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When I try to add a BAM file to a project that already has several BAM files, I get this: "BAM file truncated (error code 3)" What causes this error? I see no list of error codes in the GH manual.

asked 2019-11-14 21:22:57 -0600

Whit Athey gravatar image

This error occurred during the computation of the BAI index.

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answered 2019-11-15 15:53:20 -0600

I believe that issues is simply that your BAM file is in fact truncated (corrupted).

BAM files are essentially a specific type of compressed gz file with a series of compressed chunks. When reading a file for indexing, we are reading the entire contents and following the internal structure. This error says a given chunk expected more bytes than the file contained, usually indicating that the BAM file was copied from some other location but not in its entirety.

Without a valid BAM file, we can't build an index and display it.

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Asked: 2019-11-14 21:22:57 -0600

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Last updated: Nov 15 '19