isabl-debug-analysis

Debugging an Isabl Analysis

You are helping debug a failed or problematic Isabl analysis.

Checklist

Work through these steps systematically:

1. Get analysis details (status, application, targets)
2. Check the command script (head_job.sh)
3. Review stdout log (head_job.log)
4. Review stderr log (head_job.err)
5. Check input data exists (BAM files, dependencies)
6. Verify settings (application_settings values)
7. Identify root cause
8. Suggest fix

Step 1: Get Analysis Details

import isabl_cli as ii

# Get the analysis
analysis = ii.Analysis(ANALYSIS_PK)

print(f"Status: {analysis.status}")
print(f"Application: {analysis.application.name} v{analysis.application.version}")
print(f"Storage URL: {analysis.storage_url}")
print(f"Targets: {[t.system_id for t in analysis.targets]}")
print(f"References: {[r.system_id for r in analysis.references]}")

Step 2: Check Command Script

The generated command is in head_job.sh:

# View the command that was executed
cat {analysis.storage_url}/head_job.sh

Look for:

• Incorrect paths
• Missing environment variables
• Malformed command syntax

Step 3: Review Logs

# Standard output
cat {analysis.storage_url}/head_job.log

# Standard error (usually more informative)
cat {analysis.storage_url}/head_job.err

Common error patterns:

Error	Likely Cause
"File not found"	Input file path incorrect or missing
"Permission denied"	Storage directory permissions
"Command not found"	Tool path in settings is wrong
"Memory allocation"	Job needs more memory (batch system)
"Timeout"	Job exceeded time limit

Step 4: Check Input Data

# Verify target experiments have data
for target in analysis.targets:
    print(f"{target.system_id}:")
    print(f"  Raw data: {target.raw_data}")
    print(f"  BAM files: {target.bam_files}")

# Check files exist
ls -la {path_to_input_file}

Step 5: Check Dependencies

If the app depends on other analyses:

# Find dependency analyses
from isabl_cli import utils

# Check if dependency result exists
result, dep_analysis = utils.get_result(
    experiment=analysis.targets[0],
    application_key=DEPENDENCY_APP_PK,
    result_key="expected_result"
)
print(f"Dependency analysis: {dep_analysis}")
print(f"Dependency result: {result}")

Step 6: Verify Settings

# Get application settings
app = ii.get_instance("applications", analysis.application.pk)
print(f"Settings: {app.settings}")

# Check specific setting
from my_apps import MyApplication
instance = MyApplication()
print(f"Tool path: {instance.settings.tool_path}")

Step 7: Common Fixes

Fix 1: Re-run with --force

# Wipe failed analysis and restart
isabl myapp-1-0 --analyses pk={ANALYSIS_PK} --force --commit

Fix 2: Re-run with --restart

# Resume from checkpoint (if supported)
isabl myapp-1-0 --analyses pk={ANALYSIS_PK} --restart --commit

Fix 3: Run locally for debugging

# Execute locally instead of batch system
isabl myapp-1-0 --targets EXPERIMENT_ID --local --commit

Fix 4: Manually patch status

# If analysis completed but status is wrong
ii.patch_instance("analyses", analysis.pk, status="SUCCEEDED")

Fix 5: Check batch system logs

# For SLURM
sacct -j JOB_ID --format=JobID,State,ExitCode,MaxRSS,Elapsed

# For LSF
bjobs -l JOB_ID
bhist -l JOB_ID

Signals and Automations

If the analysis SUCCEEDED but something else failed:

# Check if signals are configured
from isabl_cli.settings import system_settings
print(f"ON_STATUS_CHANGE: {system_settings.ON_STATUS_CHANGE}")

# Manually trigger signals
from isabl_cli import signals
signals.run_on_status_change(analysis)

Reporting the Issue

When reporting, include:

1. Analysis PK and status
2. Application name and version
3. Relevant portion of head_job.err
4. Input experiment IDs
5. Steps to reproduce