Crash when creating _short_initial_contigs_extended_contigs.* files

[YannDussert]

Hello,

I have the following issue with AlignGraph: the program crashes during the creation of _short_initial_contigs_extended_contigs.* files by BLAT (corresponding to that line of code: s = "blat tmp/_extended_contigs." + itoa(i) + ".fa tmp/_short_initial_contigs." + itoa(i) + ".fa -noHead tmp/_short_initial_contigs_extended_contigs." + itoa(i) + ".psl > blat_doc.txt 2> blat_doc.txt";).

Blat give this error:
Program error: trying to allocate 0 bytes in needLargeMem (limit: 536870912)
blat: memalloc.c:90: needLargeMem: Assertion `0' failed.

After looking at temporary files, it seems that, for some of the reference genome contigs, the _extended_contigs.* and _short_initial_contigs.* files are empty.

Is this an issue with my dataset, or with the program? Can I do something to resolve this issue?

Thank you in advance for your answer.
Best regards,
Yann

[baoe]

Hi, Yann,

Sorry for reply late. The problem should be due to BLAT's version. Maybe try version v34.

Bao