Ignore sparsity flag not recognised

[Paul Munn]

Hi All,

I'm attempting to run Arrowhead and HiCCUPS using the --ignore_sparsity flag, but I get an error message saying: Unknown option '--ignore_sparsity'

Could you please point me to some documentation that shows how this flag is used.

Many thanks,

Paul

[Muhammad Saad Shamim]

Hey Paul,

Are you using the latest jar (http://aidenlab.org/commandlinetools/)?

The command should be passed like this:

arrowhead --ignore_sparsity inter.hic temp_results

hiccups --ignore_sparsity inter.hic temp_results2

Note that it'll still print a warning about the map being sparse, but instead of exiting it will print the defaults being used and continue with processing:

java -jar juicebox_tools.7.0.jar arrowhead --ignore_sparsity inter.hic temp_results

Reading file: inter.hic

HiC file version: 8

Warning: Hi-C map is too sparse to find many domains via Arrowhead.

Default settings for 10kb being used

...

java -jar juicebox_tools.7.0.jar hiccups --ignore_sparsity inter.hic temp_results2

Reading file: inter.hic

HiC file version: 8

No valid configurations specified, using default settings

Warning Hi-C map is too sparse to find many loops via HiCCUPS.

Default settings for 5kb, 10kb, and 25kb being used

...

​Best,​

- Muhammad Saad Shamim

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[Hiroyuki Kato]

Hi, 

Hope someone could help me.

I also had similar problem regarding --ignore_sparsity posted here.

My command is like this.

java -jar ~/juicer_tools.jar arrowhead  --ignore_sparsity  my.hic(input) contact_domains_list(output)

However, I get the following error.

WARN [2020-04-27T20:39:25,942]  [Globals.java:138] [main]  Development mode is enabled

Exception in thread "main" jargs.gnu.CmdLineParser$UnknownOptionException: Unknown option '--ignore_sparsity'

at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:475)

at jargs.gnu.CmdLineParser.parse(CmdLineParser.java:426)

at juicebox.tools.HiCTools.main(HiCTools.java:61)

Since, I can run the following example as shown in the website, it seems it's not a version or path matter.

java -jar ~/juicer_tools.jar arrowhead https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_30.hic contact_domains_list

I know I would get this error if my sequencing depth is not enough, but --ignore_sparsity seems not working at all.

Is there any solution?

I use JAVA1.8.

I downloaded juicer_tools_1.19.02.jar (latest version).

Thanks in advance.

Best, 

Hiroyuki

2016年9月5日月曜日 11時56分11秒 UTC+9 Muhammad Saad Shamim:

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[Muhammad Saad Shamim]

Hi!

We changed the flag to --use-sparsity (no underscore). 

In the older jar, the internal usage didn't get updated, but it should be fixed in the newer jars.

- Muhammad Saad Shamim

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[Hiroyuki Kato]

Hi Muhammad,

--ignore-sparsity (no underscore) worked perfectly!
Thank you so much for this wonderful tool!

Best, 

Hiroyuki

Sender notified by Mailtrack 20/04/28 18:05:15

2020年4月28日(火) 4:32 Muhammad Saad Shamim <sa50...@gmail.com>: