<p>I'm using <a href="https://alkesgroup.broadinstitute.org/Eagle/" rel="nofollow noreferrer">Eagle 2.4.1</a> for phasing a vcf.gz file. Whenever I give the command it gives me the following error</p>
<pre><code>Phasing samples 1-1
WARNING: Sample 1 (1-indexed) has a het count of 0
ERROR: Failed to allocate 18446744073709551596 bytes
</code></pre>
<p>The command to reproduce the error is as follows,</p>
<pre><code>eagle --vcf myprofile.vcf.gz  --geneticMapFile genetic_map_hg38_withX.txt.gz --outPrefix chr2 --chrom 2
</code></pre>
<p>Link for the vcf file <a href="https://github.com/shafayetrahat/test/blob/main/NA20298_chr2.vcf.gz" rel="nofollow noreferrer">https://github.com/shafayetrahat/test/blob/main/NA20298_chr2.vcf.gz</a>
Any help will be apreciated.</p>

CC BY-SA 4.0
2021-12-30T11:31:56.293Z
It seems like you are trying to phase a single sample without a reference panel, that’s also entirely homozygous? You need a reference panel for that and if all the sites are homs, something has gone wrong in the original vcf file.
user438383
CC BY-SA 4.0
2021-12-30T17:01:58.763Z
It looks like a negative number is being stored internally as an unsigned integer, leading to overflow.
Alex Reynolds
CC BY-SA 4.0
2021-12-30T17:38:52.047Z
@user438383 but the sample is not homozygous. I've checked it. Can the header of the vcf file cause the problem? Also in the eagle documentation, they will check it from server? Anyway can you give link to the ghch38 reference panel server?
Shafayet Rahat
CC BY-SA 4.0
2021-12-30T17:41:23.407Z
@AlexReynolds didn't understand what you mean. Can you speak more elaborately?
Shafayet Rahat
CC BY-SA 4.0
2021-12-30T17:46:36.910Z
@ShafayetRahat post a few lines from the vcf please. I believe Alex means that there may be a bug in the source code somewhere which means Eagle is confused about how much memory is actually being used.
user438383
CC BY-SA 4.0
2021-12-30T17:49:16.303Z
ok I'm adding my vcf in the question
Shafayet Rahat
CC BY-SA 4.0
2021-12-30T17:56:04.903Z
@AlexReynolds added the link for the vcf.gz file
Shafayet Rahat
CC BY-SA 4.0
2021-12-30T18:32:23.737Z
All of your genotypes are `1|1` according to that snippet. That can't be right.
user438383
CC BY-SA 4.0
2021-12-30T19:41:51.770Z
@user438383 apparently, there are big cases for 1/1, or 1|1. But there are many cases of 0/1,1/0 also. I've checked it.
Shafayet Rahat
<errors><imputation><phasing>
ERROR: Failed to allocate 18446744073709551596 bytes
# ERROR: Failed to allocate 18446744073709551596 bytes

(Asked by: username_0 on 2021-12-30)

I'm using Eagle 2.4.1 for phasing a vcf.gz file. Whenever I give the command it gives me the following error
Phasing samples 1-1
WARNING: Sample 1 (1-indexed) has a het count of 0
ERROR: Failed to allocate 18446744073709551596 bytes

The command to reproduce the error is as follows,
eagle --vcf myprofile.vcf.gz  --geneticMapFile genetic_map_hg38_withX.txt.gz --outPrefix chr2 --chrom 2

Link for the vcf file https://github.com/shafayetrahat/test/blob/main/NA20298_chr2.vcf.gz
Any help will be apreciated.

**Tags:** errors, imputation, phasing
> **Comments:**
> **username_1**: It seems like you are trying to phase a single sample without a reference panel, that’s also entirely homozygous? You need a reference panel for that and if all the sites are homs, something has gone wrong in the original vcf file.  
> **username_2**: It looks like a negative number is being stored internally as an unsigned integer, leading to overflow.  
> **username_0**: @user438383 but the sample is not homozygous. I've checked it. Can the header of the vcf file cause the problem? Also in the eagle documentation, they will check it from server? Anyway can you give link to the ghch38 reference panel server?  
> **username_0**: @AlexReynolds didn't understand what you mean. Can you speak more elaborately?  
> **username_1**: @ShafayetRahat post a few lines from the vcf please. I believe Alex means that there may be a bug in the source code somewhere which means Eagle is confused about how much memory is actually being used.  
> **username_0**: ok I'm adding my vcf in the question  
> **username_0**: @AlexReynolds added the link for the vcf.gz file  
> **username_1**: All of your genotypes are `1|1` according to that snippet. That can't be right.  
> **username_0**: @user438383 apparently, there are big cases for 1/1, or 1|1. But there are many cases of 0/1,1/0 also. I've checked it.  

---

## 0 answers

