Bad File Format

[dylanHco]

Hello - I am trying to use Waster to generate a tree for input into cactus aligner. I am trying to align chloroplast genomes from several different species. Instead of using raw fastq files, I am first taking them thru GetOrganelle (https://github.com/Kinggerm/GetOrganelle) to extract just reads associated with chloroplast in order to build a tree. GetOrganelle outputs paired in reads as fastqs that are only associated with the chloroplast. I use BBMerge to merge together the paired end files. However when I try to use these with waster, I get Bad Format errors and I am not sure why that is. Below is the first few lines of a merged fasta:

LH00305:47:22J3KWLT3:1:1106:31984:20819 1:N:0:GAATTAGT+GTCAGTAC TTTCGCTACAGCACCCGCTGCTCTAGCTAATTGTCCACCCTTTCCAAGTGTGATTTCTATGTTATGTATG GCCGTGCCTAAGGGCATATCGGTTGAAGTAGATTC LH00305:47:22J3KWLT3:1:1107:33731:12248 1:N:0:GAATTAGT+GTCAGTAC ATTCTATCTAACGAATGAGACTTCTATGGATCTATCCCATTTTTTCGGGTTATCCAAAAGAGTTTAATTA TTAATTACATGAGTTTCAAACTTGAATTTGGATTCCTAAT LH00305:47:22J3KWLT3:1:1109:18790:4269 1:N:0:GAATTAGT+GTCAGTAC TTTAATTATTATTTTTGATATTTTATTTTGTAGGATAGAGTCAAAACTTATCCTAAGTTCCCCAAATTAG ACCAACGGAATTCTGTTTGCTATATTATATAAAAAAGTGCTTCTGAATTAATCTCATCTT LH00305:47:22J3KWLT3:1:1109:44115:6367 1:N:0:GAATTCGT+GTCAGTAC GAGTTCATTCTCCGGGAAACTCCGTTTAAATTATTCCGGTGGATTCTTTACAACCTACTTCTTTTATTAT CTCATTGGAAATCATATAAAGACAATTCCTATTTAATATAGCTAT LH00305:47:22J3KWLT3:1:1109:37125:16301 1:N:0:GAATTAGT+GTCAGTAC CGCACTTCTAACACTTGTTCCACTTTTGGAAGACCCTGCGTTATGTCCCCAGATCTCGACTTTTCATATA TAAATGTAACTAATGTATCTCCTTCATAAAGGATTTCCCCATAATGGCCATGAACGGTTGCTCCTGGGGT GGCCAAATAAGGCCTAGCTGATCGTATTACTACGGAATCGACTTGAACAAATATAA LH00305:47:22J3KWLT3:1:1109:20361:19265 1:N:0:GAATTAGT+GTCAGTAC ATATAATCCCATAGACCTCCTTTAAGAATTCCAATCTGGAAAAAGAATTGATAGCTTGTATTTCGGTTGT ATCAATTATCATTTTTAACGATCAACTTCTCCCATAATGATATCTATGCTACCTAATATCGTCATAATAT CAGCCAATTTCATTCTTTTAA LH00305:47:22J3KWLT3:1:1109:43708:28927 1:N:0:GAATTAGT+GTCAGTAC TTTTCTTCTTCCATATGTAAAAAGGGAATAAACAAATCAATCAAATTCCGGGATGCTTCATGAAGTGCTT CTTTCGGAGTTAAACTTCCGTTTGTCCATATTTCTAGAAAAAGTATCTCTTGTTTTTCATTCCCATTCCC ATAAGAAAGAATACTATGATTTGCATTTCGAACAGGCA

Thanks for any suggestions! Dylan