安装好了，执行jba报错

[wwhwwxlz]

执行jba：
Error: See usage.
Execution halted
执行用例：
[root@hostnamezuyih JaBbA]# jba ${JABBA_PATH}/junctions.vcf ${JABBA_PATH}/coverage.txt --gurobi TRUE
Did not find hets file setting to NULL
Did not find nseg file setting to NULL

---

(___ ) ( \ ( ) ( _ ) | | _ _ | (_) )| |_ | (_) | _ | | /'_ )| _ <'| '\ | _ | ( )_| |( (_| || (_) )| |_) )| | | | _/'`_,)(___/'(,/'() ()

(Junction Balance Analysis)

JaBbA 2024-11-08 16:39:18: Located junction file /path/to/snphylo/R_install/lib/R/library/JaBbA/extdata//junctions.vcf
JaBbA 2024-11-08 16:39:18: Located coverage file /path/to/snphylo/R_install/lib/R/library/JaBbA/extdata//coverage.txt
JaBbA 2024-11-08 16:39:18: Loading packages ...
JaBbA 2024-11-08 16:39:18: Starting analysis in /home/JaBbA
JaBbA 2024-11-08 16:39:19: Read in 83 total input junctions
JaBbA 2024-11-08 16:39:19: In the input, There are 0 tier 1 junctions; 83 tier 2 junctions; 0 tier 3 junctions.
JaBbA 2024-11-08 16:39:20: Read in 1,805 1000bp bins of coverage data across 1 chromosomes
JaBbA 2024-11-08 16:39:20: No segmentation provided, so performing segmentation using CBS
JaBbA 2024-11-08 16:39:20: Segmentation finished
JaBbA 2024-11-08 16:39:20: Loaded 83 junctions from the input.
JaBbA 2024-11-08 16:39:20: Found tier field enforcing >=1 CN at 0 junctions
JaBbA 2024-11-08 16:39:20: Removing 0 tier 3 junctions
JaBbA 2024-11-08 16:39:20: 69 INDEL-like isolated events
JaBbA 2024-11-08 16:39:20: 69 INDEL-like isolated junctions mandatorily EXCLUDED in the final model
JaBbA 2024-11-08 16:39:20: TRUE for drop.chr, dropping chr in chromosome names.
JaBbA 2024-11-08 16:39:20: Conform the reference sequence length of: seg, coverage, and ra, to be:
12:100746000
16:90354753
19:59128983
JaBbA 2024-11-08 16:39:20: Number of gaps with nonzero width: 18
JaBbA 2024-11-08 16:39:20: Number of segments before gap filtering: 29
JaBbA 2024-11-08 16:39:21: 13 segments produced after gap filtering
JaBbA 2024-11-08 16:39:21: creating karyograph
JaBbA 2024-11-08 16:39:23: Definining coverage good quality nodes as >=50% bases covered by non-NA and non-Inf values i00KB region
JaBbA 2024-11-08 16:39:23: Hard setting 0 Mb of the genome to NA that didn't pass our quality threshold
JaBbA 2024-11-08 16:39:23: Using loess to fit mean to variance relationship in segments with greater than 1 bins
JaBbA 2024-11-08 16:39:23: Using ppgrid to estimate purity ploidy
JaBbA 2024-11-08 16:39:23: setting up ppgrid matrices ..

.....................................................................................................
.....................................................................................................
JaBbA 2024-11-08 16:39:24: Built gGraph with 82 nodes, 104 edges, purity 0.6, and ploidy 1.93
JaBbA 2024-11-08 16:39:27: Brand new function for reciprocal junctions calling.
.
JaBbA 2024-11-08 16:39:28: Excluding 14 aberrant junctions whose both breakpoints are in NA coverage regions
JaBbA 2024-11-08 16:39:28: Cancel nudge for 0 aberrant junctions where one of the 2 breakpoint is in NA coverage region
JaBbA 2024-11-08 16:39:28: In sum, we are forcing 0 junctions, excluding 14 junctions, and nudging 0 junctions
JaBbA 2024-11-08 16:39:28: Excluding aberrant junctions: 1,2,3,4,5,6,7,8,9,10,11,12,13,14
JaBbA 2024-11-08 16:39:28: Adjusting the kag (naive solution) as mipstart (initial solution).
JaBbA 2024-11-08 16:39:28: Applying mipstarts from previous jabba solution
reading karyograph from file
Marking nodes with cn contained in column: cnmle
Computing node weights using variance contained in column: loess.var
Rewards not supplied on edges!
Starting LP balance on gGraph with...
Number of nodes: 41
Number of edges: 52
detected no tier 1 junctions
No duplicate Tier 1 junctions detected
Grabbing available memory...
Currently used: 689.9 Mb
Allowed: 16000 Mb
Treemem: 14310.1 Mb
creating copy of input gGraph
Checking inputs
adding l0 penalty indicator
adding delta constraints for LP
Unique cids (A): 979
Unique cids (b): 979
Number of variables: 1072
bvec length: 979
Amat nrow: 979
Starting optimization with gurobi!
Set parameter Username
Set parameter TimeLimit to value 6000
Set parameter MIPGap to value 1e-05
Gurobi Optimizer version 11.0.3 build v11.0.3rc0 (armlinux64 - "openEuler 20.03 (LTS-SP3)")

CPU model: ARM64
Thread count: 96 physical cores, 96 logical processors, using up to 32 threads

Optimize a model with 979 rows, 1100 columns and 2166 nonzeros
Model fingerprint: 0xf6388696
Variable types: 558 continuous, 542 integer (192 binary)
Coefficient statistics:
Matrix range [1e-01, 1e+03]
Objective range [1e+00, 3e+02]
Bounds range [1e+03, 1e+03]
RHS range [1e-02, 2e+00]
Found heuristic solution: objective 2960.1239772
Presolve removed 891 rows and 1001 columns
Presolve time: 0.02s
Presolved: 88 rows, 99 columns, 304 nonzeros
Found heuristic solution: objective 1019.5978332
Variable types: 0 continuous, 99 integer (46 binary)

Explored 0 nodes (0 simplex iterations) in 0.02 seconds (0.00 work units)
Thread count was 32 (of 96 available processors)

Solution count 2: 1019.6 2960.12

Optimal solution found (tolerance 1.00e-05)
Best objective 1.019597833161e+03, best bound 1.019597833161e+03, gap 0.0000%
CPLEX epgap 0 with solution status
JaBbA 2024-11-08 16:39:37: Recording convergence status of subgraphs
JaBbA 2024-11-08 16:39:39: simplifying segments in JaBbA graph but keeping all edges (including copy 0), dumping to jab
JaBbA 2024-11-08 16:39:40: Checking for hets
JaBbA 2024-11-08 16:39:41: Skipping loose end annotation
JaBbA 2024-11-08 16:39:41: Saving results
JaBbA 2024-11-08 16:39:44: Generating figures
JaBbA 2024-11-08 16:39:48: Done .. job output in: /home/JaBbA
There were 25 warnings (use warnings() to see them)