missing target cause missing output even with -S

[diekhans]

intronProspector -C 1.0 -g tmp/hg38.fa -S --map-to-ucsc --intron-calls=merged/HS_A_Brain.introns.tsv.ku.gi.ucsc.edu.26701 --junction-bed=merged/HS_A_Brain.juncs.tsv.ku.gi.ucsc.edu.26701 --intron-bed=merged/HS_A_Brain.introns.bed.ku.gi.ucsc.edu.26701 ../bams/merged/HS_A_Brain.merged.bam

Warning: genomic sequence not found for chrMT splice junctions not available
Warning: genomic sequence not found for GL000225.1 splice junctions not available
Warning: genomic sequence not found for GL000009.2 splice junctions not available
Warning: genomic sequence not found for GL000194.1 splice junctions not available
Warning: genomic sequence not found for KI270742.1 splice junctions not available
Warning: genomic sequence not found for GL000205.2 splice junctions not available
Warning: genomic sequence not found for GL000195.1 splice junctions not available
Warning: genomic sequence not found for KI270733.1 splice junctions not available
Warning: genomic sequence not found for GL000219.1 splice junctions not available
Warning: genomic sequence not found for GL000216.2 splice junctions not available
Warning: genomic sequence not found for KI270712.1 splice junctions not available
Warning: genomic sequence not found for KI270706.1 splice junctions not available
Warning: genomic sequence not found for KI270744.1 splice junctions not available
Warning: genomic sequence not found for KI270734.1 splice junctions not available
Warning: genomic sequence not found for GL000220.1 splice junctions not available
Warning: genomic sequence not found for GL000221.1 splice junctions not available
Warning: genomic sequence not found for KI270711.1 splice junctions not available
Warning: genomic sequence not found for KI270752.1 splice junctions not available
mv: cannot stat ‘merged/HS_A_Brain.introns.tsv.ku-32.kulocal.14169’: No such file or directory