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read header error #57
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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 ***@***.***> 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_hic_header.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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Assistant Professor | Molecular and Human Genetics
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www.aidenlab.org
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@antarikshtyagi was this resolved? |
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 < ***@***.***> wrote:
@antarikshtyagi <https://github.com/antarikshtyagi> was this resolved?
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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
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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)
|
What version of the juicer jar are you using? This sounds like an issue with running juicer, not a bug in straw. |
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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_hic_header.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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