def count_kmers(tmp_dirpath, fpath, log_fpath, err_fpath, can_reuse=True):
kmc_out_fpath = join(tmp_dirpath, basename(fpath) + '.kmc')
if can_reuse and is_non_empty_file(kmc_out_fpath + '.kmc_pre') and is_non_empty_file(kmc_out_fpath + '.kmc_suf'):
return kmc_out_fpath
max_mem = max(2, get_free_memory())
run_kmc(['-m' + str(max_mem), '-k' + str(KMERS_LEN), '-fm', '-cx1', '-ci1', fpath, kmc_out_fpath, tmp_dirpath],
log_fpath, err_fpath, use_kmc_tools=False)
return kmc_out_fpath
def get_gridss_memory():
free_mem = get_free_memory()
if free_mem >= 64:
return 31
elif free_mem >= 32:
return 16
elif free_mem >= 16:
return 8
return 2
def count_kmers(tmp_dirpath, fpath, kmer_len, log_fpath, err_fpath):
kmc_out_fpath = join(tmp_dirpath, basename(fpath) + '.kmc')
max_mem = max(2, get_free_memory())
run_kmc([
'-m' + str(max_mem), '-n128', '-k' + str(kmer_len), '-fm', '-cx1',
'-ci1', fpath, kmc_out_fpath, tmp_dirpath
],
log_fpath,
err_fpath,
use_kmc_tools=False)
return kmc_out_fpath
def sort_bam(bam_fpath,
sorted_bam_fpath,
err_path,
logger,
threads=None,
sort_rule=None):
if not threads:
threads = qconfig.max_threads
mem = '%dGB' % min(100, max(2, get_free_memory()))
cmd = [
sambamba_fpath('sambamba'), 'sort', '-t',
str(threads), '--tmpdir',
dirname(sorted_bam_fpath), '-m', mem, '-o', sorted_bam_fpath, bam_fpath
]
if sort_rule:
cmd += [sort_rule]
qutils.call_subprocess(cmd, stderr=open(err_path, 'a'), logger=logger)