How to Fix Error in snpeff

Misbah Abbas

Junior Member

Join Date: Jun 2017

Posts: 2
- Share
- Tweet
#1

How to Fix Error in snpeff

08-09-2017, 05:36 AM

Asslamu Alikum

I am using snpeff to annotate vcf files, When I run command it gives some errors and warnings

" java -Xmx4g -jar snpEff.jar CanFam3.1.75 -v /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/DQ1.g.vcf > DQ1.ann.vcf"

It give error at the end of complition

ERRORS: Some errors were detected

Error type Number of errors

ERROR_CHROMOSOME_NOT_FOUND 285197

WARNINGS: Some warning were detected Warning type Number of warnings INFO_REALIGN_3_PRIME 6443 WARNING_TRANSCRIPT_INCOMPLETE 277 WARNING_TRANSCRIPT_NO_START_CODON 678825 WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME 943 WARNING_TRANSCRIPT_NO_STOP_CODON 499400 WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME 346

Is it effect on the results? I don't know how to fix it.

Please tell me about it

thankx
Tags: None

Previous template Next

Reply to Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by mylaser

Kheloyar – Everything You Need to Know About Kheloyaar Login and Kheoyar Id
If you are looking for an online gaming platform that offers a user-friendly experience, Kheloyar has become a name that many users search for. Whether you're interested in creating a new account, accessing your dashboard through Kheloyaar Login, or learning how to obtain a Kheoyar Id, understanding the platform's features and account process is essential.
This guide explains everything you need to know about...
- Channel: Articles
07-11-2026, 01:13 AM
Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by SEQadmin2

Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...
- Channel: Articles
07-09-2026, 11:10 AM
Cancer Drug Resistance: The Lingering Barrier to Rising Survival

by SEQadmin2

Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
- Channel: Articles
07-08-2026, 05:17 AM

Topics	Statistics	Last Post
New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2 Started by SEQadmin2, 07-09-2026, 10:04 AM	0 responses 22 views 0 reactions	Last Post by SEQadmin2 07-09-2026, 10:04 AM
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, 07-08-2026, 10:08 AM	0 responses 14 views 0 reactions	Last Post by SEQadmin2 07-08-2026, 10:08 AM
Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2 Started by SEQadmin2, 07-07-2026, 11:05 AM	0 responses 33 views 0 reactions	Last Post by SEQadmin2 07-07-2026, 11:05 AM
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, 07-02-2026, 11:08 AM	0 responses 31 views 0 reactions	Last Post by SEQadmin2 07-02-2026, 11:08 AM

Unconfigured Ad

How to Fix Error in snpeff

Latest Articles

ad_right_rmr

News