Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T11:31:56.293Z
Comments.Text: 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.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T17:01:58.763Z
Comments.Text: It looks like a negative number is being stored internally as an unsigned integer, leading to overflow.
Comments.UserDisplayName: Alex Reynolds
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T17:38:52.047Z
Comments.Text: @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?
Comments.UserDisplayName: Shafayet Rahat
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T17:41:23.407Z
Comments.Text: @AlexReynolds didn't understand what you mean. Can you speak more elaborately?
Comments.UserDisplayName: Shafayet Rahat
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T17:46:36.910Z
Comments.Text: @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.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T17:49:16.303Z
Comments.Text: ok I'm adding my vcf in the question
Comments.UserDisplayName: Shafayet Rahat
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T17:56:04.903Z
Comments.Text: @AlexReynolds added the link for the vcf.gz file
Comments.UserDisplayName: Shafayet Rahat
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T18:32:23.737Z
Comments.Text: All of your genotypes are `1|1` according to that snippet. That can't be right.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-30T19:41:51.770Z
Comments.Text: @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.
Comments.UserDisplayName: Shafayet Rahat
Tags: <errors><imputation><phasing>
Title: ERROR: Failed to allocate 18446744073709551596 bytes
ThreadText: # ERROR: Failed to allocate 18446744073709551596 bytes
  
  (Asked by: username_0 on 2021-12-30)
  
  I'm using [Eagle 2.4.1](https://alkesgroup.broadinstitute.org/Eagle/) 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/username_0/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**: @username_1 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**: @username_2 didn't understand what you mean. Can you speak more elaborately?  
  > **username_1**: @username_0 post a few lines from the vcf please. I believe username_2 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**: @username_2 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**: @username_1 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
  
  