Memory and CPU usage (until killed by OS) |
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too...
2012-04-18
BLAST+ memory hog with subject FASTA and XML output
We noticed a major memory problem running NCBI BLAST+ with XML output using a FASTA subject (consuming loads of swap space then getting killed). This doesn't happen with tabular output, nor if using a BLAST database:
2012-04-03
Missing feature locations in GenBank "with parts"
My last blog post was on a problem with missing NCBI GenBank feature location information for trans-spliced genes when using GenBank 'with parts'. That was fixed, but while using EFetch a colleague just stumbled over something possibly related where the location is given as just a question mark. This took a little digging to understand...
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