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grenaud / vgan

Suite of tools for pangenomics built using vg
GNU General Public License v3.0
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Unable to test vgan euka due to damageProfiles error #2

Closed morien closed 9 months ago

morien commented 10 months ago

Hello, I'm trying to test euka out on some metagenomic shotgun sequencing samples. I set up according to instructions on my CentOS 8 remote server. The installed location of vgan is /usr/bin/vgan The euka and hcfiles directories are here: /usr/bin/share/vgan/ Here's what the files look like in there. They are all owned by root and have chmod +w permissions

/usr/bin/share/vgan/
├── damageProfiles
│   └── none.prof
├── euka_dir
│   ├── euka_db.bins
│   ├── euka_db.clade
│   ├── euka_db.dist
│   ├── euka_db.gbwt
│   ├── euka_db.gfa
│   ├── euka_db.gg
│   ├── euka_db.giraffe.gbz
│   ├── euka_db_graph_path_supports
│   ├── euka_db.min
│   ├── euka_db.og
│   ├── euka_db.ry
│   ├── euka_db.snarls
│   └── euka_db.vg
└── hcfiles
    ├── children.txt
    ├── graph.dist
    ├── graph.gbwt
    ├── graph.gg
    ├── graph.giraffe.gbz
    ├── graph.og
    ├── graph_paths
    ├── graph.ry
    ├── graph.snarls
    ├── graph.xg
    ├── k17_w18.min
    ├── k31_w11.min
    ├── mappability.tsv
    ├── parents.txt
    ├── parsed_pangenome_mapping
    └── path_supports

here is the command I would like to run: vgan euka -fq1 ESW_7FEV_Library_control_36_S6_L003_R1_001.fq --euka_dir /usr/bin/share/vgan/euka_dir/ this is the only output: libgab.h getFullPath failed on /usr/bin/../share/vgan/damageProfiles/none.prof

Since I'm only running a test, not even trying to get damageProfiles info yet, I'm not sure why this error is popping up. Any help would be appreciated.

nicolaavogel commented 10 months ago

Hi morien,

All zero-damage profiles are read in by default, even if you do not specify the option. I can see that the way we specified the path for the damage profiles is not optimal (I will work on a better solution for this for our next update. Thank you.) For now, the easiest way to fix the error message would be to move the share folder out of your bin folder and one directory back into your usr folder. Then the specified path in euka should match the location of the none.prof damage profiles in the damageProfiles folder.

Let me know if there are any more issues or if you have any more questions! Best, Nicola