junlanlu
commented
8 months ago TLDR: rename your ute twix files to avoid the word dixon.
The error is can be resolved by renaming the proton twix file and avoiding the substring "Dixon". This causes the code to incorrectly use the ute file as the gas exchange file. You can see in that the main difference below is that that the proper code to read ute twix files tries to get the first element in twix_obj in case the twix_obj is a list of length 2. This is just hardcoded that way.
The dixon file doesn't have this edge case, and thus, the function to read in the dixon file would fail to read in this particular ute file.
Description from @RachelEddy :
"Good news, we appear to mostly have the pipeline working! We have 2 random cases (so far) though that fail in the pipeline, saying the raw files could not be found. Ironically, these were ones included in our mega COVID analysis, so they ran through your lab analysis, and also through the old GUI analysis in our hands. We have a range of difference sequence/file naming conventions that doesn’t seem to be the issue here."
Team Xenon / @junlanlu : I've put files for these 2 subjects on the Network Share under "shared -> David -> gx_testing -> rachel" for initial triage.