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Can't read files on s3 #1277

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BenjaminSargsyan opened this issue Apr 5, 2024 · 0 comments
Open

Can't read files on s3 #1277

BenjaminSargsyan opened this issue Apr 5, 2024 · 0 comments

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@BenjaminSargsyan
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Hi.
I am using igv-reports python package to generate igv pictures for the given sample located on s3 but it crushes on the part where it uses pysam package showing protocol not supported.
I tried to just use pysam.view but it also crushed with exit code 1 and again showed can't open file protocol not supported.
I thought that it is because of the samtools installed in my environment in Kubernetes cause the samtools in there gives the same error.
So I decided to use all of it locally with satmools version 1.18 with htslib version 1.18 but it didn't worked.
Also I searched in several packages to see where the samtools directory is located but haven't found any.

Is there any way to use pysam with s3 files ?

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