How to address location of temporary file issue when converting Homer tag directories to hi-c files?
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2.9 years ago

I am trying to convert my homer tag directories to *.hic files in order to visualize them using Juicer. I am using, 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.

If anyone has come across this or knows how to address this issue, please help! Thanks so much.

homer juicer hi-c juicer_tools • 833 views

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