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fix: improve error handling for subprocess commands in atac_seq.py #1446

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Merged
merged 4 commits into from
Sep 12, 2025
Merged

fix: improve error handling for subprocess commands in atac_seq.py #1446

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fix: improve error handling for subprocess commands in atac_seq.py
Bento007 Sep 11, 2025
6a6b527
fix: ensure proper waiting and error handling for subprocesses in ata…
Bento007 Sep 11, 2025
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34 changes: 28 additions & 6 deletions cellxgene_schema_cli/cellxgene_schema/atac_seq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -479,12 +479,21 @@ def prepare_fragment(
stdout=subprocess.PIPE,
env={**os.environ, "LC_ALL": "C"},
)
gzip_proc.stdout.close()
bgzip_proc = subprocess.Popen(["bgzip", f"--threads={num_cores}", "-c"], stdin=sort_proc.stdout, stdout=out_f)
sort_proc.stdout.close()
bgzip_proc.wait()
sort_proc.wait()
gzip_proc.wait()

# check that all processes completed successfully
errors = []
if sort_proc.returncode != 0:
errors.append(f"sort command failed with error code {sort_proc.returncode}")
if gzip_proc.returncode != 0:
errors.append(f"gzip command failed with error code {gzip_proc.returncode}")
if bgzip_proc.returncode != 0:
raise RuntimeError(f"bgzip compression failed with error code {bgzip_proc.returncode}")
errors.append(f"bgzip command failed with error code {bgzip_proc.returncode}")
if errors:
raise RuntimeError(" | ".join(errors))
logger.info(f"bgzip compression completed successfully for {bgzip_output_file}")


Expand Down Expand Up @@ -577,11 +586,24 @@ def deduplicate_fragment_rows(
bgzip_proc = subprocess.Popen(bgzip_cmd, stdin=uniq_proc.stdout, stdout=outfile)
uniq_proc.stdout.close()
bgzip_proc.wait()
if bgzip_proc.returncode != 0:
raise RuntimeError(f"bgzip compression failed with error code {bgzip_proc.returncode}")
# Wait for the rest of the pipeline to finish and check for errors
uniq_proc.wait()
sort_proc.wait()
gzip_proc.wait()

if bgzip_proc.returncode != 0:
raise RuntimeError(f"bgzip compression failed with error code {bgzip_proc.returncode}")

# check that all processes completed successfully
errors = []
if uniq_proc.returncode != 0:
errors.append(f"uniq command failed with error code {uniq_proc.returncode}")
if sort_proc.returncode != 0:
errors.append(f"sort command failed with error code {sort_proc.returncode}")
if gzip_proc.returncode != 0:
errors.append(f"gzip command failed with error code {gzip_proc.returncode}")
# bgzip_proc error already checked above; no need to check again here.
if errors:
raise RuntimeError(" | ".join(errors))

logger.info(f"bgzip compression completed successfully for {output_file_name}")
return str(output_file_name)
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