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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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License not recognized, Singularity image pull error #79

Closed CSree closed 2 months ago

CSree commented 3 months ago

Hi,

  1. I downloaded the latest mi.license, however still it is not recognized by the pipeline.
Screenshot 2024-08-09 at 12 12 52 PM
  1. Running with tcr - false, After 7hrs, this is the error:
Screenshot 2024-08-09 at 12 04 19 PM

thanks in advance Chai

riederd commented 3 months ago

Hi,

1. The mixcr license file needs to be passed to the nextNEOpi pipeline via --MIXCR_lic /path/to/yourwonderful/mi.licence

and it should look like:

$ cat mi.license | tr '[A-Z]' 'X'
X-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

2. it seems you have connection issues form the machine that runs the strelka process. I just tested manually here and it works fine:

$ singularity pull --name strelka_test.sif https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1
INFO:    Downloading network image
78.2MiB / 78.2MiB [==================================================================================================================================================] 100 % 5.5 MiB/s 0s
$ ls -l strelka_test.sif 
-rwxr-xr-x 1 user users 81948672 Aug 12 15:52 strelka_test.sif

HTH

riederd commented 2 months ago

no feedback. I'm closing the issue for now, please feel free to open it again