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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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Error querying alignments for: alignment.sort.bam Error message: Invalid GZIP header #1410

Closed daniel-es6 closed 1 year ago

daniel-es6 commented 1 year ago

Hello,

I am getting this error when loading a bam file that is sorted and indexed. I have tried to delete all the index bai files and recreate it, but still no success. What can be wrong?

The IGV version is 2.16.2, desktop version on a mac (intel chip).

Thanks

daniel-es6 commented 1 year ago

samtools view opens the bam file without problems.

jrobinso commented 1 year ago

Is this being loaded locally or from a web server? If the latter, one possible cause is the web server improperly adding a "Encoding: gzip" header to the response. I have seen this happen and it will cause the error you are experiencing. Otherwise I couldn't really say. If you could share the BAM file we will look into it.

daniel-es6 commented 1 year ago

Hi Jim, I found it was caused by a sync problem, I was opening the old bam file. After a clean sync, the problem went away. Thank you for the tip

daniel-es6 commented 1 year ago

solved.