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Canvas - Copy number variant (CNV) calling from DNA sequencing data
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tabix: Permission denied #94

Closed BenoitFiset closed 5 years ago

BenoitFiset commented 6 years ago

Hi Eric,

Moving along.... Now trying Canvas-1.38.0.1554 with dotnet 2.0.7 to get canvas Somatic-WGS to work... configured, started and got to Checkpoint 04-CanvasClean.json

Then this error:

more CanvasError.txt
2018-08-31T23:00:09-04:00,ERROR: Job tabix-index-tmp-ballele.bedgraph.gz.1 failed with exit code 126. Job logs: 
    /home/bfiset/scratch/WGS/HI.4748-008_4763-006_V418_Aligned_01_SWGS_Canvas_01/Logging/tabix-index-tmp-ballele.bedgraph.gz.1.stdout
    /home/bfiset/scratch/WGS/HI.4748-008_4763-006_V418_Aligned_01_SWGS_Canvas_01/Logging/tabix-index-tmp-ballele.bedgraph.gz.1.stderr
Job error message:
bash: /project/6014302/bfiset/Canvas/Canvas-1.38.0.1554/tabix: Permission denied
2018-08-31T23:13:37-04:00,ERROR: Canvas workflow error: Isas.Framework.WorkManagement.JobFailedException: Job tabix-index-tmp-ballele.bedgraph.gz.1 failed with exit code 12
6

In the file: tabix-index-tmp-ballele.bedgraph.gz.1.stderr has this:

bash: /project/6014302/bfiset/Canvas/Canvas-1.38.0.1554/tabix: Permission denied

Tabix and Tabix.exe are in the /project/6014302/bfiset/Canvas/Canvas-1.38.0.1554/tabix directory.

When I try to execute tabix.exe with dotnet get this:

dotnet tabix.exe
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/project/6014302/bfiset/Canvas/Canvas-1.38.0.1554/'.

Haven't seen this issue in the Cavas issues.

Any guidance possible ?

Thanks,

B.

BenoitFiset commented 6 years ago

Thanks Alexander T. for the answer:

" Make tabix executable with chmod +x tabix in the Canvas base directory."

This fixed the issue and execution resumed.

ATpoint commented 6 years ago

I just see that my comment was deleted, strange. Suggestion was to make tabix executable with chmod +x tabix in the Canvas base directory.

BenoitFiset commented 5 years ago

Canvas version Canvas-1.39.0.1598 has the same issue no "x" for tabix...

144115336520668785 512 -rw-rw-r--  1  2.5M Oct 18 15:36 tabix
144115336520668786 512 -rw-rw-r--  1  204K Oct 18 15:36 tabix.exe

Have to issue chmod +x tabix for this version to work.

tfenne commented 5 years ago

I just ran into this same issue with both 1.39 and 1.40. Would be really nice if either the tar file generation could include setting the execute permissions on tabix (and possibly also bedGraphToBigWig), or at the least putting this in the install instructions that one needs to do this before running on linux.