search

aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
402 stars 180 forks source link

Update juicer_postprocessing.sh #282

Closed adadiehl closed 2 years ago

adadiehl commented 2 years ago

Expose --threads option for Arrowhead

pna059 commented 2 years ago

With or without the -z/--threads option postprocessing is not working:

$ bash ~/Juicer_dir/scripts/common/juicer_postprocessing.sh -j ~/Juicer_dir/scripts/common/juicer_tools -i aligned/inter.hic -g ~/Juicer_dir/chrom_sizes/hv03.chr.sizes
/home/pavlan/Juicer_dir/scripts/common/juicer_tools is post-processing Hi-C for /home/pavlan/Juicer_dir/chrom_sizes/hv03.chr.sizes
Data read from aligned/inter.hic.
Motifs read from /gpfs0/juicer2/references/motif

ARROWHEAD:

Exception in thread "main" jargs.gnu.CmdLineParser$IllegalOptionValueException: Illegal value 'aligned/inter.hic' for option -z/--threads
        at jargs.gnu.CmdLineParser$Option$IntegerOption.parseValue(CmdLineParser.java:202)
        at jargs.gnu.CmdLineParser$Option.getValue(CmdLineParser.java:157)
        at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:485)
        at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:426)
        at juicebox.tools.HiCTools.main(HiCTools.java:61)
***! Problem while running Arrowhead

With the option:

$ bash ~/Juicer_dir/scripts/common/juicer_postprocessing.sh -j ~/Juicer_dir/scripts/common/juicer_tools -z 10 -i aligned/inter.hic -g ~/Juicer_dir/chrom_sizes/hv03.chr.sizes/
/home/pavlan/Juicer_dir/scripts/common/juicer_postprocessing.sh: illegal option -- z
Usage: /home/pavlan/Juicer_dir/scripts/common/juicer_postprocessing.sh [-h] -j <juicer_tools_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>
adadiehl commented 2 years ago

Sorry, realize now I did not provide -t with a default value. Will get a patch up ASAP.

On Thu, Jul 7, 2022 at 10:46 AM pna059 @.***> wrote:

With or without the -z/--threads option postprocessing is not working:

$ bash ~/Juicer_dir/scripts/common/juicer_postprocessing.sh -j ~/Juicer_dir/scripts/common/juicer_tools -i aligned/inter.hic -g ~/Juicer_dir/chrom_sizes/hv03.chr.sizes /home/pavlan/Juicer_dir/scripts/common/juicer_tools is post-processing Hi-C for /home/pavlan/Juicer_dir/chrom_sizes/hv03.chr.sizes Data read from aligned/inter.hic. Motifs read from /gpfs0/juicer2/references/motif

ARROWHEAD:

Exception in thread "main" jargs.gnu.CmdLineParser$IllegalOptionValueException: Illegal value 'aligned/inter.hic' for option -z/--threads at jargs.gnu.CmdLineParser$Option$IntegerOption.parseValue(CmdLineParser.java:202) at jargs.gnu.CmdLineParser$Option.getValue(CmdLineParser.java:157) at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:485) at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:426) at juicebox.tools.HiCTools.main(HiCTools.java:61) ***! Problem while running Arrowhead

With the option

bash ~/Juicer_dir/scripts/common/juicer_postprocessing.sh -j ~/Juicer_dir/scripts/common/juicer_tools -z 10 -i aligned/inter.hic -g ~/Juicer_dir/chrom_sizes/hv03.chr.sizes/ /home/pavlan/Juicer_dir/scripts/common/juicer_postprocessing.sh: illegal option -- z Usage: /home/pavlan/Juicer_dir/scripts/common/juicer_postprocessing.sh [-h] -j -i -m -g

— Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/pull/282#issuecomment-1177730367, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACUMZSJOUHZTTUF3EGDMD6LVS3USJANCNFSM52GEAANQ . You are receiving this because you authored the thread.Message ID: @.***>