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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Issue with bgzf_useek() in "Streaming Reads" #146

Open titoghose opened 2 years ago

titoghose commented 2 years ago

Hello,

I am trying to run Expansion Hunter on whole genome sequencing data. The data is in the form of CRAM files. I am running into the following issue when I try to run the code on JupyterLab:

2021-10-11T [Streaming reads] bgzf_useek() on reference file: Software caused connection abort bgzf_useek() on reference file: Transport endpoint is not connected ExpansionHunter: cram/cram.io.c:2501: cram_ref_load: Assertion 'r-->last->count > 0' faild Aborted

I was wondering why this issue might be occurring?

egor-dolzhenko commented 2 years ago

Apologies about this issue. Could you please confirm that the reference you are using is the same as the one used to generate the CRAM file? (All contig names in CRAM header / index must be identical to those in the reference supplied to ExpansionHunter.)