[Question] How to use aTRAM stitcher? (no tutorial available / help menu unclear)

[ClaraKoehne]

Hello there. I have run the aTRAM pipeline up to the point where I need the stitcher. I have a bunch of files now that contain aTRAM's output (contig files); they are called like Helobdella_robusta_5951at33208_6412_0_002a2c_451.all_contigs.fasta and contain DNA sequences with names like >5_NODE_1_length_7889_cov_3.702579 iteration=5 contig_id=NODE_1_length_7889_cov_3.702579 score=4001.82.. The proteins in my reference.faa are called like >Helobdella_robusta@446000at33208_6412_0:000010, so are quite obviously the origin of the file names where aTRAM saves its output contigs.
I'm not sure what to put in my taxa.txt file for the stitcher; I only have one query taxon (Dimorphilus gyrociliatus, but the name never comes up in any file or header) and one reference (Helobdella robusta). The taxa.txt file therefore currently contains exactly one line, and that is "Helobdella robusta". I've tried to run the stitcher like

aTRAM/atram_stitcher.py --taxa taxa.txt \
--refs reference.faa \
--assemblies-dir assemblies/ \
--file-filter "*.all_contigs.fasta" \
--output-prefix atram_stitcher_results/

and it produces a lot of output files (one per protein sequence in the reference file), but they are all empty. Am I using the stitcher wrong? Thanks for the help.