plot rainfall error #25
Comments
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-------Python and Package Versions------- |
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Hi @temizna, Thanks for reaching out! Best, |
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-------Python and Package Versions-------
Python Version: 3.10.8
SigProfilerMatrixGenerator Version: 1.2.14
SigProfilerPlotting version: 1.3.12
matplotlib version: 3.4.3
scipy version: 1.9.3
numpy version: 1.23.4
43_Liver_tumor_2.mut.dna.pass.ad3.dp10.vaf0.05.vcf
<https://drive.google.com/file/d/1yqyqOlvgioQGSZe73Lt0M4T0196xXIAO/view?usp=drive_web>
78_liver_tumor.mut.dna.pass.ad3.dp10.vaf0.05.vcf
<https://drive.google.com/file/d/11IJ4pizAZzL-yF76wgRbNoVuIld-JTWX/view?usp=drive_web>
131_renal_node_1.mut.dna.pass.ad3.dp10.vaf0.05.vcf
<https://drive.google.com/file/d/1UwM3iq1jd5nABSdsqwlU7zJu7bs71q9n/view?usp=drive_web>
CD_4NQO_178_tumor_S26.mut.dna.pass.ad3.dp10.vaf0.05.vcf
<https://drive.google.com/file/d/1J6Q67tlgau7_0beryJVLZgjTfZz82KOs/view?usp=drive_web>
CD_4NQO_247_tumor_S28.mut.dna.pass.ad3.dp10.vaf0.05.vcf
<https://drive.google.com/file/d/1D2PkHkovdJyOPgC83lpOvujC0EGBKvro/view?usp=drive_web>
…On Fri, Jun 21, 2024 at 12:51 AM Mousumy Kundu ***@***.***> wrote:
Hi @temizna <https://github.com/temizna>,
Thanks for reaching out!
I did run SigProfilerClusters pipeline with one of the example file and it
has run successfully. It will be great if you can share one of your input
files so that I can run at my end.
Best,
Mousumy
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Hi @temizna, Thank you for sending! Could you please let me know how you are running the cluster pipeline? Additionally please share the log files(.err and .out file). By this time my suggestion will be to create a new conda environment and re-install the tools and run it again. Best, |
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How do you create a new conda environment for the tools? I did not see an
option like that on the github pages.
I used pip to install these
A
…On Fri, Jun 21, 2024 at 12:46 PM Mousumy Kundu ***@***.***> wrote:
Hi @temizna <https://github.com/temizna>,
Thank you for sending!
Could you please let me know how you are running the cluster pipeline?
Additionally please share the log files(.err and .out file). By this time
my suggestion will be to create a new conda environment and re-install the
tools and run it again.
Best,
Mousumy
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Hi @temizna, I hope you have installed Anaconda or Miniconda in your computer. If you haven't installed Anaconda or Miniconda yet, you can download and install it from their respective websites. Then create a new conda Environment with Python 3.10. Please see below how you can create an environment: Create a new environment with Python 3.10conda create --name myenv python=3.10 Activate the new environmentconda activate myenv Next, you can re-install the tools using pip (for example: pip install SigProfilerClusters). Please follow wiki page(https://osf.io/qpmzw/wiki/home/) to install the required genome. Hope that was helpful. Please let me know which genome you are using(GRCh37 or GRCh38) to run the SigProfilerClusters tool? Best, |
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I have python 3.11. Do you think that is causing the issue?
I use grch38 and mm10 for human and mouse.
…On Tue, Jun 25, 2024 at 11:30 AM Mousumy Kundu ***@***.***> wrote:
Hi @temizna <https://github.com/temizna>,
I hope you have installed Anaconda or Miniconda in your computer. If you
haven't installed Anaconda or Miniconda yet, you can download and install
it from their respective websites.
Then create a new conda Environment with Python 3.10. Please see below how
you can create an environment:
Create a new environment with Python 3.10
conda create --name myenv python=3.10
Activate the new environment
conda activate myenv
Next, you can re-install the tools using pip (for example: pip install
SigProfilerClusters). Please follow wiki page(
https://osf.io/qpmzw/wiki/home/) to install the required genome.
Hope that was helpful. Please let me know which genome you are
using(GRCh37 or GRCh38) to run the SigProfilerClusters tool?
Best,
Mousumy
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I am guessing, it's not a python version issue. I hope the example files you have shared with me, all are human(GRCh38) sample. Please let me know if I am not correct.
I |
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mm10
…On Tue, Jun 25, 2024 at 11:50 AM Mousumy Kundu ***@***.***> wrote:
I am guessing, it's not a python version issue.
You sent me the python and package versions where it looks you are using
Python 3.10.8. However, we have checked with Python 3.11 and it works if
you run the SigProfilerClusters tool within python script by defining the
main function(please see this issue: #23
<#23>).
I hope the example files you have shared with me, all are human(GRCh38)
sample. Please let me know if I am not correct.
-------Python and Package Versions------- Python Version: 3.10.8
SigProfilerMatrixGenerator Version: 1.2.14 SigProfilerPlotting version:
1.3.12 matplotlib version: 3.4.3 scipy version: 1.9.3 numpy version: 1.23.4
I
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I followed your advice and I am still getting the same plot rainfall error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/Users/temizna/Library/Python/3.10/lib/python/site-packages/SigProfilerClusters/SigProfilerClusters.py",
line 706, in analysis
plottingFunctions.rainfall(chrom_based, project, input_path,
chrom_path, chromLengths, centromeres, contexts, includedVAFs,
includedCCFs, correction, windowSize, bedRanges)
File
"/Users/temizna/Library/Python/3.10/lib/python/site-packages/SigProfilerClusters/plottingFunctions.py",
line 1182, in rainfall
for sample in sorted(samplesSet, key=natural_sortkey):
TypeError: '<' not supported between instances of 'str' and 'int'
…On Tue, Jun 25, 2024 at 11:56 AM Nuri Temiz ***@***.***> wrote:
mm10
On Tue, Jun 25, 2024 at 11:50 AM Mousumy Kundu ***@***.***>
wrote:
> I am guessing, it's not a python version issue.
> You sent me the python and package versions where it looks you are using
> Python 3.10.8. However, we have checked with Python 3.11 and it works if
> you run the SigProfilerClusters tool within python script by defining the
> main function(please see this issue: #23
> <#23>).
>
> I hope the example files you have shared with me, all are human(GRCh38)
> sample. Please let me know if I am not correct.
>
> -------Python and Package Versions------- Python Version: 3.10.8
> SigProfilerMatrixGenerator Version: 1.2.14 SigProfilerPlotting version:
> 1.3.12 matplotlib version: 3.4.3 scipy version: 1.9.3 numpy version: 1.23.4
>
> I
>
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> <#25 (comment)>,
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HI @temizna, Sorry to hear that. This is how I am running the pipeline: from SigProfilerSimulator import SigProfilerSimulator as sigSim from SigProfilerClusters import SigProfilerClusters as hp Can I please ask you to update the packages according to the versions that I am using: Hope that will solve your issues. Please let me know if you have any questions. Best, |
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I am getting a sigplofilerplotting error and also scypy error:
temizna$ pip install --force-reinstall -v "SipProfilerPlotting==1.3.23"
Using pip 24.0 from
/Users/temizna/anaconda3/envs/sigprofiler/lib/python3.10/site-packages/pip
(python 3.10)
ERROR: Could not find a version that satisfies the requirement
SipProfilerPlotting==1.3.23 (from versions: none)
ERROR: No matching distribution found for SipProfilerPlotting==1.3.23
sigprofilermatrixgenerator 1.2.26 requires scipy>=1.12.0; python_version >=
"3.9", but you have scipy 1.10.1 which is incompatible.
…On Thu, Jun 27, 2024 at 12:27 PM Mousumy Kundu ***@***.***> wrote:
HI @temizna <https://github.com/temizna>,
Sorry to hear that.
I ran the SigProfilerClusters pipeline with one of your example file and
it works at my end(please see the attached
rainfallPlots_clustered_test_corrected.pdf
<https://github.com/user-attachments/files/16018755/rainfallPlots_clustered_test_corrected.pdf>
).
This is how I am running the pipeline:
from SigProfilerMatrixGenerator.scripts import
SigProfilerMatrixGeneratorFunc as matGen
matrices = matGen.SigProfilerMatrixGeneratorFunc("test", "mm10",
"/Desktop/SigProfilerIssues/SPC_rainfall_plot_issue/",plot=True,
exome=False, bed_file=None, chrom_based=False, tsb_stat=False,
seqInfo=False, cushion=100)
from SigProfilerSimulator import SigProfilerSimulator as sigSim
sigSim.SigProfilerSimulator("test",
"/Desktop/SigProfilerIssues/SPC_rainfall_plot_issue/", "mm10",
contexts=['96'], simulations=100, chrom_based=False, exome=False,
vcf=False, cushion=100)
from SigProfilerClusters import SigProfilerClusters as hp
hp.analysis("test", "mm10", "96", ["96"],
"/Desktop/SigProfilerIssues/SPC_rainfall_plot_issue/", analysis="all",
sortSims=True, subClassify=True, correction=True, calculateIMD=True,
includedVAFs=False, includedCCFs=False, exome=False)
Can I please ask you to update the packages according to the versions that
I am using:
-------Python and Package Versions-------
Python Version: 3.10.14
SigProfilerMatrixGenerator Version: 1.2.26
SigProfilerPlotting version: 1.3.23
matplotlib version: 3.4.3
scipy version: 1.10.1
numpy version: 1.23.5
Hope that will solve your issues. Please let me know if you have any
questions.
Best,
Mousumy
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Hi @temizna, Please create a new environment using conda and re-install the tools. Here are the commands below: Create a new environmentconda create -n SPC_new python=3.10 Install compatible versions of numpy, pandas, and scipyconda install numpy=1.23.5 pandas=1.5.3 scipy=1.12.0 #install the tool Please run the SigProfilerClusters pipeline again and let me know if that works at your end. Best, |
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did all that
still getting the following error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/Users/temizna/Library/Python/3.10/lib/python/site-packages/SigProfilerClusters/SigProfilerClusters.py",
line 706, in analysis
plottingFunctions.rainfall(chrom_based, project, input_path,
chrom_path, chromLengths, centromeres, contexts, includedVAFs,
includedCCFs, correction, windowSize, bedRanges)
File
"/Users/temizna/Library/Python/3.10/lib/python/site-packages/SigProfilerClusters/plottingFunctions.py",
line 1182, in rainfall
for sample in sorted(samplesSet, key=natural_sortkey):
TypeError: '<' not supported between instances of 'str' and 'int'
…On Thu, Jun 27, 2024 at 2:01 PM Mousumy Kundu ***@***.***> wrote:
Hi @temizna <https://github.com/temizna>,
Please create a new environment using conda and re-install the tools. Here
are the commands below:
Create a new environment
conda create -n SPC_new python=3.10
conda activate SPC_new
Install compatible versions of numpy, pandas, and scipy
conda install numpy=1.23.5 pandas=1.5.3 scipy=1.12.0
#install the tool
pip install SigProfilerClusters
Please run the SigProfilerClusters pipeline again and let me know if that
works at your end.
Best,
Mousumy
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Hi @temizna, Sorry to hear that! Best, |
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I can meet Tuesday July 9 in the afternoon central time. I am free from 1
pm central till 5 pm central.
Thanks.
Alpay
…On Mon, Jul 1, 2024 at 1:04 PM Mousumy Kundu ***@***.***> wrote:
Hi @temizna <https://github.com/temizna>,
Sorry to hear that!
It's hard to figure out why it is not working at your end. May be we can
set up a quick Zoom call this week or early next week if that works for you.
Best,
Mousumy
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Thank you for letting me know. Could you please share your email address! Best, |
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***@***.***
…On Mon, Jul 1, 2024 at 1:34 PM Mousumy Kundu ***@***.***> wrote:
Thank you for letting me know. Could you please share your email address!
Best,
Mousumy
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Sorry, but your email address is not readable to me. It will be great if you could send an email at [email protected]. Best, |
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Dont know whether this issue solved or not, but according to my reply in the other issue (#27 (comment)), it might be you are tring to use contexts=["96"] as input. Using contexts="96" may help. |
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I will try that. Thanks.
…On Wednesday, August 14, 2024, blastchinchillas ***@***.***> wrote:
Dont know whether this issue solved or not, but according to my reply in
the other issue (#27 (comment)
<#27 (comment)>),
it might be you are tring to use contexts=["96"] as input. Using
contexts="96" may help.
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Traceback (most recent call last):
File "", line 1, in
File "/Library/Python/3.10/lib/python/site-packages/SigProfilerClusters/SigProfilerClusters.py", line 706, in analysis
plottingFunctions.rainfall(chrom_based, project, input_path, chrom_path, chromLengths, centromeres, contexts, includedVAFs, includedCCFs, correction, windowSize, bedRanges)
File "/Library/Python/3.10/lib/python/site-packages/SigProfilerClusters/plottingFunctions.py", line 1182, in rainfall
for sample in sorted(samplesSet, key=natural_sortkey):
TypeError: '<' not supported between instances of 'str' and 'int'
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