problem with featureMatrix

[yamihn]

hi @timoast, I was trying to analyze the peaks of my object. I called the peaks using callpeaks, but the problem is that when I try to create the featurematrix, I get the following error:

macs2_counts <- FeatureMatrix (
+ fragments = fragments (subset_obj),
+ features = peaks,
+)
[W :: hts_idx_load2] The index file is older than the data file: /media/jan/toshiba/single_cell/Fragment/KO_d6_r1_fragments.tsv.gz.tbi
Error in h (simpleError (msg, call)):
  error evaluating the 'y' argument when selecting a method for the 'intersect' function: [internal] bgzf_seek () failed


 traceback()
12: h(simpleError(msg, call))
11: .handleSimpleError(function (cond) 
    .Internal(C_tryCatchHelper(addr, 1L, cond)), "[internal] bgzf_seek() failed", 
        base::quote(.headerTabix(file, ...)))
10: .headerTabix(file, ...)
9: seqnamesTabix(file = tbx)
8: seqnamesTabix(file = tbx)
7: intersect(x = seqnames(x = features), y = seqnamesTabix(file = tbx))
6: keepSeqlevels(x = features, value = intersect(x = seqnames(x = features), 
       y = seqnamesTabix(file = tbx)), pruning.mode = "coarse")
5: SingleFeatureMatrix(fragment = fragments[[x]], features = features, 
       cells = cells, sep = sep, verbose = verbose, process_n = process_n)
4: FUN(X[[i]], ...)
3: lapply(X = X, FUN = FUN, ...)
2: sapply(X = obj.use, FUN = function(x) {
       SingleFeatureMatrix(fragment = fragments[[x]], features = features, 
           cells = cells, sep = sep, verbose = verbose, process_n = process_n)
   })
1: FeatureMatrix(fragments = Fragments(subset24_obj), features = peaks, 
       )

Also, when I try to find the dars between two conditions (WT vs KO), I find myself with extremely low fold changes and see no difference. In latent.vars I don't have the "peak_region_fragments" file. could the problem stem from this?

[timoast]

It looks like there's an issue with your fragment file, maybe it was not constructed or indexed properly. Take a look at #242 for some suggestions