[maq-help] Indexing complex consensus file

[Tim M S. <Tim...@he...>]

We are also getting a segmentation fault when using
"maqindex -i -c consensus.cns our.map" and 11900 reference
sequences. Indexing of our.map works fine. The
segmentation fault occurs while indexing consensus.cns.

I also wonder that assemble.log shows a negative reference
length.
S0 reference length: -1376992766
S0 number of gaps in the reference: 186161294
S0 number of uncalled bases: 1256646331 (-0.68)
Mapcheck shows the correct reference length (bosTau4)
Length of reference sequences exlcuding gaps: 2731813236
Length of gaps in the reference sequences: 186161294

Thank you for any help
Tim

(OS: SLES10, maq-0.6.8, maqview-0.2.3)

Output of strace
........
read(4, "\276\351i\365\177\306u\266d\267\341\226\360M<6\334\20\177"..., 
16384) = 16384
read(4, "T\274\23\276)\3375\37\304\273-?)\376\25\267\244\'\24O\322"..., 
16384) = 16384
read(4, "\343\7\341\223\352\212\361ql]\261:\334\325\257\352\267"..., 
16384) = 16384
read(4, "\6t\242`%T\325\n\310`\32\321sU\1\347\t\334Q\313\r7\263"..., 
16384) = 16384
read(4, "\5\361\266\374&\236\350\346\243=\277H\357?\254^lq\270\30"..., 
16384) = 16384
read(4, "P\234\10/\327\326\323\232g\322\257\252\v\333|\35\315\243"..., 
16384) = 16384
--- SIGSEGV (Segmentation fault) @ 0 (0) ---
+++ killed by SIGSEGV +++


-- 

Tim M. Strom, MD                   Tel: +49 89 3187 3296
Institute of Human Genetics        Fax: +49 89 3187 3297
Helmholtz Zentrum München
German Research Center for Environmental Health
Ingolstaedter Landstr. 1
85764 Neuherberg
Germany

WWW: http://ihg.helmholtz-muenchen.de