Skip to content

Problem on genotype step #53

@stat-lab

Description

@stat-lab

Thank you for providing ScatTR. I tried to run this tool using a human dataset containing the GRCh38 reference fasta, a bam file for chr20 (30x 150 bp PE short reads), and a tandem repeat catalog corresponding to chr20 (N = 25,682). The stats, extract, and define steps appeared to complete without errors, but the final genotype step failed to generate its output file. The message displayed on the console was follows:

Dec 04 10:00:45.048 INFO Loaded haplotype depth distribution with mean = 24.932874627540574
Dec 04 10:00:45.048 INFO Loaded insert size distribution with mean = 444.2482023881525 and sd = 104.3883724298505
Dec 04 10:00:45.048 INFO Loading problem definitions
Dec 04 10:25:26.279 INFO [TR588903] Starting genotype estimation for locus
Dec 04 10:25:27.450 INFO [TR588903] Genotype = 21/149, confidence interval = 21-21/148-149
Dec 04 10:25:27.450 INFO [TR578816] Starting genotype estimation for locus

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

thread '' panicked at src/alignment.rs:305:45:
called Option::unwrap() on a None value

Any comments or solutions regarding this issue would be appreciated.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions