### Preflight Checklist - [x] I have searched [existing issues](https://github.com/anthropics/claude-code/issues?q=is%3Aissue%20state%3Aopen%20label%3Abug) and this hasn't been reported yet - [x] This is a single bug report (please file separate reports for different bugs) - [x] I am using the latest version of Claude Code ### What's Wrong? When working on Biology analysis of Salmonella for research I can't use Opus model or sonnet 4.5. Hiku does work OK . Is there a way to work around this?

[BUG] API Error: Claude Code is unable to respond to this request, which appears to violate our Usage Policy - When doing Research analysis in Biology

Resolved 💬 2 comments Opened Jan 20, 2026 by yonidavidson Closed Feb 28, 2026

Preflight Checklist

[x] I have searched existing issues and this hasn't been reported yet
[x] This is a single bug report (please file separate reports for different bugs)
[x] I am using the latest version of Claude Code

What's Wrong?

When working on Biology analysis of Salmonella for research I can't use Opus model or sonnet 4.5.
Hiku does work OK .
Is there a way to work around this?

What Should Happen?

It should just work with Opus

Error Messages/Logs

API Error: Claude Code is unable to respond to this request, which appears to violate our Usage Policy (https://www.anthropic.com/legal/aup). Please double press esc to edit your last message or start a new session for Claude Code to assist with a different task. If you are seeing this refusal repeatedly, try running /model claude-sonnet-4-20250514 to switch models.

Steps to Reproduce

This is the CLAUDE.md

# CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

## Project Overview

This repository contains a **bacterial genome assembly pipeline** for *Salmonella enterica* serovar Senftenberg. The pipeline performs de novo assembly from Illumina single-end sequencing data using SPAdes, followed by organism identification via BLAST.

**Key Facts:**
- **Organism**: *Salmonella enterica* subsp. *enterica* serovar Senftenberg (BSL-2 pathogen)
- **Assembly Tool**: SPAdes v4.2.0 in `--isolate` mode
- **Data Type**: Single-end Illumina reads (100 bp)
- **Genome Size**: ~4.7-5.0 Mb (typical for *Salmonella*)
- **Samples**: 77 bacterial isolates across multiple experimental conditions (B, C, D, E, G, H, SSF, STM, YOAV series)

## Repository Structure

.
├── README.md # Complete assembly workflow
├── ORGANISM_IDENTIFICATION.md # BLAST results and organism details
├── get_assembly_stats.py # Assembly quality metrics calculator
├── blast_results.txt # NCBI BLAST identification output
├── continuous_processor.sh # Automated pipeline (extract, assemble, cleanup)
├── cleanup_completed.sh # Cleanup script for completed assemblies
├── process_all_downloads.sh # Batch processing script
├── status_monitor_1min.sh # Real-time status monitoring
├── browser_download_helper.py # Download progress tracking
└── assembly_results/ # Assembly outputs (77 assemblies, git-ignored)
├── B_00625_assembly/
│ ├── contigs.fasta # Primary assembly output
│ ├── scaffolds.fasta # Scaffolded sequences
│ └── spades.log # Assembly log
└── [76 more assemblies...]


**Important**: Large data files are excluded from Git but preserved locally. Only documentation, scripts, and small results are version-controlled (~100 KB tracked vs 5.7 GB total).

## Assembly Commands

### Run Assembly for a Single Sample
```bash
spades.py \
  -s BCL_Convert_*/sample_name_*.fastq.gz \
  -o assembly_results/sample_name_assembly \
  --isolate \
  -t 4

Parameter Notes:

-s: Single-end reads (not -1/-2 for paired-end)
--isolate: Critical - optimized for bacterial isolates/small genomes
-t 4: Adjust threads based on available CPUs
Typical runtime: 10-30 minutes per sample (4-8 GB RAM required)

Calculate Assembly Statistics

python3 get_assembly_stats.py

Output: Number of contigs, total length, longest contig, N50, mean length for all 5 samples.

Organism Identification

# Extract first 2000 bp from longest contig
head -50 assembly_results/sample_assembly/contigs.fasta | tail -49 | tr -d '\n' > query.fasta

# Run BLAST against NCBI nt database (requires internet)
blastn -query query.fasta -db nt -remote \
  -outfmt "6 qseqid sseqid pident length stitle" \
  -max_target_seqs 5

Expected Assembly Quality

Baseline Metrics (from completed assemblies):

N50: 130-142 kb (good contiguity)
Longest contig: 289-347 kb
Total contigs: 1,100-3,100 (normal for bacterial genome from single-end reads)
Total length: 4.85-5.0 Mb

Quality Indicators:

Genome size matches S. enterica reference (4.6-4.9 Mb): ✓
N50 > 100 kb: ✓ Good
Longest contig > 200 kb: ✓ Very good
Contig count < 5,000: ✓ Acceptable for single-end data

Critical Safety Context

⚠️ BSL-2 Pathogen: All samples are Salmonella enterica - a human pathogen causing food poisoning. When discussing or working with these sequences:

Reference biosafety level 2 (BSL-2) requirements
Mention proper lab safety if discussing live cultures
Note that this is a reportable organism in many jurisdictions

Data Handling

Git Strategy:

Tracked: Documentation (.md), scripts (.py), small results (<1 MB)
Ignored: Raw FASTQ (5.3 GB), assembly outputs (392 MB), logs, intermediate files

Why: Enables version control of analysis workflow while avoiding GitHub size limits. Raw data stored separately on institutional/cloud storage.

Common Analysis Tasks

Troubleshoot Failed Assembly

# Check SPAdes log for errors
less assembly_results/sample_assembly/spades.log

# Verify input file integrity
gzip -t BCL_Convert_*/sample_*.fastq.gz

# Check disk space (assemblies need ~2-5 GB per sample)
df -h

Add New Sample

Place FASTQ in BCL_Convert_*/ directory
Run SPAdes with --isolate flag (same pattern as existing samples)
Add sample to assembly_dirs list in get_assembly_stats.py (line 5-11)
Re-run statistics script

Downstream Analysis Suggestions

Annotation: Use Prokka for gene prediction
Resistance genes: Screen with AMRFinderPlus or CARD
Virulence factors: Query against VFDB database
Serotyping: Confirm with SISTR or SeqSero2
Quality assessment: Run QUAST or CheckM

SPAdes Output Files

Primary outputs (in each assembly_results/*/ directory):

contigs.fasta: Main result - assembled contigs (use this for downstream analysis)
scaffolds.fasta: Scaffolded sequences (contigs linked by gaps)
spades.log: Detailed assembly log (check if assembly fails)

Supporting files:

assembly_graph.fastg: Assembly graph for visualization
assembly_graph_after_simplification.gfa: Simplified graph (GFA format)
K21/, K33/, K55/: k-mer specific intermediate results
tmp/: Temporary files (can delete to save space)

Assembly Statistics Script Details

get_assembly_stats.py parses contigs.fasta files and calculates:

N50: Metric for assembly contiguity (50% of bases in contigs ≥ this length)
Longest contig: Maximum single contig length
Mean contig length: Average across all contigs

Modify for new samples: Update assembly_dirs list (lines 5-11) with new sample paths.

Notes on Single-End vs Paired-End

This pipeline uses single-end reads only (one file per sample, R1 only). The original data appears to be from a single-end Illumina run, not paired-end.

Implications:

Cannot resolve certain repetitive regions (lower contiguity than paired-end)
More fragmented assemblies (higher contig counts)
Still produces good quality for ~5 Mb bacterial genomes
SPAdes --isolate mode optimizes for this scenario

If paired-end data becomes available, switch to:

spades.py -1 R1.fastq.gz -2 R2.fastq.gz -o output/ --isolate -t 4

Workflow Summary

Download: Samples downloaded from Google Drive (browser automation or gdown)
Extraction: Automated extraction of zip files to ~/Downloads
Assembly: SPAdes v4.2.0 with --isolate mode (up to 5 concurrent processes)
Cleanup: Automatic removal of processed downloads to save disk space
Monitoring: Real-time status updates every 60 seconds
Result: 77 successful assemblies, all Salmonella enterica serovar Senftenberg

Automated Pipeline

The repository includes an automated pipeline for large-scale assembly:

continuous_processor.sh

Runs continuously in the background, performing:

Extract 5 zip files per cycle
Start assemblies (maintains max 5 concurrent SPAdes processes)
Cleanup completed downloads
Cycles every 5 minutes

Usage

# Start continuous processor
nohup ./continuous_processor.sh > processor.log 2>&1 &

# Monitor status (updates every 60 seconds)
./status_monitor_1min.sh

# Process all downloads at once
./process_all_downloads.sh

All 77 samples were processed successfully using this automated approach.


IN our specific folder structure it doesn't work even once.

```tree .
lumina git:(main) ✗ tree .
.
├── ALL_SERIES_ANALYSIS_INDEX.md
├── AMINO_ACID_ANNOTATION_COMPLETE.md
├── AMINO_ACID_ANNOTATION_FINAL_SUMMARY.md
├── ANALYSIS_COMPLETE.txt
├── ANALYSIS_COMPLETE_SUMMARY.md
├── ANALYSIS_STATUS.md
├── ANNOTATED_MUTATIONS_ONLY.csv
├── ANNOTATION_COMPLETE.md
├── ANNOTATION_COMPLETE_READY_FOR_NCBI_MAPPING.md
├── ANNOTATION_CORRECTION_REPORT.md
├── ANNOTATION_FILES_INDEX.md
├── ANNOTATION_FINAL_STATUS.md
├── ANNOTATION_PROJECT_COMPLETION_SUMMARY.md
├── ANNOTATION_RESULTS_SUMMARY.txt
├── ARCHIVE_MANIFEST.md
├── ASSEMBLY_QUALITY_SUMMARY.txt
├── CE_SERIES_ANALYSIS_COMPLETE.md
├── CE_SERIES_ANALYSIS_FINAL.md
├── CE_SERIES_GENE_NAME_STATUS.md
├── CE_SERIES_MUTATION_TABLES_COMPLETE.md
├── CLAUDE.md
├── COMPARISON_FILES_INDEX.md
├── COMPARISON_SUMMARY_D_H_REFERENCE.md
├── COMPLETE_ANALYSIS_SUMMARY.txt
├── COMPLETE_GENE_MAPPING.md
├── COMPREHENSIVE_ASSEMBLY_COMPARISON.md
├── COMPREHENSIVE_C_E_MUTATION_SUMMARY.md
├── COMPREHENSIVE_GENE_ANNOTATION_REPORT.html
├── COMPREHENSIVE_GENE_ANNOTATION_REPORT.md
├── COMPREHENSIVE_PROMOTER_MUTATION_ANALYSIS.csv
├── CREATE_CE_ANALYSIS_SUMMARY.md
├── CSV_FILES_INDEX.md
├── C_0_ANNOTATION_COMPLETE_SUMMARY.md
├── C_0_ANNOTATION_SUMMARY.md
├── C_0_MUTATION_ANALYSIS_COMPLETE.csv
├── C_0_MUTATION_ANALYSIS_SSF.csv
├── C_4_ANNOTATED_MUTATIONS.md
├── C_4_ANNOTATED_NUMBERS.csv
├── C_4_COMPREHENSIVE_MUTATIONS.xlsx
├── C_4_COMPREHENSIVE_MUTATIONS_ANNOTATED.xlsx
├── C_4_DETAILED_MUTATIONS.md
├── C_4_FINAL_ANNOTATED.csv
├── C_4_FOR_NUMBERS.csv
├── C_4_MUTATIONS_DETAILED.md
├── C_4_MUTATIONS_WITH_GENE_NAMES.xlsx
├── C_4_MUTATION_ANALYSIS_COMPLETE.csv
├── C_4_MUTATION_SUMMARY_BLAST_ANNOTATED.csv
├── C_4_MUTATION_SUMMARY_ENRICHED.csv
├── C_4_MUTATION_SUMMARY_TABLE.csv
├── C_4_MUTATION_SUMMARY_TABLE.xlsx
├── C_4_MUTATION_SUMMARY_TABLE_ANNOTATED.csv
├── C_4_MUTATION_SUMMARY_TABLE_COMPREHENSIVE.csv
├── C_4_MUTATION_SUMMARY_TABLE_ENHANCED.csv
├── C_4_MUTATION_SUMMARY_TABLE_FINAL.csv
├── C_4_MUTATION_SUMMARY_TABLE_FINAL.xlsx
├── C_4_MUTATION_SUMMARY_TABLE_FINAL_ANNOTATED.csv
├── C_4_MUTATION_SUMMARY_TABLE_REFERENCE_ANNOTATED.csv
├── C_4_NUMBERS.csv
├── C_4_SNP_GENE_MAPPING.md
├── C_4_UNKNOWN_GENES_REPORT.txt
├── C_4_UNKNOWN_PROTEINS_ANALYSIS.txt
├── C_4_blast_refs.txt
├── C_4_blast_remote.txt
├── C_4_blast_results.txt
├── C_4_blast_sample.faa
├── C_4_gene_annotations.csv
├── C_4_gene_annotations_complete.csv
├── C_E_SERIES_ALL_ANNOTATED_NUMBERS.csv
├── C_E_SERIES_ALL_MUTATIONS.csv
├── C_E_SERIES_ALL_MUTATIONS_ANNOTATED.csv
├── C_E_SERIES_ANALYSIS_COMPLETE.csv
├── C_E_SERIES_COMPLETE_ANNOTATED.csv
├── C_E_SERIES_COMPREHENSIVE_MUTATIONS.xlsx
├── C_E_SERIES_MUTATIONS_COMPLETE.md
├── C_E_SERIES_MUTATIONS_SUMMARY.csv
├── C_SERIES_MUTATION_SUMMARY_TABLE.md
├── DATA_QUALITY_VERIFICATION.md
├── DELIVERABLES_COMPLETE_SUMMARY.md
├── DELIVERY_CHECKLIST.md
├── DELIVERY_MANIFEST.txt
├── DELIVERY_SUMMARY.md
├── DESIGNED_DOCUMENTS_SUMMARY.md
├── DESIGN_PHILOSOPHY_GENE_REPORT.md
├── DHL_ALL_SERIES_MUTATIONS_ANNOTATED.csv
├── DHL_ANALYSIS_INDEX.md
├── DHL_CROSS_SERIES_COMPARISON.md
├── DHL_SERIES_COMPREHENSIVE_SUMMARY.md
├── DHL_SERIES_CROSS_COMPARISON.xlsx
├── DNDS_SELECTION_ANALYSIS.md
├── D_H_LASS_SSF_ASSEMBLY_COMPARISON.md
├── D_SERIES_COMPREHENSIVE_ANALYSIS.xlsx
├── D_SERIES_COMPREHENSIVE_ANALYSIS_FINAL.xlsx
├── D_SERIES_COMPREHENSIVE_ANALYSIS_V2.xlsx
├── D_SERIES_GENES_SUMMARY.csv
├── D_SERIES_GENE_ANNOTATION_REPORT.html
├── D_SERIES_MUTATION_SUMMARY_TABLE.csv
├── D_SERIES_MUTATION_SUMMARY_TABLE.md
├── D_SERIES_STRICT_PROMOTER_ONLY.csv
├── D_SERIES_vs_SSF_ASSEMBLY_COMPARISON.md
├── E1_LA_N2_ANALYSIS_REPORT.md
├── E1_LA_N2_ASSEMBLY_STATISTICS.csv
├── E1_LA_N2_COMPARISON_SUMMARY.csv
├── E1_LA_N2_COMPLETE_MUTATION_ANALYSIS.csv
├── E1_LA_N2_COMPLETE_MUTATION_ANALYSIS_ANNOTATED.csv
├── E1_LA_N2_COMPLETE_MUTATION_ANALYSIS_PROPER.csv
├── E1_LA_N2_vs_REFERENCE_BLAST_COMPARISON.csv
├── E2_2_NONSYNONYMOUS_ANALYSIS_REPORT.md
├── E2_2_REASSEMBLY_SUMMARY.md
├── E2_LA_ALL_SAMPLES_SNP_ANNOTATED.csv
├── E2_LA_ALL_SAMPLES_SNP_SORTED_BY_CONCENTRATION.csv
├── E2_LA_ASSEMBLY_COMPLETE.md
├── E2_LA_DETAILED_FOCUS.png
├── E2_LA_DNDS_RATIOS_BY_SAMPLE.csv
├── E2_LA_ENRICHED_ANNOTATIONS_SUMMARY.md
├── E2_LA_SERIES_ASSEMBLY_SUMMARY.md
├── E2_LA_SNP_ANALYSIS_COMPLETE.md
├── E2_LA_SSF_COMPREHENSIVE_ANALYSIS.png
├── E2_LA_SSF_DETAILED_REPORT.txt
├── ENHANCED_SHEETS_GUIDE.md
├── E_0_ANNOTATED_MUTATIONS.md
├── E_0_ANNOTATED_NUMBERS.csv
├── E_0_COMPREHENSIVE_MUTATIONS.xlsx
├── E_0_COMPREHENSIVE_MUTATIONS_ANNOTATED.xlsx
├── E_0_DETAILED_MUTATIONS.md
├── E_0_FINAL_ANNOTATED.csv
├── E_0_FOR_NUMBERS.csv
├── E_0_MUTATIONS_DETAILED.md
├── E_0_MUTATIONS_WITH_GENE_NAMES.xlsx
├── E_0_MUTATION_ANALYSIS_COMPLETE.csv
├── E_0_MUTATION_SUMMARY_BLAST_ANNOTATED.csv
├── E_0_MUTATION_SUMMARY_ENRICHED.csv
├── E_0_MUTATION_SUMMARY_TABLE.csv
├── E_0_MUTATION_SUMMARY_TABLE.xlsx
├── E_0_MUTATION_SUMMARY_TABLE_ANNOTATED.csv
├── E_0_MUTATION_SUMMARY_TABLE_COMPREHENSIVE.csv
├── E_0_MUTATION_SUMMARY_TABLE_ENHANCED.csv
├── E_0_MUTATION_SUMMARY_TABLE_FINAL.csv
├── E_0_MUTATION_SUMMARY_TABLE_FINAL.xlsx
├── E_0_MUTATION_SUMMARY_TABLE_FINAL_ANNOTATED.csv
├── E_0_MUTATION_SUMMARY_TABLE_REFERENCE_ANNOTATED.csv
├── E_0_NUMBERS.csv
├── E_0_SNP_GENE_MAPPING.md
├── E_0_UNKNOWN_GENES_REPORT.txt
├── E_0_blast_refs.txt
├── E_0_gene_annotations.csv
├── E_0_gene_annotations_complete.csv
├── E_2_ANNOTATED_MUTATIONS.md
├── E_2_ANNOTATED_NUMBERS.csv
├── E_2_COMPREHENSIVE_MUTATIONS.xlsx
├── E_2_COMPREHENSIVE_MUTATIONS_ANNOTATED.xlsx
├── E_2_DETAILED_MUTATIONS.md
├── E_2_FINAL_ANNOTATED.csv
├── E_2_FOR_NUMBERS.csv
├── E_2_MUTATIONS_DETAILED.md
├── E_2_MUTATIONS_WITH_GENE_NAMES.xlsx
├── E_2_MUTATION_ANALYSIS_COMPLETE.csv
├── E_2_MUTATION_SUMMARY_BLAST_ANNOTATED.csv
├── E_2_MUTATION_SUMMARY_ENRICHED.csv
├── E_2_MUTATION_SUMMARY_TABLE.csv
├── E_2_MUTATION_SUMMARY_TABLE.xlsx
├── E_2_MUTATION_SUMMARY_TABLE_ANNOTATED.csv
├── E_2_MUTATION_SUMMARY_TABLE_COMPREHENSIVE.csv
├── E_2_MUTATION_SUMMARY_TABLE_ENHANCED.csv
├── E_2_MUTATION_SUMMARY_TABLE_FINAL.csv
├── E_2_MUTATION_SUMMARY_TABLE_FINAL.xlsx
├── E_2_MUTATION_SUMMARY_TABLE_FINAL_ANNOTATED.csv
├── E_2_MUTATION_SUMMARY_TABLE_REFERENCE_ANNOTATED.csv
├── E_2_NUMBERS.csv
├── E_2_SNP_GENE_MAPPING.md
├── E_2_UNKNOWN_GENES_REPORT.txt
├── E_2_UNKNOWN_PROTEINS_ANALYSIS.txt
├── E_2_blast_refs.txt
├── E_2_blast_remote.txt
├── E_2_blast_results.txt
├── E_2_blast_sample.faa
├── E_2_gene_annotations.csv
├── E_2_gene_annotations_complete.csv
├── E_4_ANNOTATED_MUTATIONS.md
├── E_4_ANNOTATED_NUMBERS.csv
├── E_4_COMPREHENSIVE_MUTATIONS.xlsx
├── E_4_COMPREHENSIVE_MUTATIONS_ANNOTATED.xlsx
├── E_4_DETAILED_MUTATIONS.md
├── E_4_FINAL_ANNOTATED.csv
├── E_4_FOR_NUMBERS.csv
├── E_4_MUTATIONS_DETAILED.md
├── E_4_MUTATIONS_WITH_GENE_NAMES.xlsx
├── E_4_MUTATION_ANALYSIS_COMPLETE.csv
├── E_4_MUTATION_SUMMARY_BLAST_ANNOTATED.csv
├── E_4_MUTATION_SUMMARY_ENRICHED.csv
├── E_4_MUTATION_SUMMARY_TABLE.csv
├── E_4_MUTATION_SUMMARY_TABLE.xlsx
├── E_4_MUTATION_SUMMARY_TABLE_ANNOTATED.csv
├── E_4_MUTATION_SUMMARY_TABLE_COMPREHENSIVE.csv
├── E_4_MUTATION_SUMMARY_TABLE_ENHANCED.csv
├── E_4_MUTATION_SUMMARY_TABLE_FINAL.csv
├── E_4_MUTATION_SUMMARY_TABLE_FINAL.xlsx
├── E_4_MUTATION_SUMMARY_TABLE_FINAL_ANNOTATED.csv
├── E_4_MUTATION_SUMMARY_TABLE_REFERENCE_ANNOTATED.csv
├── E_4_NUMBERS.csv
├── E_4_SNP_GENE_MAPPING.md
├── E_4_blast_refs.txt
├── E_4_blast_remote.txt
├── E_4_blast_results.txt
├── E_4_blast_sample.faa
├── E_4_gene_annotations.csv
├── E_4_gene_annotations_complete.csv
├── E_SERIES_MUTATION_SUMMARY_TABLE.md
├── FILES_ANNOTATION_COMPLETE.md
├── FILES_OPENED_SUMMARY.txt
├── FILE_MANIFEST.txt
├── FILE_NAVIGATION_INDEX.md
├── FINAL_ANALYSIS_REPORT.md
├── FINAL_ANNOTATION_REPORT.md
├── FINAL_COMPARISON_SUMMARY.txt
├── FINAL_CROSS_SERIES_SUMMARY.md
├── FINAL_DELIVERY_SUMMARY.txt
├── FINAL_DHL_ANNOTATED_SUMMARY.md
├── FINAL_FILES_REFERENCE.md
├── FINAL_GENE_IDENTIFICATIONS.csv
├── FINAL_GENE_NAMES_IDENTIFIED.md
├── GENE_6_1_IDENTIFICATION_ATTEMPT.md
├── GENE_6_1_NCBI_IDENTIFICATION_REPORT.md
├── GENE_ANNOTATION_ANALYSIS_GAP.md
├── GENE_ANNOTATION_COMPLETE.md
├── GENE_ANNOTATION_INDEX.md
├── GENE_ANNOTATION_ISSUE_RESOLVED.md
├── GENE_ANNOTATION_STATUS_UPDATE.md
├── GENE_ANNOTATION_SUMMARY.md
├── GENE_ID_INFERRED_MAPPING.csv
├── GENE_NAMES_SUMMARY.md
├── GIT_REPOSITORY_INFO.md
├── Gany
│   ├── ANALYSIS_COMPLETION_REPORT.txt
│   ├── ANALYSIS_SUMMARY.md
│   ├── B_SERIES_MUTATION_SUMMARY_TABLE.csv
│   ├── C_E_SERIES_ANALYSIS_COMPLETE 3.numbers
│   ├── C_E_SERIES_ANALYSIS_COMPLETE.csv
│   ├── C_E_SERIES_ANALYSIS_COMPLETE_gany.csv
│   ├── DESIGN_PHILOSOPHY.md
│   ├── D_SERIES_MUTATION_SUMMARY_TABLE.csv
│   ├── D_SERIES_STRICT_PROMOTER_ONLY.csv
│   ├── E1_LA_N2_1_SSF_L1-ds.961fb1b06a534a73a3801df9715796c9
│   ├── E1_LA_N2_ANALYSIS_REPORT.md
│   ├── E1_LA_N2_ASSEMBLY_STATISTICS.csv
│   ├── E1_LA_N2_COMPARISON_SUMMARY.csv
│   ├── E1_LA_N2_COMPLETE_MUTATION_ANALYSIS.csv
│   ├── E2_2_16_L1-ds.b7dfc6d0a5a843f59c580539a235a13d 2
│   ├── E2_2_ANNOTATION_SUMMARY.md
│   ├── E2_2_DELIVERABLES.txt
│   ├── E2_2_E2_2_00625_UNIQUE_MUTATIONS.csv
│   ├── E2_2_E2_2_0125_UNIQUE_MUTATIONS.csv
│   ├── E2_2_E2_2_16_UNIQUE_MUTATIONS.csv
│   ├── E2_2_E2_2_2_UNIQUE_MUTATIONS.csv
│   ├── E2_2_E2_2_4_UNIQUE_MUTATIONS.csv
│   ├── E2_2_E2_2_8_UNIQUE_MUTATIONS.csv
│   ├── E2_2_FILTERED_HIGH_CONFIDENCE.csv
│   ├── E2_2_INTER_SAMPLE_COMPARISON.csv
│   ├── E2_2_MUTATED_GENES_PER_SAMPLE.csv
│   ├── E2_2_NONSYNONYMOUS_ANALYSIS_REPORT.md
│   ├── E2_2_PROJECT_COMPLETION_SUMMARY.txt
│   ├── E2_2_QUICK_SUMMARY.txt
│   ├── E2_2_REASSEMBLY_COMPLETE.csv
│   ├── E2_2_REASSEMBLY_SUMMARY.md
│   ├── E2_2_SAMPLE_DNDS_ONLY.csv
│   ├── E2_2_vs_SSF_CONCENTRATION_DEPENDENT.csv
│   ├── E2_2_vs_SSF_NONSYNONYMOUS_ONLY.csv
│   ├── E2_2_vs_SSF_WITH_CORRECT_SAMPLE_DNDS.csv
│   ├── E2_2_vs_SSF_WITH_GENE_LABELS.csv
│   ├── E2_2_vs_SSF_WITH_GENE_NAMES.csv
│   ├── E2_2_vs_SSF_WITH_SAMPLE_DNDS.csv
│   ├── E2_LA_1_SSF_2_L1-ds.46cd19f868c442cbbaf96435561f476e 2
│   ├── E2_LA_ALL_SAMPLES_SNP_ANNOTATED.csv
│   ├── E2_LA_ALL_SAMPLES_SNP_SORTED_BY_CONCENTRATION.csv
│   ├── E2_LA_ALL_SAMPLES_SNP_WITH_GENE_NAMES.csv
│   ├── E2_LA_WITH_REAL_GENE_NAMES.csv
│   ├── E2_LA_WITH_REAL_GENE_NAMES.xlsx
│   ├── H_SERIES_MUTATION_SUMMARY_TABLE (1).csv
│   ├── H_SERIES_MUTATION_SUMMARY_TABLE.csv
│   ├── H_SERIES_STRICT_PROMOTER_ONLY.csv
│   ├── INDEX_ALL_INTERGENIC_ANALYSIS_FILES.md
│   ├── INTERGENIC_ANALYSIS_SUMMARY.txt
│   ├── README_E2_2_ANALYSIS.txt
│   ├── README_INTERGENIC_ANALYSIS.md
│   ├── SSF_ASSEMBLY_STATISTICS.csv
│   ├── SSF_REASSEMBLY_SUMMARY.md
│   ├── STM_LB_0_july_ANALYSIS_REPORT.md
│   ├── STM_LB_0_july_vs_ASSAF_COMPARISON.csv
│   ├── STM_LB_0_july_vs_ASSAF_COMPARISON_FILTERED.csv
│   ├── STM_LB_ANALYSIS_FILES_SUMMARY.md
│   ├── STM_LB_ANNOTATED_VARIANTS.csv
│   ├── STM_LB_ANNOTATED_WITH_FULL_NAMES.csv
│   ├── STM_LB_ANNOTATED_WITH_PROMOTER_ANALYSIS.xlsx
│   ├── STM_LB_COMPLETE_MUTATION_ANALYSIS.csv
│   ├── STM_LB_COMPLETE_MUTATION_INVENTORY.csv
│   ├── STM_LB_COMPREHENSIVE_ANALYSIS.csv
│   ├── STM_LB_COMPREHENSIVE_COMPARISON_REPORT.md
│   ├── STM_LB_CORRECTED_ANALYSIS_REPORT.md
│   ├── STM_LB_CORRECTED_VARIANT_ANNOTATION.csv
│   ├── STM_LB_FINAL_VARIANT_ANNOTATION.csv
│   ├── STM_LB_GENE_ANNOTATION_REFERENCE.csv
│   ├── STM_LB_INTERGENIC_ANALYSIS_COMPLETE_REPORT.md
│   ├── STM_LB_INTERGENIC_ANALYSIS_FINDINGS_AND_INSIGHTS.md
│   ├── STM_LB_INTERGENIC_COMPLETE_ANALYSIS.csv
│   ├── STM_LB_INTERGENIC_DISTRIBUTION_SUMMARY.csv
│   ├── STM_LB_INTERGENIC_MUTATION_DISTRIBUTION_CLARIFICATION.md
│   ├── STM_LB_INTERGENIC_PROMOTER_ANALYSIS.csv
│   ├── STM_LB_INTERGENIC_PROMOTER_ANALYSIS_ANNOTATED.csv
│   ├── STM_LB_INTERGENIC_PROMOTER_ANALYSIS_COMPLETE.xlsx
│   ├── STM_LB_INTERGENIC_PROMOTER_ANALYSIS_FINAL.csv
│   ├── STM_LB_INTERGENIC_PROMOTER_REPORT.md
│   ├── STM_LB_MUTATED_GENES_ANNOTATION.csv
│   ├── STM_LB_POSITION_COMPARISON_MATRIX.csv
│   ├── STM_LB_SAMPLE_COMPARISON_SUMMARY.csv
│   ├── STM_LB_SERIES_ANALYSIS_REPORT.md
│   ├── STM_LB_SERIES_ANALYSIS_SUMMARY.csv
│   ├── STM_LB_STM1_LB_00625_VARIANTS.csv
│   ├── STM_LB_STM1_LB_0125_VARIANTS.csv
│   ├── STM_LB_STM1_LB_025_VARIANTS.csv
│   ├── STM_LB_STM1_LB_05_VARIANTS.csv
│   ├── STM_LB_STM1_LB_1_VARIANTS.csv
│   ├── STM_LB_STM1_LB_2_VARIANTS.csv
│   ├── Salmonella_Genomic_Analysis_Complete
│   │   ├── ANALYSIS_SUMMARY.md
│   │   ├── B_SERIES_MUTATION_SUMMARY_TABLE.csv
│   │   ├── DESIGN_PHILOSOPHY.md
│   │   ├── D_SERIES_MUTATION_SUMMARY_TABLE.csv
│   │   ├── D_SERIES_STRICT_PROMOTER_ONLY.csv
│   │   ├── H_SERIES_MUTATION_SUMMARY_TABLE.csv
│   │   ├── H_SERIES_STRICT_PROMOTER_ONLY.csv
│   │   └── README.md
│   ├── Salmonella_Mutation_Data.zip
│   └── WHY_0.5-2.0_mM_SAMPLES_APPEAR_MISSING.md
├── H_SERIES_COMPREHENSIVE_ANALYSIS.xlsx
├── H_SERIES_COMPREHENSIVE_ANALYSIS_FINAL.xlsx
├── H_SERIES_COMPREHENSIVE_ANALYSIS_V2.xlsx
├── H_SERIES_GENES_SUMMARY.csv
├── H_SERIES_GENE_ANNOTATION_REPORT.html
├── H_SERIES_MUTATION_SUMMARY_TABLE.csv
├── H_SERIES_MUTATION_SUMMARY_TABLE.md
├── H_SERIES_STRICT_PROMOTER_ONLY.csv
├── H_SERIES_vs_SSF_ASSEMBLY_COMPARISON.md
├── H_series_analysis
│   ├── H_0_prokka
│   │   └── H_0.log
│   ├── H_0_vs_SSF_L1.1delta
│   ├── H_0_vs_SSF_L1.coords
│   ├── H_0_vs_SSF_L1.delta
│   ├── H_0_vs_SSF_L1.snps
│   ├── H_16_prokka
│   │   └── H_16.log
│   ├── H_16_vs_SSF_L1.1delta
│   ├── H_16_vs_SSF_L1.coords
│   ├── H_16_vs_SSF_L1.delta
│   ├── H_16_vs_SSF_L1.snps
│   ├── H_1_prokka
│   │   └── H_1.log
│   ├── H_1_vs_SSF_L1.1delta
│   ├── H_1_vs_SSF_L1.coords
│   ├── H_1_vs_SSF_L1.delta
│   ├── H_1_vs_SSF_L1.snps
│   ├── H_4_a_prokka
│   │   └── H_4_a.log
│   ├── H_4_a_vs_SSF_L1.1delta
│   ├── H_4_a_vs_SSF_L1.coords
│   ├── H_4_a_vs_SSF_L1.delta
│   ├── H_4_a_vs_SSF_L1.snps
│   ├── H_ALL_MUTATIONS_DETAILED.csv
│   ├── H_COMPREHENSIVE_ANALYSIS.md
│   ├── H_DETAILED_MUTATION_BREAKDOWN.md
│   ├── H_ENHANCED_ANALYSIS.md
│   ├── H_GENE_DNDS.csv
│   ├── H_INTERGENIC_ANNOTATED.csv
│   ├── H_SERIES_ALL_MUTATIONS_ANNOTATED.csv
│   ├── H_SERIES_ALL_MUTATIONS_ANNOTATED_WITH_GENE_NAMES.csv
│   ├── H_SERIES_ANALYSIS_COMPLETE.md
│   ├── H_SERIES_COMPREHENSIVE_SUMMARY.xlsx
│   ├── H_SERIES_MUTATION_FIGURE.pdf
│   ├── H_SERIES_MUTATION_SUMMARY_FIGURE.pdf
│   └── H_SERIES_SUMMARY.md
├── INTERGENIC_MUTATIONS_FOR_PROMOTER_ANALYSIS.csv
├── INTERGENIC_MUTATIONS_MAPPED_TO_GENES.csv
├── LATEST_STATUS_UPDATE.txt
├── ORGANISM_IDENTIFICATION.md
├── PROCESSING_STATUS.md
├── PROMOTER_ANALYSIS_COMPLETE_SUMMARY.md
├── PROMOTER_ANALYSIS_SUMMARY.txt
├── PROMOTER_ENRICHMENT_SUMMARY.txt
├── PROMOTER_GENES_FUNCTION_REFERENCE.txt
├── PROMOTER_GENES_SUMMARY_TABLE.csv
├── PROMOTER_MUTATIONS_BY_CATEGORY.csv
├── PROMOTER_MUTATIONS_BY_LOCATION.csv
├── PROMOTER_MUTATIONS_D_SERIES.csv
├── PROMOTER_MUTATIONS_H_SERIES.csv
├── PROMOTER_MUTATIONS_SERIES_COMPARISON.csv
├── PROMOTER_MUTATIONS_SUMMARY_TABLE.csv
├── PROMOTER_MUTATIONS_WITH_GENE_INFO.csv
├── PROMOTER_MUTATION_ANALYSIS.txt
├── PROMOTER_TO_GENE_MAPPING_GUIDE.md
├── QUICK_REFERENCE_CARD.txt
├── QUICK_REFERENCE_LASS_vs_SSF.txt
├── QUICK_START.md
├── QUICK_START_CHECKLIST.md
├── README.md
├── README_ANALYSIS.md
├── README_ANALYSIS_FILES.md
├── READY_FOR_DELIVERY.txt
├── REFERENCE_GENOME_MAPPING_RESULTS.txt
├── SEND_THESE_FILES_TO_OWNER.txt
├── SERIES_ANALYSIS_PLAN.md
├── SERIES_ANALYSIS_README.md
├── SERIES_COMPARISON_SUMMARY.md
├── SESSION_SUMMARY.md
├── SESSION_SUMMARY_COMPREHENSIVE.md
├── SSF_ASSEMBLY_STATISTICS.csv
├── SSF_COMPARISON_SUMMARY.csv
├── SSF_COMPLETE_MUTATION_ANALYSIS (1).csv
├── SSF_COMPLETE_MUTATION_ANALYSIS.csv
├── SSF_GENES_BY_EMS_CONCENTRATION.csv
├── SSF_GENES_PER_SAMPLE_CONCENTRATION.csv
├── SSF_GENES_WITH_MUTATIONS_BY_SAMPLE.csv
├── SSF_JYN29_GENE_ANALYSIS.png
├── SSF_SNP_ALIGNMENT_READY.csv
├── SSF_STM_COMPREHENSIVE_REPORT.txt
├── SSF_STM_GENE_ANALYSIS.png
├── SSF_WGS_YESNO_CHECKED (1).xlsx
├── SSF_WGS_YESNO_CHECKED (2).xlsx
├── SSF_WGS_YESNO_CHECKED.xlsx
├── SSF_vs_REFERENCE_ACTUAL_SNPS.csv
├── SSF_vs_REFERENCE_BLAST_COMPARISON.csv
├── SSF_vs_REFERENCE_COMPARISON.md
├── SSF_vs_REFERENCE_DETAILED_COMPARISON.csv
├── SSF_vs_REFERENCE_FINAL_COMPARISON.csv
├── SSF_vs_REFERENCE_MUTATION_SUMMARY.csv
├── START_HERE_ANNOTATION_STATUS.md
├── START_HERE_COMPLETE_ANALYSIS.md
├── START_HERE_GENE_ANNOTATION.md
├── START_HERE_SESSION_SUMMARY.md
├── STM_ALL_LINEAGES_CONSOLIDATED_DNDS.csv
├── STM_ALL_LINEAGES_DNDS_CORRECT.csv
├── STM_ALL_LINEAGES_DNDS_PER_SAMPLE.csv
├── STM_ALL_LINEAGES_PER_SAMPLE_DNDS.csv
├── STM_ALL_LINEAGES_POOLED_DNDS.csv
├── STM_ALL_SAMPLES_DNDS_WITH_CI.csv
├── STM_E1_LA_DNDS_ANALYSIS.csv
├── STM_E1_LA_DNDS_BY_GENE.csv
├── STM_E1_LA_DNDS_CORRECT.csv
├── STM_E1_LA_DNDS_PER_GENE.csv
├── STM_E1_LA_DNDS_PER_SAMPLE.csv
├── STM_E1_LA_DNDS_PER_SAMPLE_CORRECTED.csv
├── STM_E1_LA_DNDS_WITH_CI.csv
├── STM_E1_LA_vs_STM_LB_COMPARISON.csv
├── STM_E1_LA_vs_STM_LB_DETAILED_COMPARISON.csv
├── STM_E1_LA_vs_STM_LB_ENHANCED.csv
├── STM_E1_LA_vs_STM_LB_FULLY_ANNOTATED.csv
├── STM_LB_0_july_ANALYSIS_REPORT.md
├── STM_LB_0_july_DNDS_CORRECT.csv
├── STM_LB_0_july_DNDS_PER_SAMPLE.csv
├── STM_LB_0_july_DNDS_WITH_CI.csv
├── STM_LB_0_july_genes.gbk
├── STM_LB_0_july_genes.gff
├── STM_LB_0_july_vs_ASSAF_COMPARISON.csv
├── STM_LB_0_july_vs_ASSAF_COMPARISON_FILTERED.csv
├── STM_LB_COMPREHENSIVE_ANALYSIS.csv
├── STM_LB_COMPREHENSIVE_COMPARISON_REPORT.md
├── STM_LB_COMPREHENSIVE_VARIANT_ANALYSIS.csv
├── STM_LB_DETAILED_VARIANT_ANNOTATION.csv
├── STM_LB_DNDS_ANALYSIS.csv
├── STM_LB_DNDS_BY_GENE.csv
├── STM_LB_DNDS_CORRECT.csv
├── STM_LB_DNDS_FROM_COMPLETE_ANALYSIS.csv
├── STM_LB_DNDS_PER_GENE.csv
├── STM_LB_DNDS_PER_SAMPLE.csv
├── STM_LB_DNDS_PER_SAMPLE_CORRECTED.csv
├── STM_LB_DNDS_WITH_CI.csv
├── STM_LB_FINAL_DETAILED_ANALYSIS.csv
├── STM_LB_JULY_ASSEMBLY_SUMMARY.txt
├── STM_LB_JULY_COMPLETE_ASSEMBLY_SUMMARY.txt
├── STM_LB_JULY_MUTATION_ANALYSIS_REPORT.md
├── STM_LB_JULY_MUTATION_COMPREHENSIVE.csv
├── STM_LB_JULY_MUTATION_COMPREHENSIVE_WITH_NAMES.csv
├── STM_LB_JULY_VARIANT_ANALYSIS_SUMMARY.txt
├── STM_LB_MUTATION_ANALYSIS_FINAL_REPORT.txt
├── STM_LB_POSITION_COMPARISON_MATRIX.csv
├── STM_LB_PROMOTER_BOX_CLASSIFICATION.csv
├── STM_LB_REFINED_PROMOTER_ANALYSIS.csv
├── STM_LB_SAMPLE_COMPARISON_SUMMARY.csv
├── STM_LB_SERIES_ANALYSIS_REPORT.md
├── STM_LB_SERIES_ANALYSIS_SUMMARY.csv
├── STM_LB_STM1_LB_00625_VARIANTS.csv
├── STM_LB_STM1_LB_0125_VARIANTS.csv
├── STM_LB_STM1_LB_025_VARIANTS.csv
├── STM_LB_STM1_LB_05_VARIANTS.csv
├── STM_LB_STM1_LB_1_VARIANTS.csv
├── STM_LB_STM1_LB_2_VARIANTS.csv
├── STM_LB_VARIANT_SUMMARY_BY_SAMPLE.csv
├── STM_LB_emailJULY_MUTATION_COMPREHENSIVE.csv
├── STM_LB_email_JULY_FINAL.csv
├── STM_LINEAGES_DNDS_COMBINED.csv
├── STM_LINEAGES_DNDS_PER_SAMPLE.csv
├── STM_WGS_YESno (1).xlsx
├── STM_WGS_YESno (2).xlsx
├── STM_WGS_YESno.xlsx
├── WINDOWS_EXTRACTION_GUIDE.md
├── WORK_COMPLETED_SUMMARY.txt
├── add_dnds_to_summary.py
├── add_gene_labels.py
├── add_gene_names_embl.py
├── add_intergenic_flanking_genes.py
├── add_intergenic_with_real_names.py
├── add_more_gene_names.py
├── add_per_sample_dnds.py
├── add_synonymy_and_names.py
├── add_synonymy_final.py
├── advanced_annotation.py
├── advanced_blast_annotation.py
├── analyze_b_series_complete.sh
├── analyze_convergent_mutations.py
├── analyze_g_series_complete.sh
├── analyze_intergenic_and_dnds.py
├── analyze_promoter_mutations.py
├── analyze_series.sh
├── annotate_STM_E1_LA.py
├── annotate_STM_E1_LA_v2.py
├── annotate_ce_series_complete.py
├── annotate_ce_series_with_blast.py
├── annotate_dhl_mutations.py
├── annotate_e2_2.sh
├── annotate_from_reference.py
├── annotate_g_mutations_fast.py
├── annotate_genes_blast.py
├── annotate_remaining_genes_blast.py
├── annotate_remaining_mutations.py
├── annotate_unknown_with_features.py
├── annotate_using_reference_mapping.py
├── annotate_variants_with_blast.py
├── annotate_with_blast_ncbi.py
├── apply_gene_name_mappings.py
├── apply_gene_names_to_dhl.py
├── b_series_monitor.log
├── blast_annotate_gene_names.sh
├── blast_annotate_genes.py
├── blast_results.txt
├── browser_download_helper.py
├── calculate_dnds_per_strain.py
├── calculate_g_dnds.py
├── calculate_proper_dnds.py
├── calculate_synonymy_corrected.py
├── check_b_series_download.sh
├── clean_gene_names.py
├── clean_unknown_genes.py
├── cleanup_completed.sh
├── compare_b_series.sh
├── compare_b_series_CORRECTED.sh
├── compare_b_series_test.sh
├── comprehensive_annotation.py
├── consolidate_enriched_annotations.py
├── continuous_processor.sh
├── convert_to_csv.py
├── correct_amino_acid_changes.py
├── correct_c0_dnds_final.py
├── correct_c0_dnds_ratio.py
├── correct_c0_dnds_v2.py
├── create_b_series_comprehensive_analysis.py
├── create_ce_formatted_tables.py
├── create_ce_mutation_reports.py
├── create_comprehensive_gene_map.py
├── create_comprehensive_promoter_csv.py
├── create_csv_for_numbers.py
├── create_d_mutation_summary_figure.py
├── create_d_series_comprehensive.py
├── create_detailed_mutation_table.py
├── create_dhl_comprehensive_summary.py
├── create_dhl_excel_comprehensive.py
├── create_enhanced_series_analysis.py
├── create_excel_summary.py
├── create_final_annotated_series.py
├── create_final_comprehensive_table.py
├── create_final_excel_with_real_names.py
├── create_g_excel_summary.py
├── create_g_mutation_summary_figure.py
├── create_g_summary_table.py
├── create_gene_annotated_csvs.py
├── create_h_mutation_summary_figure.py
├── create_h_series_comprehensive.py
├── create_mutation_summary_figure.py
├── create_mutation_summary_figure_fixed.py
├── create_mutation_summary_table.py
├── create_promoter_visualization.py
├── create_proper_d_h_tables.py
├── create_salmonella_db.py
├── create_salmonella_gene_database.py
├── create_series_summaries.py
├── create_series_summary.py
├── create_strain_analysis_figures.py
├── create_visual_mutation_table.py
├── csv_reports
│   ├── ANNOTATION_STATUS_GUIDE.md
│   ├── ASSEMBLY_QUALITY_COMPARISON.csv
│   ├── B_SERIES_NAMED_GENES_REFERENCE.csv
│   ├── D_SERIES_ALL_MUTATIONS_DETAIL.csv
│   ├── D_SERIES_ANALYSIS_SUMMARY.csv
│   ├── D_SERIES_COMPLETE_MUTATIONS_WITH_GENES.csv
│   ├── D_SERIES_DNDS_ANNOTATED.csv
│   ├── D_SERIES_DNDS_BY_GENE.csv
│   ├── D_SERIES_FINAL_WITH_GENE_NAMES.csv
│   ├── D_SERIES_FINAL_WITH_GENE_NAMES_UPDATED.csv
│   ├── D_SERIES_GENES_IDENTIFIED.csv
│   ├── D_SERIES_GENE_ANNOTATIONS.csv
│   ├── D_SERIES_GENE_SUMMARY.csv
│   ├── D_SERIES_HYPOTHETICAL_PROTEINS.csv
│   ├── D_SERIES_INTERGENIC_MUTATIONS.csv
│   ├── D_SERIES_MUTATIONS_ANNOTATED.csv
│   ├── D_SERIES_MUTATIONS_FULLY_ANNOTATED.csv
│   ├── D_SERIES_MUTATIONS_WITH_DNDS.csv
│   ├── D_SERIES_SAMPLE_METRICS.csv
│   ├── D_SERIES_TOP20_GENES.csv
│   ├── D_SERIES_WITH_GENE_NAMES.csv
│   ├── D_vs_H_GENE_COMPARISON.csv
│   ├── GENE_ID_COMPREHENSIVE_ANNOTATION.csv
│   ├── GENE_NAMES_CURATED_MAPPING.csv
│   ├── GENE_NAMES_SUMMARY.csv
│   ├── H_CONVERGENT_EVOLUTION_ANALYSIS.csv
│   ├── H_SERIES_ALL_MUTATIONS_DETAIL.csv
│   ├── H_SERIES_ANALYSIS_SUMMARY.csv
│   ├── H_SERIES_COMPLETE_MUTATIONS_WITH_GENES.csv
│   ├── H_SERIES_DNDS_ANNOTATED.csv
│   ├── H_SERIES_DNDS_BY_GENE.csv
│   ├── H_SERIES_FINAL_WITH_GENE_NAMES.csv
│   ├── H_SERIES_FINAL_WITH_GENE_NAMES_UPDATED.csv
│   ├── H_SERIES_GENES_IDENTIFIED.csv
│   ├── H_SERIES_GENE_ANNOTATIONS.csv
│   ├── H_SERIES_GENE_SUMMARY.csv
│   ├── H_SERIES_HYPOTHETICAL_PROTEINS.csv
│   ├── H_SERIES_INTERGENIC_MUTATIONS.csv
│   ├── H_SERIES_MUTATIONS_ANNOTATED.csv
│   ├── H_SERIES_MUTATIONS_FULLY_ANNOTATED.csv
│   ├── H_SERIES_MUTATIONS_WITH_DNDS.csv
│   ├── H_SERIES_SAMPLE_METRICS.csv
│   ├── H_SERIES_TOP20_GENES.csv
│   ├── H_SERIES_WITH_GENE_NAMES.csv
│   ├── MUTATION_STATISTICS_COMPARISON.csv
│   └── QUICK_REFERENCE_SUMMARY.csv
├── debug_amino_acids.py
├── debug_codon_extraction.py
├── download_log.txt
├── download_reference_genes.py
├── download_samples_individually.sh
├── e2_2_comprehensive_snp_analysis.py
├── e2la_16_careful.log
├── e2la_blast_results.txt
├── e2la_local_blast_results.txt
├── e2la_samples.txt
├── e2la_snp_analysis
│   ├── E2_LA_16_SNP_ANALYSIS.csv
│   ├── E2_LA_16_SNP_ANNOTATED.csv
│   ├── E2_LA_16_SNPs.txt
│   ├── E2_LA_16_vs_SSF.delta
│   ├── E2_LA_1_SSF_0125_SNP_ANALYSIS.csv
│   ├── E2_LA_1_SSF_0125_SNP_ANNOTATED.csv
│   ├── E2_LA_1_SSF_0125_SNPs.txt
│   ├── E2_LA_1_SSF_0125_vs_SSF.delta
│   ├── E2_LA_ALL_SAMPLES_SNP_ANNOTATED.csv
│   ├── E2_LA_ALL_SAMPLES_SNP_SORTED_BY_CONCENTRATION.csv
│   ├── E2_LA_N1_00625_SSF_SNP_ANALYSIS.csv
│   ├── E2_LA_N1_00625_SSF_SNP_ANNOTATED.csv
│   ├── E2_LA_N1_00625_SSF_SNPs.txt
│   ├── E2_LA_N1_00625_SSF_vs_SSF.delta
│   ├── E2_SSF_LA_1_05_a_SNP_ANALYSIS.csv
│   ├── E2_SSF_LA_1_05_a_SNP_ANNOTATED.csv
│   ├── E2_SSF_LA_1_05_a_SNPs.txt
│   ├── E2_SSF_LA_1_05_a_vs_SSF.delta
│   ├── E2_SSF_LA_1_05_b_SNP_ANALYSIS.csv
│   ├── E2_SSF_LA_1_05_b_SNP_ANNOTATED.csv
│   ├── E2_SSF_LA_1_05_b_SNPs.txt
│   ├── E2_SSF_LA_1_05_b_vs_SSF.delta
│   ├── E2_SSF_LA_1_2_SNP_ANALYSIS.csv
│   ├── E2_SSF_LA_1_2_SNP_ANNOTATED.csv
│   ├── E2_SSF_LA_1_2_SNPs.txt
│   ├── E2_SSF_LA_1_2_vs_SSF.delta
│   ├── E2_SSF_LA_1_4_SNP_ANALYSIS.csv
│   ├── E2_SSF_LA_1_4_SNP_ANNOTATED.csv
│   ├── E2_SSF_LA_1_4_SNPs.txt
│   ├── E2_SSF_LA_1_4_vs_SSF.delta
│   ├── E2_SSF_LA_1_8_SNP_ANALYSIS.csv
│   ├── E2_SSF_LA_1_8_SNP_ANNOTATED.csv
│   ├── E2_SSF_LA_1_8_SNPs.txt
│   ├── E2_SSF_LA_1_8_vs_SSF.delta
│   └── README_SNP_ANNOTATION.md
├── e2la_snp_calling_fixed.log
├── e2la_snp_calling_fixed2.log
├── e2la_snp_calling_pipeline.py
├── e2la_snp_pipeline.log
├── e2la_variant_annotation.log
├── e2la_variant_annotation.py
├── e2la_variant_annotation_CORRECTED.py
├── e2la_variant_annotation_FIXED.py
├── enhance_gene_name_with_aa_change.py
├── enhance_master_with_dnds.py
├── enhance_mutation_classification.py
├── enhance_with_blast_gene_names.py
├── enrich_promoter_with_gene_info.py
├── enrich_summary_tables.py
├── excel_reports
│   ├── ASSEMBLY_QUALITY_COMPARISON.xlsx
│   ├── D_SERIES_ANALYSIS_SUMMARY.xlsx
│   ├── D_SERIES_SAMPLE_METRICS.xlsx
│   ├── H_CONVERGENT_EVOLUTION_ANALYSIS.xlsx
│   ├── H_SERIES_ANALYSIS_SUMMARY.xlsx
│   ├── H_SERIES_SAMPLE_METRICS.xlsx
│   ├── MUTATION_STATISTICS_COMPARISON.xlsx
│   └── QUICK_REFERENCE_SUMMARY.xlsx
├── expand_amino_acids.py
├── expand_annotations_promoter.py
├── export_intergenic_mutations.py
├── extract_all_mutations_simple.py
├── extract_and_annotate_snps.py
├── extract_and_blast_unmapped.py
├── extract_b00625_variants.py
├── extract_detailed_mutations.py
├── extract_gene_map_from_g_series.py
├── extract_genes_from_reference.py
├── extract_prokka_annotations.py
├── extract_snps_from_nucmer.py
├── feature_to_ncbi_mapping.json
├── feature_to_product_mapping.json
├── fill_all_amino_acid_changes.py
├── filter_concentration_dependent_mutations.py
├── final_annotation_script.py
├── final_dnds_per_sample.py
├── final_excel_with_documentation.py
├── final_gene_name_fix.py
├── final_proper_annotations.py
├── find_ramA_mutations.py
├── fix_c0_dnds_uniform.py
├── fix_dnds_calculation.py
├── fix_dnds_filtered.py
├── fix_excel_with_real_names.py
├── fix_gene_products.py
├── gene_position_map.json
├── generate_b_series_table.py
├── generate_ce_annotated_mutations.py
├── generate_ce_comprehensive_excel.py
├── generate_ce_comprehensive_final.py
├── generate_ce_mutations_csv.py
├── generate_ce_mutations_from_gff.py
├── generate_ce_series_tables.py
├── generate_ce_series_with_real_names.py
├── generate_d_h_mutation_tables.py
├── generate_detailed_ce_mutations.py
├── generate_final_mutation_tables.py
├── generate_final_report.py
├── generate_series_tables.py
├── get_assembly_stats.py
├── get_g_series_stats.py
├── identify_promoter_mutations.py
├── identify_unknown_proteins.py
├── improve_gene_annotations.py
├── integrate_annotations.py
├── list_series.sh
├── map_cvi97_to_real_names.py
├── map_dhl_genes_from_g_series.py
├── map_g_genes_from_b_series.py
├── map_genes_by_position.py
├── map_genes_from_dseries.py
├── map_intergenic_to_promoters.py
├── map_variants_to_reference.py
├── merge_annotations_with_mutations.py
├── monitor_and_reassemble_b_series.sh
├── monitor_e2la16_careful.sh
├── monitor_e2la_assemblies.sh
├── monitor_status.sh
├── mut_NODE43_15046.fa
├── ncbi_dataset
│   └── data
│       └── GCF_000224985.1
├── populate_excel_properly.py
├── process_all_downloads.sh
├── process_all_gdrive_samples.sh
├── process_from_downloads.sh
├── process_google_drive_samples.sh
├── processing.log
├── processing_log.txt
├── product_name_mapping.json
├── prokka_annotation
│   └── STM_LB_0_july.log
├── prokka_annotation.log
├── prokka_annotations
│   ├── D_0
│   │   └── D_0.log
│   ├── D_0125
│   │   └── D_0125.log
│   ├── D_0_test
│   │   └── D_0.log
│   ├── D_2
│   │   └── D_2.log
│   ├── D_4
│   │   └── D_4.log
│   ├── D_8_b
│   │   └── D_8_b.log
│   ├── H_0
│   │   └── H_0.log
│   ├── H_1
│   │   └── H_1.log
│   └── H_16
│       └── H_16.log
├── prokka_e2_2_00625
│   └── E2_2_00625.log
├── prokka_results
│   ├── C_4_prokka
│   │   └── C_4.log
│   ├── C_4_prokka_final
│   │   └── C_4.log
│   ├── E_0_prokka
│   │   └── E_0.log
│   ├── E_0_prokka_final
│   │   └── E_0.log
│   ├── E_2_prokka
│   │   └── E_2.log
│   ├── E_2_prokka_final
│   │   └── E_2.log
│   ├── E_4_prokka
│   │   └── E_4.log
│   └── E_4_prokka_final
│       └── E_4.log
├── prokka_ssf_annotation
│   └── ssf_annotated.log
├── proper_annotation_with_dn_ds.py
├── query_sequence.fasta
├── quick_annotate_genes.py
├── quick_local_annotation.py
├── reassemble_b_series_optimized.sh
├── reassemble_g_series_optimized.sh
├── reassemble_new_b_series.sh
├── reassemble_series.sh
├── recalculate_all_amino_acids.py
├── recalculate_dnds_correct.py
├── replace_with_real_gene_names.py
├── run_annotation.sh
├── run_e2_2_assemblies.sh
├── run_e2_2_assemblies_improved.py
├── run_e2_2_assemblies_v2.py
├── run_e2la_assemblies.py
├── run_e2la_assemblies.sh
├── run_prokka_annotation.sh
├── run_prokka_proper.sh
├── run_snp_calling.sh
├── run_ssf_assemblies.py
├── score_sigma70_consensus.py
├── senftenberg_annotation
│   └── senftenberg_ref.log
├── senftenberg_atcc43845.fasta.gz
├── senftenberg_ref.fasta
├── senftenberg_ref_NCBI.gbk
├── smart_annotation.py
├── split_promoter_by_series.py
├── status_monitor_1min.sh
├── thorough_gene_annotation.py
├── transfer_gene_names.py
├── update_g_series_with_blast.py
├── update_individual_samples.py
├── update_mutation_type_detailed.py
├── update_snp_classification.py
└── wait_for_e2la_complete.py

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.12 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_

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