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hwc2021 / GSAT

Graph-based Sequence Assembly Toolkit
MIT License
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Arrays and negative indexes in Perl #1

Open chlorophyllb opened 1 year ago

chlorophyllb commented 1 year ago

Hi, i ran with this command:

gsat graphCorrection -conf mytest1.conf

im getting this error:

BLAST ran out of memory: Query sequence buffer

Reading gfa file ... Reading path file ... Reading reads file ... Constructing index for reads ...

Modification of non-creatable array value attempted, subscript -1 at /public/home/softwares/GSAT-main/bin/../lib/GSAT/graphIO.pm line 21.

what could be the reason?

thank.

hwc2021 commented 1 year ago

It seems that the problem occurred during the blast process: the input query and subject files are too large which made the blastn program ran out of the memory and failed to output the alignments.

Please change the minimap2 option (in your config file, e.g., mytest1.conf) to use the minimap2, instead of blastn, for large sequencing dataset.