Can't Bio.pairwise2 align two very long sequences(50kbp and 100kbp)?

[tanger-code]

Hi.
I am aligning two long sequence(seq1 is 5wbp, seq2 is 10wbp) using Bio.pairwise2, but there is an error:
Process finished with exit code -1073741819 (0xC0000005)

Can't Bio.pairwise2 align such long sequence? Or is there other method to do this in Bio?

Any advice would help me a lot.

[MarkusPiotrowski]

Sorry for my ignorance, but what is 'w' standing for?

[tanger-code]

Sorry for my ignorance, but what is 'w' standing for?

Sorry, it means 50,000bp and 100,000bp

[MarkusPiotrowski]

Yes, that's probably too long, although I'm not sure if the error messages that you see is indicative for a memory overflow.

However, please use the 'new' PairwiseAligner, as described here: https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec127

[tanger-code]

Ok, I will try it.
Thank you.

[peterjc]

I'd have written this as 50kbp and 100kbp, with k for kilo meaning a thousand from the SI units https://en.wikipedia.org/wiki/Metric_prefix

Was the "w" for 10,000 from another language perhaps? I know Japanese use this unit a lot.

[tanger-code]

I'd have written this as 50kbp and 100kbp, with k for kilo meaning a thousand from the SI units https://en.wikipedia.org/wiki/Metric_prefix

Was the "w" for 10,000 from another language perhaps? I know Japanese use this unit a lot.

Haha, you guessed close, I'm Chinese.

[mdehoon]

@tanger-code Were you able to use the PairwiseAligner for this problem? It will require a lot of memory (more than 50000 * 100000 bytes).