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maickrau / GraphAligner

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Error: Alignment broke with some reads. #52

Closed AntoineHo closed 1 year ago

AntoineHo commented 2 years ago

Hello,

I am trying to align MinION reads to a .gfa graph obtained with Flye. Some reads caused the alignement to break with this stderr:

GraphAligner bioconda 1.0.14-
src/GraphAlignerBitvectorCommon.h:1118: Assertion 'previous.node(neighbor).endSlice.scoreEnd >= scoreHere-(eq?0:1)' failed. Read: read1. Seed: 0+,0,0,0

I do not really understand what is wrong with the reads, I attached a .fq file of one read that cause this error. Is this a problem in the formatting of the fastq file?

Cheers, Antoine

failed_minion_read_graphaligner.fq.txt

maickrau commented 2 years ago

The formatting of the fastq file is fine. This looks like a bug in GraphAligner instead. Could you also add the graph here?

AntoineHo commented 2 years ago

No problems,

Here is the file containing the graph (~3Gb): https://www.dropbox.com/s/m8039sxxkgutt8z/assembly_graph.gfa.gz?dl=0

AntoineHo commented 2 years ago

I just tried to align one of the problematic reads with the previous version of GraphAligner (v1.0.13) and it worked without error. I will try the whole dataset now.

maickrau commented 1 year ago

This should now work with the most recent commit, please open a new issue if it happens again.