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aidenlab / straw

Extract data quickly from Juicebox via straw
MIT License
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read header error #57

Closed antarikshtyagi closed 3 years ago

antarikshtyagi commented 3 years ago

hello,

Running read header I am getting this error. Can you please help resolving this:

$ python3 ./read_hic_header.py NlaIII_run01_UCSC_hg38.hic Traceback (most recent call last): File "./read_hicheader.py", line 19, in =straw_module.read_metadata(sys.argv[1],verbose=verbose) AttributeError: module 'straw.straw' has no attribute 'read_metadata'

Thanks Ant

nchernia commented 3 years ago

I haven't seen this error.

I wonder if there's an old version of straw on your system? Try running

pip install ./python --upgrade

On Fri, Feb 5, 2021 at 1:07 AM antarikshtyagi notifications@github.com wrote:

hello,

Running read header I am getting this error. Can you please help resolving this:

$ python3 ./read_hic_header.py NlaIII_run01_UCSC_hg38.hic Traceback (most recent call last): File "./read_hicheader.py", line 19, in =straw_module.read_metadata(sys.argv[1],verbose=verbose) AttributeError: module 'straw.straw' has no attribute 'read_metadata'

Thanks Ant

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

sa501428 commented 3 years ago

@antarikshtyagi was this resolved?

antarikshtyagi commented 3 years ago

Hello Muhammad,

Thanks for reaching out again. I am still waiting for a solution using juicer. In the meantime, I tried HiCExplorer and it worked fine in calling TADs and loops. It makes me wonder even more what may be wrong using juicer with my data. Attaching here is stdout from juicertools pre step where there is "ArrayIndexOutOfBoundsException". Just guessing if that may be the reason. Let me know if you need any other information/data.

Thank you Ant

On Thu, Mar 4, 2021 at 12:00 PM Muhammad Saad Shamim < notifications@github.com> wrote:

@antarikshtyagi https://github.com/antarikshtyagi was this resolved?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/aidenlab/straw/issues/57#issuecomment-790812272, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHESEUSWIY4NYT57PNX5PH3TB7DC7ANCNFSM4XEFOIBA .

-- antariksh

WARN [2020-11-04T21:46:46,359] [Globals.java:138] [main] Development mode is enabled Using 32 CPU thread(s) Start preprocess Writing header Writing body ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Writing footer

Finished preprocess

Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000 Calculating norms for zoom BP_10000 Calculating norms for zoom BP_5000 Calculating norms for zoom BP_1000 Calculating norms for zoom FRAG_500java.lang.ArrayIndexOutOfBoundsException: 2170 at juicebox.tools.utils.norm.NormalizationCalculations.computeVC(NormalizationCalculations.java:353) at juicebox.tools.utils.norm.NormalizationVectorUpdater.buildVCOrVCSQRT(NormalizationVectorUpdater.java:186) at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:139) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:151) at juicebox.tools.HiCTools.main(HiCTools.java:94)

sa501428 commented 3 years ago

What version of the juicer jar are you using? For help with juicer, please use our forum: aidenlab.org/forum.html.

This sounds like an issue with running juicer, not a bug in straw. So I'm going to close this issue.