Update DNAscope LongRead pipeline to use the new scheduler

sentieon_cli/command_strings.py

@@ -14,22 +14,19 @@
 logger = get_logger(__name__)
 
 
+def cmd_fai_to_bed(
+    fai: pathlib.Path,
+    bed: pathlib.Path,
+) -> str:
+    cmd = ["awk", "-v", "OFS=\t", "{print $1,0,$2}", str(fai)]
+    return shlex.join(cmd) + " > " + shlex.quote(str(bed))
+
+
 def cmd_bedtools_subtract(
-    regions_bed: typing.Optional[pathlib.Path],
+    regions_bed: pathlib.Path,
     phased_bed: pathlib.Path,
     unphased_bed: pathlib.Path,
-    tmp_dir: pathlib.Path,
-    reference: pathlib.Path,
-    dry_run: bool,
-):
-    if regions_bed is None:
-        # set region to the full genome
-        regions_bed = tmp_dir.joinpath("reference.bed")
-        if not dry_run:
-            with open(regions_bed, "wt", encoding="utf-8") as f:
-                for line in open(name(reference) + ".fai", encoding="utf-8"):
-                    toks = line.strip().split("\t")
-                    f.write(f"{toks[0]}\t0\t{toks[1]}\n")
+) -> str:
     cmd = [
         "bedtools",
         "subtract",

sentieon_cli/dnascope.py

@@ -120,7 +120,10 @@ def check_shm(
         )
         total_input_size += total
 
-    shm_free = shutil.disk_usage("/dev/shm").free
+    try:
+        shm_free = shutil.disk_usage("/dev/shm").free
+    except Exception:
+        return None
     total_mem = total_memory()
 
     if (