Uncaught exception running RNApeg floating_junction_fix

[skeating63]

Hello, I'm trying to use RNApeg to prepare data for Cicero and cannot figure out this error I'm getting. When I run the test data from the CICERO github it works, but when I run other data I get an error I can't figure out.

I'm testing with the bam files from https://www.stjude.org/research/labs/zhang-lab/cicero.html. My command is:
docker run -v /Users/shannonkeating/Documents/rna_variantskipping/cicero/test_data/RNApeg:/results -v /Applications/CICERO-master/reference:/reference -v /Users/shannonkeating/Documents/rna_variantskipping/cicero/test_data:/data ghcr.io/stjude/rnapeg:v2.7.7 -b /data/MV4_11_RNAseq_1.bam -f /reference/Homo_sapiens/GRCh37-lite/FASTA/GRCh37-lite.fa -r /reference/Homo_sapiens/GRCh37-lite/mRNA/Combined/all_refFlats.txt

This creates the initial MV4_11_RNAseq_1.bam.junctions.tab file but at the pass 2 step, I get this error:

pass 2: detect shifts... Uncaught exception from user code: error calling floating_junction_fix.pl -jf-shift MV4_11_RNAseq_1.bam.junctions.tab -now -force 1 -no-config -jf-db /reference/Homo_sapiens/GRCh37-lite/mRNA/Combined/all_refFlats.txt -fasta /reference/Homo_sapiens/GRCh37-lite/FASTA/GRCh37-lite.fa -write-both, exit 9 at /RNApeg/src/bin/junction_extraction_wrapper.pl line 338. main::run_cmd("floating_junction_fix.pl -jf-shift MV4_11_RNAseq_1.bam.junctions.tab -now -force 1 -no-config -jf-db /reference/Homo_sapiens/GRCh37-lite/mRNA/Combined/all_refFlats.txt -fasta /reference/Homo_sapiens/GRCh37-lite/FASTA/GRCh37-lite.fa -write-both", "MV4_11_RNAseq_1.bam.junctions.tab.shifted.tab") called at /RNApeg/src/bin/junction_extraction_wrapper.pl line 253 main::run_cmd("floating_junction_fix.pl -jf-shift MV4_11_RNAseq_1.bam.junctions.tab -now -force 1 -no-config -jf-db /reference/Homo_sapiens/GRCh37-lite/mRNA/Combined/all_refFlats.txt -fasta /reference/Homo_sapiens/GRCh37-lite/FASTA/GRCh37-lite.fa -write-both", [MV4_11__RNAseq_output.txt](https://github.com/stjude/RNApeg/files/12339210/MV4_11__RNAseq_output.txt) "MV4_11_RNAseq_1.bam.junctions.tab.shifted.tab") called at /RNApeg/src/bin/junction_extraction_wrapper.pl line 253

I've attached the full output as well.

I'm not sure if this is due to something with the GRCh37-lite reference genome because both the demo data from https://www.stjude.org/research/labs/zhang-lab/cicero.html and my own data are mapped to this reference, but the test data from https://github.com/stjude/CICERO are mapped to GRCh38_no_alt and that works properly. Any help trying to interpret this error would be greatly appreciated.