Move vcf with shutil instead of rename

metagenopolis · Nov 18, 2024 · 621efa9 · 621efa9
1 parent 22a56a8
commit 621efa9
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/meteor/variantcalling.py b/meteor/variantcalling.py
@@ -17,6 +17,7 @@
 import lzma
 import bgzip
 import pickle
+import shutil
 from subprocess import CalledProcessError, run, Popen, PIPE
 from dataclasses import dataclass
 from pathlib import Path
@@ -31,7 +32,6 @@
 import pandas as pd
 from typing import ClassVar
 import numpy as np
-import pysam
 
 
 def run_freebayes_chunk(
@@ -666,7 +666,7 @@ def execute(self) -> None:
                 logging.info("Merging vcf")
                 self.merge_vcf_files(vcf_chunk_files, vcf_file)
             else:
-                Path(vcf_chunk_files[0]).rename(vcf_file)
+                shutil.move(str(vcf_chunk_files[0]), str(vcf_file.resolve()))
         logging.info(
             "Completed freebayes step in %f seconds", perf_counter() - startfreebayes
         )