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[Bug]: NIRSpec Stage 3 crashes when 'src_pos_type' is 'gaussian' #732

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sarthakpatel7 opened this issue Dec 24, 2024 · 4 comments
Open
2 tasks done

[Bug]: NIRSpec Stage 3 crashes when 'src_pos_type' is 'gaussian' #732

sarthakpatel7 opened this issue Dec 24, 2024 · 4 comments
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@AarynnCarter
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bug Something isn't working NIRSpec

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@sarthakpatel7
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sarthakpatel7 commented Dec 24, 2024 •
edited by taylorbell57
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FAQ check

  • Yes, I checked the FAQ and my question has not been addressed.

Instrument

NIRSpec (Stages 1-3)

What happened?

Stage 3 crashes when 'src_pos_type' is set to 'gaussian' for NIRSpec. It works fine if an integer is given instead.

Error traceback output

Traceback (most recent call last):
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/eureka/S3_data_reduction/source_pos.py", line 162, in source_pos
    src_ypos, src_ywidth = source_pos_gauss(flux, meta, m, n, plot)
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/eureka/S3_data_reduction/source_pos.py", line 416, in source_pos_gauss
    popt, _ = curve_fit(gauss, y_pixels, med_row, p0, maxfev=10000)
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/scipy/optimize/_minpack_py.py", line 925, in curve_fit
    ydata = np.asarray_chkfinite(ydata, float)
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/numpy/lib/function_base.py", line 627, in asarray_chkfinite
    raise ValueError(
ValueError: array must not contain infs or NaNs
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/mnt/data/spatel/DataAnalysis/g395h/input/demos/run_eureka.py", line 29, in <module>
    spec, meta = s3.reduce(eventlabel, ecf_path=ecf_path)
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/eureka/S3_data_reduction/s3_reduce.py", line 418, in reduce
    source_pos.source_pos_wrapper(data, meta, log,
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/eureka/S3_data_reduction/source_pos.py", line 89, in source_pos_wrapper
    job.get()
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/multiprocessing/pool.py", line 774, in get
    raise self._value
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/eureka/S3_data_reduction/source_pos.py", line 162, in source_pos
    src_ypos, src_ywidth = source_pos_gauss(flux, meta, m, n, plot)
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/eureka/S3_data_reduction/source_pos.py", line 416, in source_pos_gauss
    popt, _ = curve_fit(gauss, y_pixels, med_row, p0, maxfev=10000)
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/scipy/optimize/_minpack_py.py", line 925, in curve_fit
    ydata = np.asarray_chkfinite(ydata, float)
  File "/home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/numpy/lib/function_base.py", line 627, in asarray_chkfinite
    raise ValueError(
ValueError: array must not contain infs or NaNs
2024-12-25 01:19:28,658 - stpipe - WARNING - /home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/numpy/core/shape_base.py:65: UserWarning: Warning: converting a masked element to nan.
  ary = asanyarray(ary)

2024-12-25 01:19:28,665 - stpipe - WARNING - /home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/numpy/core/shape_base.py:65: UserWarning: Warning: converting a masked element to nan.
  ary = asanyarray(ary)

2024-12-25 01:19:28,668 - stpipe - WARNING - /home/spatel/anaconda3/envs/eurekav1_1/lib/python3.10/site-packages/numpy/core/shape_base.py:65: UserWarning: Warning: converting a masked element to nan.
  ary = asanyarray(ary)

What operating system are you using?

KDE Neon

What version of Python are you running?

Python 3.10.14

What Python packages do you have installed?

#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
affine                    2.4.0              pyhd8ed1ab_1    conda-forge
alabaster                 1.0.0              pyhd8ed1ab_1    conda-forge
alsa-lib                  1.2.13               hb9d3cd8_0    conda-forge
anyio                     4.7.0              pyhd8ed1ab_0    conda-forge
aom                       3.9.1                hac33072_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_1    conda-forge
argon2-cffi-bindings      21.2.0          py310ha75aee5_5    conda-forge
arrow                     1.3.0              pyhd8ed1ab_1    conda-forge
arviz                     0.20.0             pyhd8ed1ab_0    conda-forge
asciitree                 0.3.3                      py_2    conda-forge
asdf                      3.5.0                    pypi_0    pypi
asdf-astropy              0.6.1              pyhd8ed1ab_0    conda-forge
asdf-coordinates-schemas  0.3.0              pyhd8ed1ab_0    conda-forge
asdf-standard             1.1.1              pyhd8ed1ab_0    conda-forge
asdf-transform-schemas    0.5.0              pyhd8ed1ab_0    conda-forge
asdf-wcs-schemas          0.4.0              pyhd8ed1ab_0    conda-forge
asteval                   1.0.5              pyhd8ed1ab_0    conda-forge
astraeus                  0.3                      pypi_0    pypi
astropy                   6.1.6           py310hf462985_0    conda-forge
astropy-base              6.1.6                h65202da_0    conda-forge
astropy-healpix           1.0.3           py310hf462985_3    conda-forge
astropy-iers-data         0.2024.12.9.0.36.21    pyhd8ed1ab_0    conda-forge
astroquery                0.4.7              pyhd8ed1ab_1    conda-forge
astroscrappy              1.2.0           py310ha75aee5_1    conda-forge
asttokens                 3.0.0              pyhd8ed1ab_1    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_1    conda-forge
attrs                     24.2.0             pyh71513ae_1    conda-forge
aws-c-auth                0.8.0               h8c8080f_14    conda-forge
aws-c-cal                 0.8.1                h0f28dba_2    conda-forge
aws-c-common              0.10.5               hb9d3cd8_0    conda-forge
aws-c-compression         0.3.0                h9cc6398_4    conda-forge
aws-c-event-stream        0.5.0               hf811eff_10    conda-forge
aws-c-http                0.9.2                hce7dc5d_3    conda-forge
aws-c-io                  0.15.3               hfd54f12_3    conda-forge
aws-c-mqtt                0.11.0              ha3c2ba9_11    conda-forge
aws-c-s3                  0.7.5                h55e9418_4    conda-forge
aws-c-sdkutils            0.2.1                h9cc6398_3    conda-forge
aws-checksums             0.2.2                h9cc6398_3    conda-forge
aws-crt-cpp               0.29.7               hed26007_5    conda-forge
aws-sdk-cpp               1.11.458             h571fd1c_3    conda-forge
azure-core-cpp            1.14.0               h5cfcd09_0    conda-forge
azure-identity-cpp        1.10.0               h113e628_0    conda-forge
azure-storage-blobs-cpp   12.13.0              h3cf044e_1    conda-forge
azure-storage-common-cpp  12.8.0               h736e048_1    conda-forge
azure-storage-files-datalake-cpp 12.12.0              ha633028_1    conda-forge
babel                     2.16.0             pyhd8ed1ab_1    conda-forge
backports                 1.0                pyhd8ed1ab_5    conda-forge
backports.tarfile         1.2.0              pyhd8ed1ab_1    conda-forge
batman-package            2.4.9           py310h91a95bf_3    conda-forge
bayesicfitting            3.2.3                    pypi_0    pypi
beautifulsoup4            4.12.3             pyha770c72_1    conda-forge
bleach                    6.2.0              pyhd8ed1ab_1    conda-forge
blosc                     1.21.6               hef167b5_0    conda-forge
bokeh                     2.4.3              pyhd8ed1ab_3    conda-forge
bottleneck                1.4.2           py310hf462985_0    conda-forge
brotli                    1.1.0                hb9d3cd8_2    conda-forge
brotli-bin                1.1.0                hb9d3cd8_2    conda-forge
brotli-python             1.1.0           py310hf71b8c6_2    conda-forge
brunsli                   0.1                  h9c3ff4c_0    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.34.3               hb9d3cd8_1    conda-forge
c-blosc2                  2.15.2               h68e2383_0    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.18.2               h3394656_1    conda-forge
catwoman                  1.0.14                   pypi_0    pypi
ccdproc                   2.4.2              pyhd8ed1ab_1    conda-forge
celerite2                 0.3.2                    pypi_0    pypi
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py310h8deb56e_0    conda-forge
cftime                    1.6.4.post1              pypi_0    pypi
charls                    2.4.2                h59595ed_0    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_1    conda-forge
click                     8.1.7           unix_pyh707e725_1    conda-forge
click-plugins             1.1.1              pyhd8ed1ab_1    conda-forge
cligj                     0.7.2              pyhd8ed1ab_2    conda-forge
cloudpickle               3.1.0              pyhd8ed1ab_1    conda-forge
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
comm                      0.2.2              pyhd8ed1ab_1    conda-forge
contourpy                 1.3.1           py310h3788b33_0    conda-forge
corner                    2.2.3              pyhff2d567_0    conda-forge
coverage                  7.6.9           py310h89163eb_0    conda-forge
crds                      11.18.4                  pypi_0    pypi
cryptography              44.0.0          py310h6c63255_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_1    conda-forge
cyrus-sasl                2.1.27               h54b06d7_7    conda-forge
cytoolz                   1.0.0           py310ha75aee5_1    conda-forge
dask                      2024.8.2           pyhd8ed1ab_0    conda-forge
dask-core                 2024.8.2           pyhd8ed1ab_0    conda-forge
dask-expr                 1.1.13             pyhd8ed1ab_0    conda-forge
dav1d                     1.2.1                hd590300_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
debugpy                   1.8.10          py310hf71b8c6_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_1    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.9              pyhd8ed1ab_1    conda-forge
distributed               2024.8.2           pyhd8ed1ab_0    conda-forge
docutils                  0.21.2             pyhd8ed1ab_1    conda-forge
double-conversion         3.3.0                h59595ed_0    conda-forge
drizzle                   2.0.0                    pypi_0    pypi
dynesty                   2.1.4              pyhd8ed1ab_0    conda-forge
emcee                     3.1.6              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_1    conda-forge
eureka                    1.2.dev0+g41e611f9.d20241212          pypi_0    pypi
exceptiongroup            1.2.2              pyhd8ed1ab_1    conda-forge
executing                 2.1.0              pyhd8ed1ab_1    conda-forge
exotic-ld                 3.2.0                    pypi_0    pypi
expat                     2.6.4                h5888daf_0    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
filelock                  3.16.1                   pypi_0    pypi
flake8                    7.1.1              pyhd8ed1ab_1    conda-forge
fleck                     1.1.2                    pypi_0    pypi
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_3    conda-forge
fontconfig                2.15.0               h7e30c49_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.55.3          py310h89163eb_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_1    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
freexl                    2.0.0                h743c826_0    conda-forge
fsspec                    2024.10.0          pyhd8ed1ab_1    conda-forge
future                    1.0.0              pyhd8ed1ab_1    conda-forge
george                    0.4.3           py310h3788b33_1    conda-forge
geos                      3.13.0               h5888daf_0    conda-forge
geotiff                   1.7.3                h77b800c_3    conda-forge
gflags                    2.2.2             h5888daf_1005    conda-forge
giflib                    5.2.2                hd590300_0    conda-forge
glog                      0.7.1                hbabe93e_0    conda-forge
graphite2                 1.3.13            h59595ed_1003    conda-forge
gwcs                      0.21.0             pyhd8ed1ab_1    conda-forge
h11                       0.14.0             pyhd8ed1ab_1    conda-forge
h2                        4.1.0              pyhd8ed1ab_1    conda-forge
h5netcdf                  1.4.1              pyhd8ed1ab_1    conda-forge
h5py                      3.12.1          nompi_py310h60e0fe6_102    conda-forge
harfbuzz                  9.0.0                hda332d3_1    conda-forge
hdf5                      1.14.3          nompi_h2d575fe_108    conda-forge
hpack                     4.0.0              pyhd8ed1ab_1    conda-forge
html5lib                  1.1                pyhd8ed1ab_1    conda-forge
httpcore                  1.0.7              pyh29332c3_1    conda-forge
httpx                     0.28.1             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_1    conda-forge
icu                       75.1                 he02047a_0    conda-forge
idna                      3.10               pyhd8ed1ab_1    conda-forge
image-registration        0.2.10.dev7+g70e3880          pypi_0    pypi
imagecodecs               2024.9.22       py310hdbe5077_0    conda-forge
imageio                   2.36.1             pyh12aca89_1    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        8.5.0              pyha770c72_1    conda-forge
importlib_metadata        8.5.0                hd8ed1ab_1    conda-forge
importlib_resources       6.4.5              pyhd8ed1ab_1    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_1    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.30.0             pyh707e725_0    conda-forge
ipywidgets                8.1.5              pyhd8ed1ab_1    conda-forge
isoduration               20.11.0            pyhd8ed1ab_1    conda-forge
jaraco.classes            3.4.0              pyhd8ed1ab_2    conda-forge
jaraco.context            6.0.1              pyhd8ed1ab_0    conda-forge
jaraco.functools          4.1.0              pyhd8ed1ab_0    conda-forge
jedi                      0.19.2             pyhd8ed1ab_1    conda-forge
jeepney                   0.8.0              pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_1    conda-forge
jmespath                  1.0.1              pyhd8ed1ab_1    conda-forge
json-c                    0.18                 h6688a6e_0    conda-forge
json5                     0.10.0             pyhd8ed1ab_1    conda-forge
jsonpointer               3.0.0           py310hff52083_1    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_1    conda-forge
jsonschema-specifications 2024.10.1          pyhd8ed1ab_1    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_1    conda-forge
jupyter                   1.1.1              pyhd8ed1ab_1    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_1    conda-forge
jupyter_client            8.6.3              pyhd8ed1ab_1    conda-forge
jupyter_console           6.6.3              pyhd8ed1ab_1    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_1    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_1    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_1    conda-forge
jupyterlab                4.3.3              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_2    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_1    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_1    conda-forge
jwst                      1.15.1                   pypi_0    pypi
jxrlib                    1.1                  hd590300_3    conda-forge
keyring                   25.5.0             pyha804496_1    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.7           py310h3788b33_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
lazy-loader               0.4                pyhd8ed1ab_2    conda-forge
lazy_loader               0.4                pyhd8ed1ab_2    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20240722.0      cxx17_h5888daf_1    conda-forge
libaec                    1.1.3                h59595ed_0    conda-forge
libarchive                3.7.7                hadbb8c3_0    conda-forge
libarrow                  18.1.0           h3b07799_4_cpu    conda-forge
libarrow-acero            18.1.0           h8bbc2ab_4_cpu    conda-forge
libarrow-dataset          18.1.0           h8bbc2ab_4_cpu    conda-forge
libarrow-substrait        18.1.0           had74209_4_cpu    conda-forge
libavif16                 1.1.1                h1909e37_2    conda-forge
libblas                   3.9.0           25_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hb9d3cd8_2    conda-forge
libbrotlidec              1.1.0                hb9d3cd8_2    conda-forge
libbrotlienc              1.1.0                hb9d3cd8_2    conda-forge
libcblas                  3.9.0           25_linux64_openblas    conda-forge
libclang-cpp19.1          19.1.5          default_hb5137d0_0    conda-forge
libclang13                19.1.5          default_h9c6a7e4_0    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcups                   2.3.3                h4637d8d_4    conda-forge
libcurl                   8.10.1               hbbe4b11_0    conda-forge
libde265                  1.0.15               h00ab1b0_0    conda-forge
libdeflate                1.22                 hb9d3cd8_0    conda-forge
libdrm                    2.4.124              hb9d3cd8_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libegl                    1.7.0                ha4b6fd6_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.6.4                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgdal-core              3.10.0               h7250d82_6    conda-forge
libgfortran               14.2.0               h69a702a_1    conda-forge
libgfortran-ng            14.2.0               h69a702a_1    conda-forge
libgfortran5              14.2.0               hd5240d6_1    conda-forge
libgl                     1.7.0                ha4b6fd6_2    conda-forge
libglib                   2.82.2               h2ff4ddf_0    conda-forge
libglvnd                  1.7.0                ha4b6fd6_2    conda-forge
libglx                    1.7.0                ha4b6fd6_2    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libgoogle-cloud           2.31.0               h804f50b_0    conda-forge
libgoogle-cloud-storage   2.31.0               h0121fbd_0    conda-forge
libgrpc                   1.67.1               hc2c308b_0    conda-forge
libheif                   1.18.2          gpl_hffcb242_100    conda-forge
libhwy                    1.1.0                h00ab1b0_0    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
libjxl                    0.11.1               hdb8da77_0    conda-forge
libkml                    1.3.0             hf539b9f_1021    conda-forge
liblapack                 3.9.0           25_linux64_openblas    conda-forge
libllvm19                 19.1.5               ha7bfdaf_0    conda-forge
liblzma                   5.6.3                hb9d3cd8_1    conda-forge
liblzma-devel             5.6.3                hb9d3cd8_1    conda-forge
libnghttp2                1.64.0               h161d5f1_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libntlm                   1.4               h7f98852_1002    conda-forge
libopenblas               0.3.28          pthreads_h94d23a6_1    conda-forge
libopengl                 1.7.0                ha4b6fd6_2    conda-forge
libparquet                18.1.0           hf4f6db6_4_cpu    conda-forge
libpciaccess              0.18                 hd590300_0    conda-forge
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@sarthakpatel7 sarthakpatel7 added the bug Something isn't working label Dec 24, 2024
@kevin218
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As the error suggests, there are Infs or NaNs in the data. This could result from a multitude of user-related errors.

I suggest inspecting your input FITS files, the xwindow and ywindow values, and any Stage 3 figures for indicators of a problem.

@sarthakpatel7
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Sorry for the late reply; one thing I wanted to share is that I didn't face this error when I ran it with the previous version of Eureka (v0.9, I believe). However, after I installed v1.1 (by creating a new environment), I faced this issue.

@kevin218
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A lot has changed between v0.9 and v1.1, including the loss of backwards compatibility, so using the same settings will not lead to the same result.

Try comparing outputs between runs to see what has changed. Also, compare your ECFs to those in the demos folder to make sure you're not missing something important.

@taylorbell57
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@sarthakpatel7, are you still dealing with this issue? If so, please first check if there are any updates needed to your ECFs by looking at the newer templates here, and also look at any output figures you get.

If none of that works, please copy-paste the contents your Stage 3 ECF file so that we can troubleshoot this further.

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