I am attempting to use prepDE.py to prepare my stringtie output for DEseq2. My stringtie command is as follows:

stringtie -e -G Gmax_275_Wm82.a2.v1.gene.gff3 -o ${name}.gtf ${bam}.

My prepDE.py command is as follows:

prepDE.py --input "./output/stringtie"

where the "stringtie" directory contains subdirectories corresponding to my sample names (for example OT89-5_LD_BF_2_short) and each of those subdirectories contain the following file

OT89-5_LD_BF_2_short.gtf

When I run the prepDE command above, I get the following error:

Error: could not locate transcript Glyma.02G158500.1.Wm82.a2.v1 entry for sample OT89-5_SD_DF_1_short
Traceback (most recent call last):
File "prepDE.py", line 286, in
geneDict[geneIDs[i]][s[0]]+=v[s[0]]
~^^^^^^
KeyError: 'OT89-5_SD_DF_1_short'`

Please let me know if I am doing something incorrectly. Thank you for your help