FAQs and troubleshooting

Below are some frequently asked questions or bugs that have arisen during our use of the pipeline.

The allocation code fails and says "Some magnets are fully blocked!"

This means that there is no way for the Robot to place the magnets in the desired positions. The robot arm itself has a set clearance when it picks up and puts down magnets, and so some magnet configurations which don't clash aren't actually possible to put on the plate.

In this case, you'll need to go back and use the interactive configuration tool to change the magnet positions to have a bit more clearance. The error message will let you know which magnets are affected.

Snakemake has an error which mentions "The files below seem to be incomplete".

This happens when a snakemake task doesn't finish properly- often because it's been killed by someone pressing Ctrl-C. It's basically saying "I don't know if the files below are finished or not!".

If you want to re-run the task which snakemake was in the middle of before it was killed, add --rerun-incomplete to the beginning of your command (e.g snakemake --rerun-incomplete --configfile ... etc).

If you don't want to re-run the command that was killed, there are two options. I've found the best thing to do is delete the .snakemake folder: rm -r .snakemake. This deletes snakemake's history and it just forgets that it was halfway through a step. You can also follow the commands that snakemake suggests, about "cleaning up metadata", but I've found that this often doesn't work for some reason... (see e.g. this github issue).

Snakemake complains about "Index 0 is out of bounds for axis with size 0" and mentions the _get_tile_filename function.

This happens because Snakemake is trying to select a row from your {start_date}_{end_date}_galaxy_tiles.csv but there aren't any matches. Check that you've typed the tile filename exactly right on the command line (it's very easy to type G12_tile_220 instead of G15_tile_220, for example!)

Snakemake says "there is no rule to make {filename}"

This happens when snakemake can't figure out how to create the output file you've asked for.

The most common cause of this is a typo in the filename you've passed it (e.g. asking it to make G155_tile_220.tar.gz will fail, for example). Another possible cause would be if you're asking it to make a tile which you haven't entered in the resources/{run_dates}/{run_dates}_galaxy_tiles.csv file. Check that the tile is located there and doesn't have any typos.

Snakemake says "Looks like we have a mismatch between the tile numbers and the filenames somewhere"

This occurs when one (or more) of the rows in the resources/{run_dates}/{run_dates}_galaxy_tiles.csv is incorrect. If you tell snakemake to use a tile file from one tile number and a guide tile from another (e.g. one row references two different numbers), or if your tile number column in that file doesn't match the filenames, you'll see this error. Go back and check that all of the rows in that file are correct!

The distortion correction code complains about "Reading past the end of a file"

This means a sky mask fits file the code is trying to read is corrupted or damaged.

The distortion correction code reads all fits files in the folder path you give it, so make sure there aren't any files in there which aren't sky masks. We've seen this error before when the distortion correction code tried to read a hidden file called ._segmap_waves_18.0_-34.1_1.41_1.17.fits. After deleting this file and all the others like it, everything worked as expected.

Snakemake complains about "Error Tokenizing data: Expecting 5 lines of data, saw {n}"

This is almost certainly caused by a typo in the resources/{run_dates}/{run_dates}_galaxy_tiles.csv. Check that you haven't added or forgotten a comma somewhere.