How to solve break line in ".filtered_polymorphic_sites.fasta"?

[Rathanin-github]

Hi sir Sorry that bother you again, since I am very new bioinformatic user. I have attempt to construct the ML tree of two chromosome bacteria. I split chr1 and chr2 before running gubbins to test that running gubbins with chr1 and chr2 separately is different from running gubbins with both chromosomes. I have already run gubbins of each chromosome and I am attempting to concatenate chr1. filtered_polymorphic_sites.fasta and chr2. filtered_polymorphic_sites.fasta together before constructing tree. I prefer to use "paste chr1.filtered_polymorphic_sites.fastn chr2. filtered_polymorphic_sites.fasta | awk '{if (NR%2==0) {print $1 $2} else {print $1}}' " to concatenate them. However, the command line does not work because I got various break line in my both chr1.filtered_polymorphic_sites.fastn and chr2. filtered_polymorphic_sites.fasta. Could you please tell me how to close the break line? The break line without sequence ID looks like this: 308 >seq1 AGACCCTGGGCTGCCACGTGGAGTCCGCGCAAGCCGCTGGCGCCAGCAGTCCCCCGTCGAGAGCTGCCCGAGGCATACTCGGGCGTGGTCTGCCCACCTCGTTTGCGTCCGCGGGGCTAGTTGAAATTGGCAGCCAACACGAGCTTATTTTGCCCCCCGTGCGCTTGCAACAGTCTGTGGCTCGTGTCCATCCTGTGCCATCTTGTCGCGTGTTACCTTCGCTACGAGCCTGGGCCGCCGCGCCGCACATATCCGCCTGCTGCGCGGGGATTTG 309 CATTACCGGGCGCCGTATAGGGCGACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATCAGCAAGCCAAGTTGCCGACGTGGCTGTGGGAGAGACAACACAACACAACCCCGCCGCTCCGGCTCGCGCCTCGCCCACAGT

I would like the sequence like this: 308 >seq1 AGACCCTGGGCTGCCACGTGGAGTCCGCGCAAGCCGCTGGCGCCAGCAGTCCCCCGTCGAGAGCTGCCCGAGGCATACTCGGGCGTGGTCTGCCCACCTCGTTTGCGTCCGCGGGGCTAGTTGAAATTGGCAGCCAACACGAGCTTATTTTGCCCCCCGTGCGCTTGCAACAGTCTGTGGCTCGTGTCCATCCTGTGCCATCTTGTCGCGTGTTACCTTCGCTACGAGCCTGGGCCGCCGCGCCGCACATATCCGCCTGCTGCGCGGGGATTTGCATTACCGGGCGCCGTATAGGGCGACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATCAGCAAGCCAAGTTGCCGACGTGGCTGTGGGAGAGACAACACAACACAACCCCGCCGCTCCGGCTCGCGCCTCGCCCACAGT

Thanks in advance!