I want to use samtools to create a .bcf file using this command:

samtools mpileup -C 50 -E -t SP -t DP -u -I -f /my/path/Geospiza_fortis.scaf.noBacterial.fa -b bam_list.txt > output_test.bcf

But I get this error:

[fai_fetch_seq] The sequence "JH739887" not found

I know that the problem is that the name "JH739887" doesn't exist in the reference genome. But How I'm I supposed to change this name so that it can be mapped on the reference genome?

head Geospiza_fortis.scaf.noBacterial.fa
>Scaffold410    275
TGCATTAATATGAGTGTGTGCTGCAAAAGTTCAGGTCATGGTCCGATCATACTTCACATTTTGGTAGCACTTTAAGCAGAGATCGGTTATCCCATTCTGTGGAAGACTCAACACTATCATAAGGTCCCACAGTTTTATTATCCCTCTGCCTCCCGGAATGCCCCCGGCAGTGAGGGGTACCATCTTCTCAGCAGTAAGGATATTCTTCAGGAGTTCCGTGTGAGCTTTCCCGGATTTAGTTCCATTTTTTAAATACTTCCCAATTCTTTGCTTTG
>Scaffold430    374
CTTTGTTAACTGAAAGAGCCTCTAAGTAGATGACCAGTGCTCAGTTAGTACAGTATGAATTTTGTTTAATGGAACAGGAAGATTTAGTATTGAGAAGCGGTTAAGGGTTTAACCCAGCCTCCTGTCTGAATGGACCTGAAGAGGGGGGCCGGGAAGAAACCCATGACTGCATTAAAGTGATAGATCTCCAGACATGGGCTAGGGAAGATTTACAAGACACTCCCTGGCCTGAGGGAGAAAATATGTTTATTGATGAGTCTTCAAGGGTGGCAGAAGGGAAGCGATTTACAGGATACACAATCATTAATGGAAGGAAATTAAAGGAAGGGGGGAGATTGTCACCCACCTGGTCAGTTCAGACAGCAGAGCTGTAT

head Geospiza_fortis.scaf.noBacterial.fa.fai 
# Scaffold410       275     17      275     276
# Scaffold430       374     310     374     375
# Scaffold1010      597     703     597     598
# scaffold260       820     1314    820     821
# scaffold980       554     2148    554     555
# scaffold440       1463    2716    1463    1464

samtools view Bamboum_sorted.bam | head 
24016062    16  JH739887    2197    37  94M *   0   0   ACCATTTAAAACACTCTTCAGGGAAGGCTTTAGCTTTTCATTCAGTTTTGTATTTTACTACATGAATATAAAGCAGTTTTGCTTCTGTGTTTTT  >@BB@>>>;;?>;@A>AAABBBBBBBBBBBBBBBBBBA?A?9<===<<BAABBABA=BBABBBBBBBBCBB>CCCACCC73?@2+<2+0+A<+=  NH:i:1  NM:i:3  RG:Z:JP3750_for_sorted
27522854    0   JH739887    2921    37  94M *   0   0   AATTTCCAACACTCTGCAAGAAGCTGCAAGAGTTCGCCTGCACCTGTGTCTTATTGCCACAAGAGCTCTCTGTTCTATACTCTGAAATTCTCAC  BCFFFFFHHHHHJJJJJJJJIJIJIJJJJJJJFGHIIJJJIJJJIIIIIHHIJJJJJJJJJJHIJJJJHHHHHHFFFFFFFEEEEEEEDDEDED  NH:i:1  NM:i:0  RG:Z:JP3923_for_sorted
31888152    0   JH739887    4964    37  94M *   0   0   AAAGCCCACCTGCATTATACAACATGAAGCCGTAGAATAGACAGTCTGATGGTTTACAATGTTTAGGAGATGTTACCATGTTAAGGATCATTAT  C@FFDFFHHHHHJIJJJJJJJJJJJIJJJJJJGIJJJJJ*?GHIEHIJIHIIHIIJJIJJJHII===CHEHGHHFFFFFFEEEDEEEDDDDEEE  NH:i:1  NM:i:5  RG:Z:JP3752_for_sorted