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AlphaMissense_hg38.tsv.gz tabix indexing issue VEP #7

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Katerina10-cloud opened this issue Nov 15, 2023 · 1 comment
Open

AlphaMissense_hg38.tsv.gz tabix indexing issue VEP #7

Katerina10-cloud opened this issue Nov 15, 2023 · 1 comment
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@Katerina10-cloud
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Katerina10-cloud commented Nov 15, 2023

I'm experiencing the issue with the tabix indexing of AlphaMissense_hg38.tsv.gz file.
I've installed alphamissense plugin in VEP and have downloaded the requested files and launch the tabix command before use it.
As I know IIRC file is already compressed with bgzip.
For indexing I use tabix Singularity image tabix_v0.2.6.sif
The command is: singularity exec tabix_v0.2.6.sif tabix -s 1 -b 2 -e 2 -f -S 1 AlphaMissense_hg38.tsv.gz
The error of command run:

INFO:    Converting SIF file to temporary sandbox...
open: No such file or directory
[tabix] was bgzip used to compress this file? AlphaMissense_hg38.tsv.gz
INFO:    Cleaning up image...

Any suggestions and ideas regarding this issue will be appreciated

@Katerina10-cloud Katerina10-cloud added the bug Something isn't working label Nov 15, 2023
@Katerina10-cloud Katerina10-cloud changed the title AlphaMissense_hg38.tsv.gz file indexing issue AlphaMissense_hg38.tsv.gz tabix indexing issue Nov 15, 2023
@Katerina10-cloud Katerina10-cloud changed the title AlphaMissense_hg38.tsv.gz tabix indexing issue AlphaMissense_hg38.tsv.gz tabix indexing issue VEP Nov 15, 2023
@Katerina10-cloud
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Katerina10-cloud commented Nov 16, 2023

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