HATCHet check failing for Gurobi

回答済み

Soubhadra Datta

2025年05月19日 21:36

• 
• 

We are trying to run  HATCHet with Gurobi as the default Solver. However, hatchet check is failing.  As per  https://raphael-group.github.io/hatchet/README.html#usingasolver  
Gurobi is the default Solver in HATCHet. I followed the instruction in the above URL and installed hatchet and loaded gurobi module file in a conda environment. However, hatchet fails at solver check. 

Are there any known  issues with Gurobi and HATCHet that is causing this issue? I

We have a floating license for Gurobi Optimizer. The  license appears to be working  with Gurobi. When I run gurobi_cl from the compute  node, I see "grb" entries in the token  server logs. However, when we run hatchet check, there are no “grb” entries in token server logs.

 

(hatchet) [jws@node116 ~]$ module list

Currently Loaded Modulefiles:

 1) conda3/202311(default)   2) gurobi/12.0.1 

 

(hatchet) [jws@node101 ~]$ hatchet check

======================

Running HATCHet checks

======================

----------------------

Command: count-reads

----------------------

  tabix check SUCCESSFUL. 

  samtools check SUCCESSFUL. 

  mosdepth check SUCCESSFUL. 

----------------------

Command: genotype-snps

----------------------

  samtools check SUCCESSFUL. 

  bcftools check SUCCESSFUL. 

----------------------

Command: count-alleles

----------------------

  samtools check SUCCESSFUL. 

  bcftools check SUCCESSFUL. 

----------------------

Command: combine-counts

----------------------

  bedtools check SUCCESSFUL. 

----------------------

Command: compute-cn

----------------------

  solver check FAILED.

    See http://compbio.cs.brown.edu/hatchet/README.html#using-a-solver

----------------------

Command: phase-snps

----------------------

  bcftools check SUCCESSFUL. 

  picard check SUCCESSFUL. 

  shapeit check SUCCESSFUL. 

  bgzip check SUCCESSFUL.

 

0

• 

  Riley Clement

  • Gurobi Staff

  2025年05月20日 10:48

  Hi Soubhadra,

  I don't expect anyone at Gurobi will have heard of hatchet (with only 86k downloads in 6 years this is not a popular package).

  My only advice is to have a read of the following article, move your license file to a default location (if it is not already) and set the GRB_LICENSE_FILE environment variable.

  https://support.gurobi.com/hc/en-us/articles/360013417211-Where-do-I-place-the-Gurobi-license-file-gurobi-lic

  Otherwise, perhaps you can open an issue with the creators of hatchet:

  https://github.com/raphael-group/hatchet

  - Riley

  0

サインインしてコメントを残してください。