Your fasta file should like:
>chr1
ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTG
TGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAG
ACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCG
ATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGT
TAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGA
TGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAG
CTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCC
GTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCG
GGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTG
GTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTG
TGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCG
TGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTA
GCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA
>chr2
CATCGGGTAGCTAGCGTCGTAGCTGTACG
...




Your fastq.gz file should like:

@TPNB500399:426:HJ5WKBGXM:1:11101:5602:1064 1:N:0:CCGGTCAG+TGTATC
CTTCTNTGGGATGTTTATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATGTTTGCATTCAAGTCACATC
+
AAAAA#E/EAEEEEEEEEAEEEEEEEEEEEAEEEEAEEAEA<AEEAEE/EEEEEEAEA6EEEEEEEEEEAEE<E//
@TPNB500399:426:HJ5WKBGXM:1:11101:2962:1070 1:N:0:CCGGTCAG+TGTATC
GTGGCNCACGCCTGTAGCATTCAAGTCACAGAGTAGAACATTAGATCGAGACAGGTTTGAAACACTCTTT
+
AAAAA#E6EEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEE/EEEE/EEEEEEE//EEEEEEEEAAEEEEEAEEEEE
...