I use this command to filter the chrM RNA.
$bowtie2 -x ./chrM/chrM_index ./S1_R1.fastq --un ./S1_R1_nochrM.fastq
And got this error after quite a long time of running:
libc++abi.dylib: terminate called throwing an exception (ERR): bowtie2-align died with signal 6 (ABRT)
It still gave me the output file.
My question is that, is the output file is complete and how to fix this error.
Thanks a lot~~