Version 0.7.5 of kneaddata does not handle FASTQ headers as seamlessly as earlier versions. With paired FASTQ files for which the headers for both read_1.fastq and read_2.fastq are,
'at’SRR7280791.1 1 length=101
'at’SRR7280791.2 2 length=101
'at’SRR7280791.3 3 length=101
where ‘at’ represents the at symbol. ( The forum script interprets the at symbol as a reference to another user. )
kneaddata reports different read counts for paired output files kneaddata_paired_1.fastq and kneaddata_paired_2.fastq. After massaging the headers to,
for read_1.fastq and,
for read_2.fastq, kneaddata reports identical read counts for the paired output files.