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BAM reader could not create index

asked 2013-03-22 09:32:14 -0700

Tony Popish gravatar image

I've loaded an ancient Neanderthal y-chromosome BAM file and the 1k Homo Sapiens reference sequence, but now I get the following error: could not create index, could not read data from block (error code 3). This seems kinda major - Any ideas

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Thanks for the response, Gabe - you have mail! BTW, the sequencing was done by the Max Planck lab in Leipzig, Germany using a newly-developed single strand protocol.

Tony Popish ( 2013-03-25 09:29:30 -0700 )edit

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answered 2013-03-28 14:08:47 -0700

Tony Popish gravatar image

Gabe's guess turned out to be the case - the original file was truncated. I returned to the source and re-downloaded the y-chromosome BAM file - this time it was much larger. GenomeBrowse was able to index and display the sequence - thanks much for the troubleshooting assistance!

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answered 2013-03-25 08:09:13 -0700

Hey Tony,

Neanderthal Y-Chromosome! That sounds pretty neat!

That error is a internal one where the number of bytes we expect in a BAM block are more than the number we are able to read.

My guess is that the file might be truncated or corrupted.

If you would like us to take a look at the file, feel free to email us at

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Asked: 2013-03-22 09:32:14 -0700

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Last updated: Mar 28 '13