,
addGeneScoreMat = TRUE)
Error in .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProject", :
Input value for 'ArchRProj' is not a null,archrproject, (ArchRProj = character) please supply valid input!

Any suggestion will be of great help.

[rcorces]

Hi @zara03! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.