[Known problem with BLAST module]500+ results gives no output in blast

[bradfordcondon]

The user experienced an error that there were 500 + results. Even tightening the evalue gave this error: i suspect that it is not a blast issue but a bug in the module.

[bradfordcondon]

Also, if there are 500 + results, why not just skim the top 20 and return those?

[bradfordcondon]

Sequences are below to troubleshoot. Meg has verified setting a reasonable e value should not give 500+ results.

>54Downstream-Mine_F12.ab1
NNNNNNNNNNNNNNNNNNNNNCANNAANGTGACAGANTAGCTTGGGCAANGGAANNCCGAAGGAAGGTTNNCGGATATTACCCTTNGTTGAAAAGTCTCAATTGCCCTTTGGTCTTCTGAGACTGTATCTTTGATATTTTTGGAGTAGACAAGTGTGTCGTGCTCCACCATGTTGACCTCTGCAGGCATGCAAGCTTCTGTTAACTTGCTAGCTTCTGCAGGTACCTTAATTAAAAGTTTAAACTATCAAGTGACTGCATATACGTTCCTGCACCAACTTTGGCAAAGAAAAGGCAACCCACTTCATCATGTGAAGAATGCTGACTATCACCACTAATGGAAACTAATGGAAGATTTGGACAAGCCAGGACGCCCAACACTACTTTCCCTTCATCTAGCAATCCCAGTGCTATAGCATATTGGTCTCCTCTTAGAAATCTATTACAAAATATGAAGCACTCAATTGACAAGTGAATGCATAAAAAAAATAAGCACTCGGTTGACAAGTGAATCATTGATAAAATATATAAATCAGCAAATAGAAAGTACAAAACAAAGCAATGAAAAAGGAAGTTTCGCCAAAGAGAGTTAGCGACCACTGATTTTTGTCTAGTTCCTTAAGTCTTCTAAACGTACTTCATTTCCTATCACAATGCNACACNCTNNNNNNNANNNNAAA
>58Upstream-Mine_G12.ab1
NNNNNNNNNNNNNNNNCTGACCGCTTCCTCGTGCTTTACGGTATCGCCGCTCCCGATTCGCAGCGCATCGCCTTCTATCGCCTTCTTGACGAGTTCTTCTGAGGGATCGTTCAAACATTTGGCAATAAAGTTTCTTAAGATTGAATCCTGTTGCCGGTCTTGCGATGATTATCATATAATTTCTGTTGAATTACGTTAAGCATGTAATAATTAACATGTAATCTTGTTTCTTTTATCAAAAGGTATACATGTGTAGGTTTTAATGTTTTATAAATCGAATGAAGAAAGTCAAATAATGTAAAAGAGAAAAACAAGAGCAATGGTTTTAATATAATTCGATTTCACGGTCGACCCATGTCCACACCCAAAAATAAAATAAATAAATAAAATCCAAAAAACCTAAATTTTTATGATTCTAAATTATTTTTGTATGTTACAATGAAACCGTGCACGCAAGTAGACATGGCAAAACGAGTTGGGATTCACCAACCTGACCCAAATCCAAAGGAAAATATTTGATCCAAATCTGATTTTTTGACCCGAATATAAAACAAGTTGACCTGTGACCTGACCNNNCCCNNNNNNNNAANNN
>58Downstream-Mine_H12.ab1
NNNNNNTNNNNTCTTCNCATAAAGTGACAGATAGCTGGGCAATGGAATCCGAGGAGGTTTCCGGATATTACCCTTTGTTGAAAAGTCTCAATTGCCCTTTGGTCTTCTGAGACTGTATCTTTGATATTTTTGGAGTAGACAAGTGTGTCGTGCTCCACCATGTTGACCTCTGCAGGCATGCAAGCTTCTGTTAACTTGCTAGCTTCTGCAGGTACCTTAATTAAAAGTTTAAATGCATGTTAAGAGCATACAGAACATGTGATTCAATGGTTGAATTTTCAAAATATAGATTCAATAAATTATTAAGTACATCCAATTGGCATGAAAATTGGCATGCATATTAAGAATATATAGAACATATGATTCAACAGTTGAATTTTCAAAATATAAATTCAATAACAAGTTATTGGATGATGTAACATATAATGTCATTCAAATACAATGGCNNNNNNAAAGCAAA

we're talking about the bottom sequence, >58Downstream-Mine_H12.ab1

[bradfordcondon]

default blast parameters: error, 500+ sequences

evalue of 0.00000000001, max target = 50

e value: 0.00000000001 no max target

[bradfordcondon]

Created an issue in the module to resolve tripal/tripal_blast#25

I think the ideal behavior is obvious: display the first 500 results. (realistically the first 50 results...)

[bradfordcondon]

Secondary issue with #203

Setting the max number of hits to 250 instead of 50 puts you somewhere between. at 500, the module cuts users off. at 50, theres no problem. at 250, the module allows the request to run, and i believe the server runs out of memory, ie, we experience the problem that Lacey put in the failsafe to prevent in tripal/tripal_blast#12.

Solutions

temporary

• Change the cutoff in the code from 500 to 101

Long term

• Reimplement how they read in the xml in the module itself, see Lacey's issue on the module

[bradfordcondon]

hard coded solution:

default:

? $options['max_target_seqs'] : 500; changed to 50

options: remove 250, 500 +

Done on dev, testing

[bradfordcondon]

changes made live as well.

What I should do is change the admin form to accept an array of choices...