Summary table generation does not work with prokka genomes

[hgscott]

Now that I have switched to using the prokka-generated GenBank files, I am getting errors when I run my summary table generation script, make_summary_table.py:

Starting analysis. Make sure you have installed biopython: pip install biopython
Successfully loaded metadata file.
Found 48 samples to analyze...

Processing sample: citrea
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000238375.3_ASM23837v4_genomic/GCF_000238375.3_ASM23837v4_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/citrea/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: salex
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2523533559/2523533559.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/2523533559/2523533559.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       G533DRAFT_scaffold00001.1574834 bp   DNA   linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/salex/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: nitzsch
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/Sulfitobacter_pseudonitzschiae_SMR1/Sulfitobacter_pseudonitzschiae_SMR1.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/Sulfitobacter_pseudonitzschiae_SMR1/Sulfitobacter_pseudonitzschiae_SMR1.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       S_pseudonitzschiae_SMR1.chrom3572445 bp   DNA linear

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/nitzsch/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: fagar
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/HG315671/HG315671.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/fagar/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: atcc26499
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2545824627/2545824627.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/2545824627/2545824627.gbk. Error: Name and length collide in the LOCUS line:
LOCUS       2545824627.25458497164397537 bp    DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/atcc26499/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: t6c
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/t6c/plasmidsaurus_vs_ref/output/output.tsv: No columns to parse from file

Processing sample: hot5_c3
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/HOT5_C03/HOT5_C03.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/hot5_c3/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: azure
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2600255073/2600255073.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/azure/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: bdim
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_004102925.1_ASM410292v1_genomic/GCF_004102925.1_ASM410292v1_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/bdim/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: hot5_b10
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/HOT5_B10/HOT5_B10.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/hot5_b10/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: fang
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2515154119/2515154119.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/2515154119/2515154119.gbk. Error: Name and length collide in the LOCUS line:
LOCUS       A37QDRAFT_scaffold_0.1282200 bp    DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/fang/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: pgall
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000511385/GCA_000511385.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000511385/GCA_000511385.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000511385.CP0069663776653 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/pgall/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: t2
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000160775.2_ASM16077v2_genomic/GCF_000160775.2_ASM16077v2_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/t2/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: dfl-12
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000018145/GCA_000018145.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000018145/GCA_000018145.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000018145.CP0008303789584 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/dfl-12/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: vnat
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_001456255.1_ASM145625v1_genomic/GCF_001456255.1_ASM145625v1_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/vnat/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: abie
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2667527211/2667527211.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/abie/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: hot5_b8
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/HOT5_B08/HOT5_B08.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/hot5_b8/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: atlcs
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2526164557/2526164557.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/atlcs/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: luca8
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/Sulfitobacter_pseudonitzschiae_SMR1/Sulfitobacter_pseudonitzschiae_SMR1.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/Sulfitobacter_pseudonitzschiae_SMR1/Sulfitobacter_pseudonitzschiae_SMR1.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       S_pseudonitzschiae_SMR1.chrom3572445 bp   DNA linear

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/luca8/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: hot5_e6
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/HOT5_E06/HOT5_E06.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/hot5_e6/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: rsphaer
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000012905.2_ASM1290v2_genomic/GCF_000012905.2_ASM1290v2_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/rsphaer/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: dss-3
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000011965/GCA_000011965.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000011965/GCA_000011965.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000011965.CP0000314109437 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/dss-3/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: kuro
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2523533634/2523533634.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/2523533634/2523533634.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       H615DRAFT_scaffold00010.10117691 bp   DNA  linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/kuro/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: relong
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000590925.1_ASM59092v1_genomic/GCF_000590925.1_ASM59092v1_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/relong/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: exig
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2562617200/2562617200.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/2562617200/2562617200.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       P403DRAFT_scf7180000000006_quiver.13078684 bp   DNA linear

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/exig/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: sflavi
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/Sphingorhabdus_flavimaris_SMR4y/Sphingorhabdus_flavimaris_SMR4y.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/Sphingorhabdus_flavimaris_SMR4y/Sphingorhabdus_flavimaris_SMR4y.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       S_flavimaris_SMR4y_SMR4y.chrom3479724 bp   DNA linear

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/sflavi/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: bs11
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000299995/GCA_000299995.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000299995/GCA_000299995.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000299995.CP0038454480507 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/bs11/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: serr
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2526164535-custom-contig-name/2526164535-custom-contig-name.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/2526164535-custom-contig-name/2526164535-custom-contig-name.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       SER39009_Serratia_390064947661 bp   DNA    linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/serr/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: pr1red
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000166275.1_ASM16627v1_genomic/GCF_000166275.1_ASM16627v1_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/pr1red/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: vcamp
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000464435/GCA_000464435.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000464435/GCA_000464435.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000464435.CP0066053746887 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/vcamp/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: hot1a3
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2687453488/2687453488.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/2687453488/2687453488.gbk. Error: Name and length collide in the LOCUS line:
LOCUS       2687454166.26874541664652873 bp    DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/hot1a3/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: phalo
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000230555/GCA_000230555.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000230555/GCA_000230555.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000230555.CP0030753944837 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/phalo/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: atcc27126
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000172635/GCA_000172635.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000172635/GCA_000172635.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000172635.CP0038414653851 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/atcc27126/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: cstat
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2623620535/2623620535.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/cstat/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: parctic
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000482725.1_ASM48272v1_genomic/GCF_000482725.1_ASM48272v1_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/parctic/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: aalgi
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/Arenibacter_algicola_SMS7/Arenibacter_algicola_SMS7.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/Arenibacter_algicola_SMS7/Arenibacter_algicola_SMS7.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       Arenibacter_algicola_SMS7.chromosome5793053 bp   DNA linear

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/aalgi/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: pinhib
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000154765/GCA_000154765.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000154765/GCA_000154765.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000154765.CP0029763821831 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/pinhib/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: shewden
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2524023135/2524023135.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/shewden/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: kordia
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000154725.1_ASM15472v1_genomic/GCF_000154725.1_ASM15472v1_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/kordia/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: de1
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000310085.1_ASM31008v1_genomic/GCF_000310085.1_ASM31008v1_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/de1/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: eryth
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000010105/GCA_000010105.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000010105/GCA_000010105.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000010105.AP0089576516310 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/eryth/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: crono
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2667527511/2667527511.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/crono/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: owen
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2508501098/2508501098.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/owen/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: fors
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000060345/GCA_000060345.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000060345/GCA_000060345.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000060345.CU2073663798465 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/fors/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: bermu
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCF_000153725.1_ASM15372v1_genomic/GCF_000153725.1_ASM15372v1_genomic.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/bermu/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: hp15
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/650377991/650377991.gbk
Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/hp15/plasmidsaurus_vs_ref/output/output.tsv: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

Processing sample: b2china
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000230555/GCA_000230555.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/GCA_000230555/GCA_000230555.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       GCA_000230555.CP0030753944837 bp   DNA     linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/b2china/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

Processing sample: koree
  - Parsing GenBank file: /projectnb/hfsp/IAMM_reference_files/prokka_results/2524614539/2524614539.gbk
  - WARNING: Could not parse GenBank file /projectnb/hfsp/IAMM_reference_files/prokka_results/2524614539/2524614539.gbk. Error: Did not recognise the LOCUS line layout:
LOCUS       G523DRAFT_scaffold00001.12348061 bp   DNA  linear       23-JUL-2025

Error processing file /projectnb/hfsp/SNP23/breseq_results/raw_files/koree/plasmidsaurus_vs_ref/output/output.tsv: cannot access local variable 'genbank_df' where it is not associated with a value

No data was processed. Output file will not be created.

[hgscott]

To resolve the "Could not parse GenBank file", I think I can use this flag when I run prokka:
--compliant Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX (default OFF)

I believe that the --compliant option forces Prokka to produce GenBank files that conform to the official GenBank/ENA/DDJB standards. This means the LOCUS line (and other fields) will follow the NCBI GenBank format much more closely, which is required for BioPython's SeqIO.parse to work reliably.

It also sets other options: --addgenes --mincontiglen 200 --centre XXX

• --addgenes: Ensures gene features are present, like I did separately in Add "gene" entries to prokka's GenBank files iamm-collection#10, so now I can remove that flag
• --mincontiglen 200: Only contigs longer than 200bp are included.
• --centre XXX: Sets the sequencing center code (required for compliance).

[hgscott]

I want to test this on just one file, since last time, I had to wait forever to be allocated enough cores to run prokka.

How can I test if I will get the error without running the whole script?

Just try loading the file with SeqIO? E.g. for a file I know I got an error with in the script (see the last error in the original comment).

from Bio import SeqIO
foo = SeqIO.parse("prokka_results/2524614539/2524614539.gbk", "genbank")

But that works, that doesn't throw an error:

So maybe I actually need to iterate through the objects like I do in the script:

gbk_path = "prokka_results/2524614539/2524614539.gbk"

genbank_info = []
for record in SeqIO.parse(gbk_path, "genbank"):
    for feature in record.features:
        if feature.type == 'CDS':
            gene_name = feature.qualifiers.get('gene', [None])[0]
            if gene_name:
                feature_info = {}
                feature_info['gene_name'] = gene_name
                feature_info['length'] = len(feature)
                feature_info['start_pos'] = feature.location.start
                feature_info['end_pos'] = feature.location.end
                # Add the feature info to the list
                genbank_info.append(feature_info)

And that throws the following error:

When I use a different file (prokka_results/650377991/650377991.gbk), it works fine, so I guess some of them are okay.

So I regenerated the file with:

prokka --force --compliant --outdir prokka_results/2524614539 --prefix 2524614539 fasta/2524614539.fna 

And now, when I run the same test as before, it passes (doesn't throw an error):

[hgscott]

Since this looks like an issue in the prokka files, not this script, I will address it in segrelab/iamm-collection#11.