When I run bwa(v 0.7.17-r1188) through a scheduler on an HPC it randomly fails with a core dump and the log file mentions the error as
glibc: double free or corruption.
A google search on the error pointed to a env variable
MALLOC_CHECK_ whose value if changed can prevent this core dump. Accordingly I changed the value to
1 which should only put a warning in the log files and not abort.
With this the alignment works fine however I wanted to get more inputs on if it is advisable to change this env variable and would it potentially affect the accuracy of alignment in any way.
EDIT: Some details on the command and the operating system
The full command I am using is.
bsub -n 6 -q <queue_name> 'bwa mem -t 6 Homo_sapiens_assembly38.fasta L001_R1_001.fastq.gz L001_R2_001.fastq.gz 2> log.txt|samtools sort -o test.bam'
The scheduler is LSF and the operating system is RedHatEnterpriseServer(Linux 2.6.32). The executable was installed via make install and not through conda.