Error trying to replicate your pipeline with your data

[olaraym]

Code used:
poolData(cellFiles = cell_files, sep = ",", chrNames = "chr1", writeDir = "C:/Users/larasaki/Downloads")

Error Message:
Start processing chromosome-by-chromosome...
...chr1: 'zcat' is not recognized as an internal or external command,
operable program or batch file.
'zcat' is not recognized as an internal or external command,
operable program or batch file.
'zcat' is not recognized as an internal or external command,
operable program or batch file.
coordinates gathered; 'zcat' is not recognized as an internal or external command,
operable program or batch file.

Error in setnames(x, value) :
Can't assign 3 names to a 0-column data.table
In addition: Warning messages:
1: In (if (.Platform$OS.type == "unix") system else shell)(paste0("(", :
'(zcat C:/Users/larasaki/Downloads/cell_1.csv | awk -F ',' '$1=="chr1"' | awk -F ',' '{print $2}') > C:\Users\larasaki\AppData\Local\Temp\Rtmpgf8DN3\file15d45f932f7' execution failed with error code 255
2: In data.table::fread(cmd = paste0("zcat ", file, " | awk -F '", :
File 'C:\Users\larasaki\AppData\Local\Temp\Rtmpgf8DN3\file15d45f932f7' has size 0. Returning a NULL data.table.
3: In (if (.Platform$OS.type == "unix") system else shell)(paste0("(", :
'(zcat C:/Users/larasaki/Downloads/cell_2.csv | awk -F ',' '$1=="chr1"' | awk -F ',' '{print $2}') > C:\Users\larasaki\AppData\Local\Temp\Rtmpgf8DN3\file15d47b302d08' execution failed with error code 255
4: In data.table::fread(cmd = paste0("zcat ", file, " | awk -F '", :
File 'C:\Users\larasaki\AppData\Local\Temp\Rtmpgf8DN3\file15d47b302d08' has size 0. Returning a NULL data.table.
5: In (if (.Platform$OS.type == "unix") system else shell)(paste0("(", :
'(zcat C:/Users/larasaki/Downloads/cell_3.csv | awk -F ',' '$1=="chr1"' | awk -F ',' '{print $2}') > C:\Users\larasaki\AppData\Local\Temp\Rtmpgf8DN3\file15d442e84e3b' execution failed with error code 255
6: In data.table::fread(cmd = paste0("zcat ", file, " | awk -F '", :
File 'C:\Users\larasaki\AppData\Local\Temp\Rtmpgf8DN3\file15d442e84e3b' has size 0. Returning a NULL data.table.
7: In (if (.Platform$OS.type == "unix") system else shell)(paste0("(", :
'(zcat C:/Users/larasaki/Downloads/cell_1.csv | awk -F ',' '$1=="chr1"' | awk -F ',' '{print $2" "$4" "$5}') > C:\Users\larasaki\AppData\Local\Temp\Rtmpgf8DN3\file15d417dc40dc' execution failed with error code 255
8: In data.table::fread(cmd = paste0("zcat ", file, " | awk -F '", :
File 'C:\Users\larasaki\AppData\Local\Temp\Rtmpgf8DN3\file15d417dc40dc' has size 0. Returning a NULL data.table.