Dear Bowtie2 developers,
I get a "Floating point exception" when using the last version of Bowtie2 (2.0.4) with some (but not all) of my data files. The input files are fastq files were adapter sequences were trimmed off the reads using cutadapt.
I originally launched Tophat2, but I could track down that the error was occurring when the following command line was launched:
bowtie2-align -q -k 60 --very-fast --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-20,0 -p 4 --sam-no-hd -x Homo_sapiens.GRCh37.69.gtf test.fastq
Interestingly, this bug did not occur with older versions of Bowtie2 (I tested 184.108.40.206, 220.127.116.11, 2.0.1 and 2.0.2)
However it occurred with versions 2.0.3 and 2.0.4
I didn't noticed any obvious difference between the input fastq leading to an error or not.