I'm using bowtie2 as my aliner to align my sequence. I'm getting an error Fewer reads in the file specified with -2 than in file specified with -1. i used the same file to align with BWA-mem it does not show any error. but botie2 is still running for more than 1week with the same file size.
the command i used to run bowtie2
bowtie2 -p 30 -x Reference/bowti_hg38 -1 Data/SRR622457_1.fastq -2 Data/SRR622457_2.fastq -S Output/Bowtie/Alignment/bowtie.sam