jingmeng-bioinformatics

OSError: [Errno 12] Cannot allocate memory

2

ERROR 2019-11-06 16:21:08,570 __main__ Aborting! ERROR 2019-11-06 16:21:08,598 __main__ preprocess.py failure on arguments: Namespace(dbsnp_to_filter=None, del_merge_min_af=0, del_min_af=0.05, ensemble_tsv=None, filter_duplicate=False, first_do_without_qual=False, good_ao=10, ins_merge_min_af=0, ins_min_af=0.05, long_read=False, matrix_base_pad=7, matrix_width=32, max_dp=100000, merge_r=0.5, min_ao=1, min_dp=5, min_ev_frac_per_col=0.06,...

It takes several days to preprocess BAM files for testing

2

Hi Sayed, I started preprocessing the whole genome bam files (tumor and matched normal) for testing on my local computer (--number_threads 1) four days ago, and it has not finished...