UPDATING error probabilities of each edge

[mainguyenanhvu]

I used kourami with IMGTHLA version: 3.49.0 (the latest update from https://github.com/ANHIG/IMGTHLA/). I run with four options of HGV favor: hs38,hs38D,hs38DH,hs38NoAltDH.

However, all outputs are empty and logs are the same:

 -d custom_db/v3.48.0-alpha-10-g50e92c6/3.49.0 -a -o output/tesths38 extracted_bam_files/VN_01_00_0016_01_01_on_KouramiPanel.bam
----------------REF GRAPH CONSTRUCTION--------------
Merging HLA sequences and building HLA graphs
processing HLA gene:	A
Traversing (7560)
DONE Traversing
processing HLA gene:	B
Traversing (8999)
DONE Traversing
processing HLA gene:	C
Traversing (7512)
DONE Traversing
processing HLA gene:	DQA1
Traversing (483)
DONE Traversing
processing HLA gene:	DQB1
Traversing (2278)
DONE Traversing
processing HLA gene:	DRB1
Traversing (3298)
DONE Traversing
processing HLA gene:	DOA
Traversing (15)
DONE Traversing
processing HLA gene:	DMA
Traversing (58)
DONE Traversing
processing HLA gene:	DMB
Traversing (71)
DONE Traversing
processing HLA gene:	DPA1
Traversing (455)
DONE Traversing
processing HLA gene:	DPB1
Traversing (2067)
DONE Traversing
processing HLA gene:	DRA
Traversing (32)
DONE Traversing
processing HLA gene:	DRB3
Traversing (436)
DONE Traversing
processing HLA gene:	DRB5
Traversing (181)
DONE Traversing
processing HLA gene:	F
Traversing (56)
DONE Traversing
processing HLA gene:	G
Traversing (104)
DONE Traversing
processing HLA gene:	H
Traversing (67)
DONE Traversing
processing HLA gene:	J
Traversing (32)
DONE Traversing
processing HLA gene:	L
Traversing (5)
DONE Traversing
Done building	19	graphs.
----------------     READ LOADING     --------------
Loading reads from:	VN_01_00_0016_01_01_on_KouramiPanel.bam
Loaded a total of 0 mapped reads.
A total of 0 bases
----------------    GRAPH CLEANING    --------------
A	>>>>> FLATTENED InsertionBubble:	0
B	>>>>> FLATTENED InsertionBubble:	0
C	>>>>> FLATTENED InsertionBubble:	0
DQA1	>>>>> FLATTENED InsertionBubble:	0
DQB1	>>>>> FLATTENED InsertionBubble:	0
DRB1	>>>>> FLATTENED InsertionBubble:	0
DOA	>>>>> FLATTENED InsertionBubble:	0
DMA	>>>>> FLATTENED InsertionBubble:	0
DMB	>>>>> FLATTENED InsertionBubble:	0
DPA1	>>>>> FLATTENED InsertionBubble:	0
DPB1	>>>>> FLATTENED InsertionBubble:	0
DRA	>>>>> FLATTENED InsertionBubble:	0
DRB3	>>>>> FLATTENED InsertionBubble:	0
DRB5	>>>>> FLATTENED InsertionBubble:	0
F	>>>>> FLATTENED InsertionBubble:	0
G	>>>>> FLATTENED InsertionBubble:	0
H	>>>>> FLATTENED InsertionBubble:	0
J	>>>>> FLATTENED InsertionBubble:	0
L	>>>>> FLATTENED InsertionBubble:	0
A	:removed	11634	Edges.
A	:removed	8124	Vertices.
B	:removed	12035	Edges.
B	:removed	8626	Vertices.
C	:removed	11945	Edges.
C	:removed	8596	Vertices.
DQA1	:removed	9912	Edges.
DQA1	:removed	8564	Vertices.
DQB1	:removed	14917	Edges.
DQB1	:removed	12440	Vertices.
DRB1	:removed	35249	Edges.
DRB1	:removed	30950	Vertices.
DOA	:removed	3714	Edges.
DOA	:removed	3682	Vertices.
DMA	:removed	5148	Edges.
DMA	:removed	5081	Vertices.
DMB	:removed	6905	Edges.
DMB	:removed	6823	Vertices.
DPA1	:removed	11529	Edges.
DPA1	:removed	10752	Vertices.
DPB1	:removed	14785	Edges.
DPB1	:removed	13300	Vertices.
DRA	:removed	5928	Edges.
DRA	:removed	5839	Vertices.
DRB3	:removed	15805	Edges.
DRB3	:removed	15172	Vertices.
DRB5	:removed	14126	Edges.
DRB5	:removed	13887	Vertices.
F	:removed	3714	Edges.
F	:removed	3647	Vertices.
G	:removed	3410	Edges.
G	:removed	3280	Vertices.
H	:removed	3925	Edges.
H	:removed	3741	Vertices.
J	:removed	3770	Edges.
J	:removed	3674	Vertices.
L	:removed	3931	Edges.
L	:removed	3887	Vertices.
A	:removed	[DE]:1	[UN]:1	[NumVertices]:2
B	:removed	[DE]:1	[UN]:1	[NumVertices]:2
C	:removed	[DE]:1	[UN]:1	[NumVertices]:2
DQA1	:removed	[DE]:1	[UN]:1	[NumVertices]:2
DQB1	:removed	[DE]:2	[UN]:1	[NumVertices]:3
DRB1	:removed	[DE]:2	[UN]:2	[NumVertices]:4
DOA	:removed	[DE]:1	[UN]:1	[NumVertices]:2
DMA	:removed	[DE]:1	[UN]:1	[NumVertices]:2
DMB	:removed	[DE]:1	[UN]:1	[NumVertices]:2
DPA1	:removed	[DE]:1	[UN]:2	[NumVertices]:3
DPB1	:removed	[DE]:1	[UN]:1	[NumVertices]:2
DRA	:removed	[DE]:1	[UN]:1	[NumVertices]:2
DRB3	:removed	[DE]:2	[UN]:2	[NumVertices]:4
DRB5	:removed	[DE]:1	[UN]:1	[NumVertices]:2
F	:removed	[DE]:1	[UN]:1	[NumVertices]:2
G	:removed	[DE]:1	[UN]:2	[NumVertices]:3
H	:removed	[DE]:1	[UN]:1	[NumVertices]:2
J	:removed	[DE]:1	[UN]:1	[NumVertices]:2
L	:removed	[DE]:1	[UN]:1	[NumVertices]:2
------------ UPDATING error probabilities of each edge ---------
------------     DONE UPDATING error probabilities     ---------
=========================
=  A
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	A
=========================
=  B
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	B
=========================
=  C
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	C
=========================
=  DQA1
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DQA1
=========================
=  DQB1
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DQB1
=========================
=  DRB1
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DRB1
=========================
=  DOA
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DOA
=========================
=  DMA
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DMA
=========================
=  DMB
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DMB
=========================
=  DPA1
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DPA1
=========================
=  DPB1
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DPB1
=========================
=  DRA
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DRA
=========================
=  DRB3
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DRB3
=========================
=  DRB5
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	DRB5
=========================
=  F
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	F
=========================
=  G
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	G
=========================
=  H
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	H
=========================
=  J
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	J
=========================
=  L
=========================
Disconnected Graph. Probably due to not enough coverage to fully assemble or check for any biases in sequencing libraries used.
CANNOT PROCEED for HLA gene:	L

Please help me to solve it. Thank you very much.