I am trying to convert my homer tag directories to *.hic files in order to visualize them using Juicer. I am using TagDir2Hic.pl, for converting the tag directories to these *.hic files, with the following command options:
1_merged_R6 -juicer auto -juicerExe 'java -jar juicer_tools_1.14.08.jar' -genome mm10
where "-juicer auto" indicates to create the .hic files in this folder, and "-juicerExe" indicates the executable juicer_tools file. When removing the -juicer_auto option and listing -juicerExe, I receive an output of the file on the Terminal, but when I include the -juicer auto option, I am receiving an error that the temporary file has not been found or that there are no reads. The output is below:
Will use "1_merged_R6/1_merged_R6.hic" for hic output file Will output a juicer hic file to 1_merged_R6/1_merged_R6.hic Will use "java -jar juicer_tools_1.14.08.jar" to execute juicer. Sorting file by chormosome interaction block to work with juicer... i.e. sort --parallel=1 -k2,2d -k6,6d 0.50584760688162.tmp > 0.50584760688162.2.tmp sort: unrecognized option `--parallel=1' Usage: sort [-bcCdfigMmnrsuz] [-kPOS1[,POS2] ... ] [+POS1 [-POS2]] [-S memsize] [-T tmpdir] [-t separator] [-o outfile] [--batch-size size] [--files0-from file] [--heapsort] [--mergesort] [--radixsort] [--qsort] [--mmap] [--human-numeric-sort] [--version-sort] [--random-sort [--random-source file]] [--compress-program program] [file ...] Done sorting, now creating *.hic file with java -jar juicer_tools_1.14.08.jar: 0.50584760688162.2.tmp does not exist or does not contain any reads. Finished.
If anyone has come across this or knows how to address this issue, please help! Thanks so much.