addReproduciblePeakSet causing error

[jacobHog]

Hello,
I am getting an error that I do not understand by using methods used in Full Manual #10 "Calling Peaks with ArchR"

Full Manual #8: Cluster identity was not defined by using scRNA, therefore Cluster2 was not generated.
Full Manual #9: Pseudo-bulk replicates were generated using addGroupCoverages().
Full Manual #10: I am calling peaks with TileMatrix by using addReproduciblePeakSet().

My code for Full Manual #10
Clean_merged_3_tmp <- addReproduciblePeakSet(
ArchRProj = Clean_merged_3,
groupBy = "Clusters",
peakMethod = "Tiles",
method = "p"
)

My error:
ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-a1552a5b3eaa-Date-2021-11-05_Time-08-36-16.log
If there is an issue, please report to github with logFile!
Group Coverages Already Computed Returning Groups, Set force = TRUE to Recompute!
List of length 22
names(22): C1 C2 C3 C4 C5 C6 C7 C8 C9 ... C14 C15 C16 C17 C18 C19 C20 C21 C22
2021-11-05 08:36:17 : Peak Calling Parameters!, 0.01 mins elapsed.
Group nCells nCellsUsed nReplicates nMin nMax maxPeaks
C1 C1 386 366 4 43 124 150000
C2 C2 1009 1009 4 43 491 150000
C3 C3 655 652 3 77 444 150000
C4 C4 316 288 3 63 156 144000
C5 C5 196 196 2 40 156 98000
C6 C6 1502 1332 5 188 332 150000
C7 C7 5986 2045 5 268 500 150000
C8 C8 10540 2500 5 500 500 150000
C9 C9 538 523 4 64 199 150000
C10 C10 152 152 3 47 57 76000
C11 C11 274 274 3 44 146 137000
C12 C12 1514 1464 5 90 444 150000
C13 C13 193 158 3 43 61 79000
C14 C14 2900 1431 5 68 500 150000
C15 C15 9835 2500 5 500 500 150000
C16 C16 1152 1101 5 64 463 150000
C17 C17 248 211 3 42 98 105500
C18 C18 819 709 4 50 500 150000
C19 C19 6318 1741 5 114 500 150000
C20 C20 4881 1182 4 83 500 150000
C21 C21 493 469 5 46 152 150000
C22 C22 54 54 2 40 40 27000
2021-11-05 08:36:23 : Computing Total Accessibility Across All Features, 0.116 mins elapsed.
2021-11-05 08:36:26 : Computing Pseudo-Grouped Tile Matrix, 0.168 mins elapsed.
2021-11-05 08:37:10 : Created Pseudo-Grouped Tile Matrix (0.801 GB), 0.897 mins elapsed.
2021-11-05 08:37:11 : Computing Peaks from Tile Matrix Group (1 of 22), 0.917 mins elapsed.
2021-11-05 08:37:11 : Computing Peaks from Tile Matrix Group (2 of 22), 0.922 mins elapsed.
2021-11-05 08:37:11 : Computing Peaks from Tile Matrix Group (3 of 22), 0.925 mins elapsed.
2021-11-05 08:37:12 : Computing Peaks from Tile Matrix Group (4 of 22), 0.929 mins elapsed.
2021-11-05 08:37:12 : Computing Peaks from Tile Matrix Group (5 of 22), 0.933 mins elapsed.
2021-11-05 08:37:12 : Computing Peaks from Tile Matrix Group (6 of 22), 0.937 mins elapsed.
2021-11-05 08:37:12 : Computing Peaks from Tile Matrix Group (7 of 22), 0.94 mins elapsed.
2021-11-05 08:37:12 : Computing Peaks from Tile Matrix Group (8 of 22), 0.942 mins elapsed.
2021-11-05 08:37:13 : Computing Peaks from Tile Matrix Group (9 of 22), 0.945 mins elapsed.
2021-11-05 08:37:13 : Computing Peaks from Tile Matrix Group (10 of 22), 0.947 mins elapsed.
2021-11-05 08:37:13 : Computing Peaks from Tile Matrix Group (11 of 22), 0.95 mins elapsed.
2021-11-05 08:37:13 : Computing Peaks from Tile Matrix Group (12 of 22), 0.952 mins elapsed.
2021-11-05 08:37:13 : Computing Peaks from Tile Matrix Group (13 of 22), 0.955 mins elapsed.
2021-11-05 08:37:13 : Computing Peaks from Tile Matrix Group (14 of 22), 0.958 mins elapsed.
2021-11-05 08:37:14 : Computing Peaks from Tile Matrix Group (15 of 22), 0.96 mins elapsed.
2021-11-05 08:37:14 : Computing Peaks from Tile Matrix Group (16 of 22), 0.963 mins elapsed.
2021-11-05 08:37:14 : Computing Peaks from Tile Matrix Group (17 of 22), 0.966 mins elapsed.
2021-11-05 08:37:14 : Computing Peaks from Tile Matrix Group (18 of 22), 0.969 mins elapsed.
2021-11-05 08:37:14 : Computing Peaks from Tile Matrix Group (19 of 22), 0.972 mins elapsed.
2021-11-05 08:37:14 : Computing Peaks from Tile Matrix Group (20 of 22), 0.975 mins elapsed.
2021-11-05 08:37:15 : Computing Peaks from Tile Matrix Group (21 of 22), 0.978 mins elapsed.
2021-11-05 08:37:15 : Computing Peaks from Tile Matrix Group (22 of 22), 0.981 mins elapsed.
2021-11-05 08:38:22 : Creating Group Peak Sets with Annotations!, 2.105 mins elapsed.
Error in .safelapply(seq_along(cellGroups), function(i) { :
Error Found Iteration 1 :
[1] "Error in gzfile(file, mode) : cannot open the connection\n"
<simpleError in gzfile(file, mode): cannot open the connection>
Error Found Iteration 2 :
[1] "Error in gzfile(file, mode) : cannot open the connection\n"
<simpleError in gzfile(file, mode): cannot open the connection>
Error Found Iteration 3 :
[1] "Error in gzfile(file, mode) : cannot open the connection\n"
<simpleError in gzfile(file, mode): cannot open the connection>
Error Found Iteration 4 :
[1] "Error in gzfile(file, mode) : cannot open the connection\n"
<simpleError in gzfile(file, mode): cannot open the connection>
Error Found Iteration 5 :
[1] "Error in gzfile(file, mode) : cannot open the connection\n"
<simpleError in gzfile(file, mode): cannot open the connection>
Error Found Iteration 6 :
[1] "Error in gzfile(file, mode) : cannot open the connection\n"
<simpleError in gzfile(file, mode): cannot open the connection>
Error Found Iteration 7 :
[1] "Error in
In addition: Warning message:
In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) :
22 function calls resulted in an error

Any suggestions what to debug, to avoid the errors?

[rcorces]

I cant be sure what the problem is but I would strongly caution against calling peaks using the Tiles method. In fact, we are planning on getting rid of that option in the future. It is really only meant for people who are unable to install MACS2 for whatever reason. Given how simple MACS2 install is, there really should never be a reason to use the Tiles method.

Also, since this is an error report, it should have gone to Issues.