[Biodevelopers] Blastall core dump on Alpha running Redhat 7.2

[Iddo Friedberg]

Less facetiously, I experienced something similar on an Alpha sometime 
ago. I recompiled everything w/o optimizations, and it worked... then I 
started raising the O levels, at some point I got the dreaded core dump.

HTH,

./I


Iddo Friedberg wrote:
> How not to use BLAST... ;)
> 
> Chris Dwan wrote:
> 
>>
>> I have an odd blastall behavior:  We have two sequences, which appear 
>> to be anathema to blastall version 2.2.8 running on an AlphaServer 
>> E40, Redhat 7.2 as distributed by HP.  The error occurs both with the 
>> downloaded binaries, and with a version of the ncbi toolbox which I 
>> built locally.
>>
>> If I attempt to align these sequences in nucleic acid space using 
>> bl2seq (or blastall, searching with either against a formatted target 
>> containing the other) then I get a core dump.  The core file indicates 
>> that an "error 8:  Arithmetic error" was the cause of death.  Tblastx 
>> also works fine.
>>
>> Everything works just peachy on an Intel Linux system, or an Apple OS 
>> X system.
>>
>> I would appreciate any suggestions, hints, or fixes.  The sequences 
>> are below.
>>
>> -Chris Dwan
>>
>>  >93-NE-13
>> ATGTTGGGGAAATGCTTGACCGCGGGCTGTTGCTCGCGATTGCTTTTTTTGTGGTGTATC
>> GTGCCGTCCTGTTTTGTTGCGCTCGTCAGCGCCAGCAACAGCAACAGCTCCCATTTACAG
>> CTGATTTACAACTTGACGCTATGTGAGCTGAATGGCACGGATTGGCTAGCTAATAGATTT
>> GATTGGGCAGTGGAATGTTTTGTCATTTTTCCTGTGCTGACTCACATTGTCTCCTATGGT
>> GCCCTCACTACTAGCCATTTCCTTGACACAGTCGGTCTGGTCACTGTGTCTACCGCCGGT
>> TTTCGTCACGGGCGGTATGTTCTGAGTAGCATCTACGCGGTCTGTGCCCTGGCTGCGTTG
>> TTTTGCTTCGTCATTAGATTTGTGAAGAATTGCATGTCCTGGCGCTATTCATGTACCAGA
>> TATACCAACTTTCTTCTGGATACTAAGGGCAGACTCTATCGTTGGCGGTCGCCCGTCATC
>> ATAGAGAAAAATGGTAAAGTTGAGGTCGAAGGTCATCTGATCGACCTCAAGAGAGTTGTG
>> CTTGATGGTTCCGTGGCAACCCCTGTAACCAGAGTTTCAGCGGAACAATGGGGTCGTCCT
>> TAG
>>
>>  >91-KY-3
>> ATGTTGGGGAAATGCTTGACCGCGGGCTGTTGCTCGCGATTGCTTTTTTTGTGGTGTATC
>> GTGCCGTCCTGTTTTGTTGCGCTCGTCAGCGCCAACAGCAACAGCAGCTCCCATTTACAG
>> CTGATTTACAACTTGACGCTATGTGAGCTGAATGGCACAGATTGGCTAGCTAGTAGATTT
>> GATTGGGCAGTGGAGTGTTTTGTCATCTTTCCTGTGCTGACTCACATTGTCTCCTATGGC
>> GCCCTCACTACCAGCCATTTCCTTGACACAGTCGGTCTGGCCACTGTGTCTACCGCCGGT
>> TTTCTTCGCGGGCGGTATGTTCTGAGTAGCATCTACGCGGTCTGTGCCCTGGCTGCGTTG
>> TTTTGCTTCGTCATTAGATTGGCGAAGAATTGCATGTCCTGGCGCTATTCATGTACCAGA
>> TATACCAACTTTCTTCTGGATACTAAGGGCAGACTCTATCGTTGGCGGTCGCCCGTCATC
>> ATAGAGAAAAAGGGTAAAGTTGAGGTCGAAGGTCATCTGATCGACCTCAAGAGAGTTGTG
>> CTTGATGGTTCCGTGGCAACCCCTGTAACCAGAGTTTCAGCGGAACAATGGGGTCGTCCT
>> TAG
>>
>>
>>
>>
>>
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>>
> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo