Issue ingesting files with newly installed pipeline

Support
#1

Hello I am part of an undergraduate computer science capstone team at the University of Portland. We recently ran into some issues and ended up having to reinstall the pipeline on our Ubuntu 18 machine. We have been working from the tutorial (https://pipelines.lsst.io/getting-started/index.html) and followed the instructions to set up and install the pipeline given here: https://pipelines.lsst.io/install/newinstall.html. The install seemed to work just fine, however when I continued to follow the tutorial and attempted to ingest images I am faced with errors. I have tried to reinstall the pipeline using just the instructions in the newinstall.sh (i.e. just doing eups distrib install lsst_apps without the version numbers in the tutorial, I thought maybe the version is out of date in the tutorial, but I get an error saying there is no such package). Anyway here is the error I am getting:

(lsst-scipipe-fcd27eb) lsst@lsst-ThinkCentre-M93p:~/lsst_stack$ ingestImages.py DATA 
$CI_HSC_DIR/raw/*.fits --mode=link
root INFO: Loading config overrride file '/home/lsst/lsst_stack/stack/miniconda3-4.5.4-                
fcd27eb/Linux64/obs_subaru/16.0+1/config/ingest.py'
HscMapper WARN: Unable to find calib root directory
CameraMapper INFO: Loading Posix exposure registry from /home/lsst/lsst_stack/DATA
ingest WARN: Failed to ingest file /home/lsst/lsst_stack/ci_hsc/raw/HSCA90333426.fits: 
  File "src/fits.cc", line 1420, in lsst::afw::fits::Fits::Fits(const string&, const string&, int)
    cfitsio error: error reading from FITS file (108) : Opening file 
'/home/lsst/lsst_stack/ci_hsc/raw/HSCA90333426.fits' with mode 'r'
cfitsio error stack:
  Error reading data buffer from file:
  /home/lsst/lsst_stack/ci_hsc/raw/HSCA90333426.fits
  ffopen could not interpret primary array header of file: 
  /home/lsst/lsst_stack/ci_hsc/raw/HSCA90333426.fits
 {0}
lsst::afw::fits::FitsError: 'cfitsio error: error reading from FITS file (108) : Opening file 
'/home/lsst/lsst_stack/ci_hsc/raw/HSCA90333426.fits' with mode 'r'
cfitsio error stack:
  Error reading data buffer from file:
  /home/lsst/lsst_stack/ci_hsc/raw/HSCA90333426.fits
  ffopen could not interpret primary array header of file: 
  /home/lsst/lsst_stack/ci_hsc/raw/HSCA90333426.fits

Any help or suggestions would be greatly appreciated! Thanks!
Mikayla

#2

Is this really a FITS file? I am wondering if you have not configured git-lfs properly so when you cloned the repo you only got the stub files that point to the real files.
See https://developer.lsst.io/git/git-lfs.html?highlight=lfs

#3

Yup, there was an issue with our git lfs set up. Fixing that cleared everything right up. Thank you so much for your help and quick response!

Thanks!
Mikayla