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fastq in and output produces a fastq with a longer phred score line than actual bases #2

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johnrandallia opened this issue Apr 8, 2024 · 1 comment

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@johnrandallia
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Hi,
I was using debar on my fastq file with the input and output (default) as fastq.
Later, I wanted to process the file further with usearch (dereplication) but it says
---Fatal error--- Bad FASTQ record: 418 bases, 493 quals line 152 file XX.fq label AA

I looked up the label and the bases
@AA AATAAATAATATGAGATTTTGACTTTTACCTCCTGCTTTAACATTGCTGCTAACTAGCAGCATAGTAGAAACTGGAGCTGGAACAGGATGAACTGTTTAC CCCCCACTATCATCTAATATTGCTCATGGAGGAGCCTCTGTTGATTTAGCTATTTTTTCCCTTCATTTAGCAGGAATCTCCTCTCTTCTAGGAGCCGTAA ATTTTATTACAACTGTAATTAATATACGATCAATAGGAATTACATTCGATCGCATACCTTTATTTGTATGATCAGTAGTAATTACAGCTTTATTATTACT TTTATCATTACCTGTTTTAGCAGGAGCTATTACAATATTATTGACAGATCGAAATTTAAATACATCTTTTTTTGACCCTGCAGGAGGAGGAGATCCAGTA TTATACCAGCATTTATTT + .... .... AGH:HFAFGGHG=GHGGA@AA
There seems to be a case where the label is not written in a new line?
I'm continuing with outformat ="fasta"

@johnrandallia
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and with fasta input it says:
Error in data.frame(header_data = head_line, sequence = data[seq(2, length(data), : arguments imply differing number of rows: 145786, 145785

with fastq input and fasta output it worked

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