len(contig) == NoneType

[StefanFrankBio]

Hey PPanGGOLiN-Team,

I get the below when running ppanggolin all version 2.1.2. I want to make the switch from version 2.0.5, where analysis of the same input data works fine.

Traceback (most recent call last):
  File "/Users/stefanfrank/Projects/PanAdapt/work/conda/ppanggolin-3b3a97db1cb8123576ebce8a9e97f31b/lib/python3.12/site-packages/ppanggolin/annotate/annotate.py", line 1163, in read_anno_file
    org, has_fasta = read_org_gff(
                     ^^^^^^^^^^^^^
  File "/Users/stefanfrank/Projects/PanAdapt/work/conda/ppanggolin-3b3a97db1cb8123576ebce8a9e97f31b/lib/python3.12/site-packages/ppanggolin/annotate/annotate.py", line 956, in read_org_gff
    correct_putative_overlaps(org.contigs)
  File "/Users/stefanfrank/Projects/PanAdapt/work/conda/ppanggolin-3b3a97db1cb8123576ebce8a9e97f31b/lib/python3.12/site-packages/ppanggolin/annotate/annotate.py", line 1096, in correct_putative_overlaps
    if gene.stop > len(contig):
                   ^^^^^^^^^^^
TypeError: 'NoneType' object cannot be interpreted as an integer

This is an example of the gff files provided.

##gff-version 3
# Liftoff v1.6.3
# /Users/stefanfrank/Projects/PanAdapt/work/conda/liftoff-f0c55c74ebf8bf74c2ec2ca40350a2c8/bin/liftoff -db /Users/stefanfrank/Projects/PanAdapt/work/90/2a19bed407a1fa28bbd5a0b0031a09/NC_045512_2.db -o NC_045512_2.gff -f types.tmp -cds -polish NC_045512_2.fasta /Users/stefanfrank/Projects/data/SC2/NC_045512_2.fasta
NC_045512.2	Liftoff	region	1	29903	.	+	.	ID=NC_045512.2:1..29903;Dbxref=taxon:2697049;collection-date=Dec-2019;country=China;gb-acronym=SARS-CoV-2;gbkey=Src;genome=genomic;isolate=Wuhan-Hu-1;mol_type=genomic RNA;nat-host=Homo sapiens;old-name=Wuhan seafood market pneumonia virus;coverage=1.0;sequence_ID=1.0;extra_copy_number=0;copy_num_ID=NC_045512.2:1..29903_0
NC_045512.2	Liftoff	gene	266	21555	.	+	.	ID=gene-GU280_gp01;Dbxref=GeneID:43740578;Name=ORF1ab;gbkey=Gene;gene=ORF1ab;gene_biotype=protein_coding;locus_tag=GU280_gp01;coverage=1.0;sequence_ID=1.0;matches_ref_protein=False;valid_ORF=False;missing_stop_codon=True;valid_ORFs=0;extra_copy_number=0;copy_num_ID=gene-GU280_gp01_0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	266	805	.	+	.	ID=id-YP_009724389.1:1..180;Note=nsp1; produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=leader protein;protein_id=YP_009725297.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	806	2719	.	+	.	ID=id-YP_009724389.1:181..818;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp2;protein_id=YP_009725298.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	2720	8554	.	+	.	ID=id-YP_009724389.1:819..2763;Note=former nsp1; conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP); produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp3;protein_id=YP_009725299.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	8555	10054	.	+	.	ID=id-YP_009724389.1:2764..3263;Note=nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp4;protein_id=YP_009725300.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	10055	10972	.	+	.	ID=id-YP_009724389.1:3264..3569;Note=nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003); produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=3C-like proteinase;protein_id=YP_009725301.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	10973	11842	.	+	.	ID=id-YP_009724389.1:3570..3859;Note=nsp6_TM; putative transmembrane domain; produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp6;protein_id=YP_009725302.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	11843	12091	.	+	.	ID=id-YP_009724389.1:3860..3942;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp7;protein_id=YP_009725303.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	12092	12685	.	+	.	ID=id-YP_009724389.1:3943..4140;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp8;protein_id=YP_009725304.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	12686	13024	.	+	.	ID=id-YP_009724389.1:4141..4253;Note=ssRNA-binding protein; produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp9;protein_id=YP_009725305.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	13025	13441	.	+	.	ID=id-YP_009724389.1:4254..4392;Note=nsp10_CysHis; formerly known as growth-factor-like protein (GFL); produced by both pp1a and pp1ab;Parent=cds-YP_009724389.1;gbkey=Prot;product=nsp10;protein_id=YP_009725306.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	13442	13468	.	+	.	ID=id-YP_009724389.1:4393..5324;Note=nsp12; NiRAN and RdRp; produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=RNA-dependent RNA polymerase;protein_id=YP_009725307.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	13468	16236	.	+	.	ID=id-YP_009724389.1:4393..5324;Note=nsp12; NiRAN and RdRp; produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=RNA-dependent RNA polymerase;protein_id=YP_009725307.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	16237	18039	.	+	.	ID=id-YP_009724389.1:5325..5925;Note=nsp13_ZBD, nsp13_TB, and nsp_HEL1core; zinc-binding domain (ZD), NTPase/helicase domain (HEL), RNA 5'-triphosphatase; produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=helicase;protein_id=YP_009725308.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	18040	19620	.	+	.	ID=id-YP_009724389.1:5926..6452;Note=nsp14A2_ExoN and nsp14B_NMT; produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=3'-to-5' exonuclease;protein_id=YP_009725309.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	19621	20658	.	+	.	ID=id-YP_009724389.1:6453..6798;Note=nsp15-A1 and nsp15B-NendoU; produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=endoRNAse;protein_id=YP_009725310.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	20659	21552	.	+	.	ID=id-YP_009724389.1:6799..7096;Note=nsp16_OMT; 2'-o-MT; produced by pp1ab only;Parent=cds-YP_009724389.1;gbkey=Prot;product=2'-O-ribose methyltransferase;protein_id=YP_009725311.1;extra_copy_number=0
NC_045512.2	Liftoff	CDS	266	13480	.	+	.	ID=cds-YP_009725295.1;Parent=gene-GU280_gp01;Dbxref=GenBank:YP_009725295.1,GeneID:43740578;Name=YP_009725295.1;Note=pp1a;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1a polyprotein;protein_id=YP_009725295.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	266	805	.	+	.	ID=id-YP_009725295.1:1..180;Note=nsp1; produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=leader protein;protein_id=YP_009742608.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	806	2719	.	+	.	ID=id-YP_009725295.1:181..818;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp2;protein_id=YP_009742609.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	2720	8554	.	+	.	ID=id-YP_009725295.1:819..2763;Note=former nsp1; conserved domains are: N-terminal acidic (Ac), predicted phosphoesterase, papain-like proteinase, Y-domain, transmembrane domain 1 (TM1), adenosine diphosphate-ribose 1''-phosphatase (ADRP); produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp3;protein_id=YP_009742610.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	8555	10054	.	+	.	ID=id-YP_009725295.1:2764..3263;Note=nsp4B_TM; contains transmembrane domain 2 (TM2); produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp4;protein_id=YP_009742611.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	10055	10972	.	+	.	ID=id-YP_009725295.1:3264..3569;Note=nsp5A_3CLpro and nsp5B_3CLpro; main proteinase (Mpro); mediates cleavages downstream of nsp4. 3D structure of the SARSr-CoV homolog has been determined (Yang et al., 2003); produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=3C-like proteinase;protein_id=YP_009742612.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	10973	11842	.	+	.	ID=id-YP_009725295.1:3570..3859;Note=nsp6_TM; putative transmembrane domain; produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp6;protein_id=YP_009742613.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	11843	12091	.	+	.	ID=id-YP_009725295.1:3860..3942;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp7;protein_id=YP_009742614.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	12092	12685	.	+	.	ID=id-YP_009725295.1:3943..4140;Note=produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp8;protein_id=YP_009742615.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	12686	13024	.	+	.	ID=id-YP_009725295.1:4141..4253;Note=ssRNA-binding protein; produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp9;protein_id=YP_009742616.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	13025	13441	.	+	.	ID=id-YP_009725295.1:4254..4392;Note=nsp10_CysHis; formerly known as growth-factor-like protein (GFL); produced by both pp1a and pp1ab;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp10;protein_id=YP_009742617.1;extra_copy_number=0
NC_045512.2	Liftoff	mature_protein_region_of_CDS	13442	13480	.	+	.	ID=id-YP_009725295.1:4393..4405;Note=produced by pp1a only;Parent=cds-YP_009725295.1;gbkey=Prot;product=nsp11;protein_id=YP_009725312.1;extra_copy_number=0
NC_045512.2	Liftoff	CDS	13468	21555	.	+	.	ID=cds-YP_009724389.1;Parent=gene-GU280_gp01;Dbxref=GenBank:YP_009724389.1,GeneID:43740578;Name=YP_009724389.1;Note=pp1ab; translated by -1 ribosomal frameshift;exception=ribosomal slippage;gbkey=CDS;gene=ORF1ab;locus_tag=GU280_gp01;product=ORF1ab polyprotein;protein_id=YP_009724389.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	21563	25384	.	+	.	ID=gene-GU280_gp02;Dbxref=GeneID:43740568;Name=S;gbkey=Gene;gene=S;gene_biotype=protein_coding;gene_synonym=spike glycoprotein;locus_tag=GU280_gp02;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp02_0
NC_045512.2	Liftoff	CDS	21563	25384	.	+	.	ID=cds-YP_009724390.1;Parent=gene-GU280_gp02;Dbxref=GenBank:YP_009724390.1,GeneID:43740568;Name=YP_009724390.1;Note=structural protein; spike protein;gbkey=CDS;gene=S;locus_tag=GU280_gp02;product=surface glycoprotein;protein_id=YP_009724390.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	25393	26220	.	+	.	ID=gene-GU280_gp03;Dbxref=GeneID:43740569;Name=ORF3a;gbkey=Gene;gene=ORF3a;gene_biotype=protein_coding;locus_tag=GU280_gp03;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp03_0
NC_045512.2	Liftoff	CDS	25393	26220	.	+	.	ID=cds-YP_009724391.1;Parent=gene-GU280_gp03;Dbxref=GenBank:YP_009724391.1,GeneID:43740569;Name=YP_009724391.1;gbkey=CDS;gene=ORF3a;locus_tag=GU280_gp03;product=ORF3a protein;protein_id=YP_009724391.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	26245	26472	.	+	.	ID=gene-GU280_gp04;Dbxref=GeneID:43740570;Name=E;gbkey=Gene;gene=E;gene_biotype=protein_coding;locus_tag=GU280_gp04;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp04_0
NC_045512.2	Liftoff	CDS	26245	26472	.	+	.	ID=cds-YP_009724392.1;Parent=gene-GU280_gp04;Dbxref=GenBank:YP_009724392.1,GeneID:43740570;Name=YP_009724392.1;Note=ORF4; structural protein; E protein;gbkey=CDS;gene=E;locus_tag=GU280_gp04;product=envelope protein;protein_id=YP_009724392.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	26523	27191	.	+	.	ID=gene-GU280_gp05;Dbxref=GeneID:43740571;Name=M;gbkey=Gene;gene=M;gene_biotype=protein_coding;locus_tag=GU280_gp05;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp05_0
NC_045512.2	Liftoff	CDS	26523	27191	.	+	.	ID=cds-YP_009724393.1;Parent=gene-GU280_gp05;Dbxref=GenBank:YP_009724393.1,GeneID:43740571;Name=YP_009724393.1;Note=ORF5; structural protein;gbkey=CDS;gene=M;locus_tag=GU280_gp05;product=membrane glycoprotein;protein_id=YP_009724393.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	27202	27387	.	+	.	ID=gene-GU280_gp06;Dbxref=GeneID:43740572;Name=ORF6;gbkey=Gene;gene=ORF6;gene_biotype=protein_coding;locus_tag=GU280_gp06;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp06_0
NC_045512.2	Liftoff	CDS	27202	27387	.	+	.	ID=cds-YP_009724394.1;Parent=gene-GU280_gp06;Dbxref=GenBank:YP_009724394.1,GeneID:43740572;Name=YP_009724394.1;gbkey=CDS;gene=ORF6;locus_tag=GU280_gp06;product=ORF6 protein;protein_id=YP_009724394.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	27394	27759	.	+	.	ID=gene-GU280_gp07;Dbxref=GeneID:43740573;Name=ORF7a;gbkey=Gene;gene=ORF7a;gene_biotype=protein_coding;locus_tag=GU280_gp07;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp07_0
NC_045512.2	Liftoff	CDS	27394	27759	.	+	.	ID=cds-YP_009724395.1;Parent=gene-GU280_gp07;Dbxref=GenBank:YP_009724395.1,GeneID:43740573;Name=YP_009724395.1;gbkey=CDS;gene=ORF7a;locus_tag=GU280_gp07;product=ORF7a protein;protein_id=YP_009724395.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	27756	27887	.	+	.	ID=gene-GU280_gp08;Dbxref=GeneID:43740574;Name=ORF7b;gbkey=Gene;gene=ORF7b;gene_biotype=protein_coding;locus_tag=GU280_gp08;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp08_0
NC_045512.2	Liftoff	CDS	27756	27887	.	+	.	ID=cds-YP_009725318.1;Parent=gene-GU280_gp08;Dbxref=GenBank:YP_009725318.1,GeneID:43740574;Name=YP_009725318.1;gbkey=CDS;gene=ORF7b;locus_tag=GU280_gp08;product=ORF7b;protein_id=YP_009725318.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	27894	28259	.	+	.	ID=gene-GU280_gp09;Dbxref=GeneID:43740577;Name=ORF8;gbkey=Gene;gene=ORF8;gene_biotype=protein_coding;locus_tag=GU280_gp09;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp09_0
NC_045512.2	Liftoff	CDS	27894	28259	.	+	.	ID=cds-YP_009724396.1;Parent=gene-GU280_gp09;Dbxref=GenBank:YP_009724396.1,GeneID:43740577;Name=YP_009724396.1;gbkey=CDS;gene=ORF8;locus_tag=GU280_gp09;product=ORF8 protein;protein_id=YP_009724396.1;extra_copy_number=0
NC_045512.2	Liftoff	gene	28274	29533	.	+	.	ID=gene-GU280_gp10;Dbxref=GeneID:43740575;Name=N;gbkey=Gene;gene=N;gene_biotype=protein_coding;locus_tag=GU280_gp10;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp10_0
NC_045512.2	Liftoff	CDS	28274	29533	.	+	.	ID=cds-YP_009724397.2;Parent=gene-GU280_gp10;Dbxref=GenBank:YP_009724397.2,GeneID:43740575;Name=YP_009724397.2;Note=ORF9; structural protein;gbkey=CDS;gene=N;locus_tag=GU280_gp10;product=nucleocapsid phosphoprotein;protein_id=YP_009724397.2;extra_copy_number=0
NC_045512.2	Liftoff	gene	29558	29674	.	+	.	ID=gene-GU280_gp11;Dbxref=GeneID:43740576;Name=ORF10;gbkey=Gene;gene=ORF10;gene_biotype=protein_coding;locus_tag=GU280_gp11;coverage=1.0;sequence_ID=1.0;matches_ref_protein=True;valid_ORF=True;valid_ORFs=1;extra_copy_number=0;copy_num_ID=gene-GU280_gp11_0
NC_045512.2	Liftoff	CDS	29558	29674	.	+	.	ID=cds-YP_009725255.1;Parent=gene-GU280_gp11;Dbxref=GenBank:YP_009725255.1,GeneID:43740576;Name=YP_009725255.1;gbkey=CDS;gene=ORF10;locus_tag=GU280_gp11;product=ORF10 protein;protein_id=YP_009725255.1;extra_copy_number=0
##FASTA
ACCGACTAG...

Can you help me figure out why the len(contig) is of type None.

Appreciate your help!

[axbazin]

Hi,

I think this is coming from the missing "##sequence-region" which is often found at the beginning of gff3.

The code is supposed to be resilient to this pragma being missing (since it is not mandatory), but it looks like there was a hickup in dealing with it with your particular file.

Any chance you could share that one file so we can reproduce the bug and try to find a fix?

Have a nice day,
Adelme

[StefanFrankBio]

Hi Adelme,

adding the '##sequene-region' line fixed the error. Attached below is one of the unmodified gff files, that caused the error.

Thank you for your help!
Stefan

NC_045512_2.gff

[axbazin]

Thank you for the file share ! And I'm glad you found a workaround.
We'll try to get that fixed for next release hopefully :)

[JeanMainguy]

Hi,

We’ve fixed this issue and released a new version with the fix. PPanGGOLiN should now correctly retrieve contig lengths even when the ##sequence-region directive is missing.

Thank you for reporting the bug!

I’ll close this issue for now, but please don’t hesitate to reopen it if needed.