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Cannot generate EMBL-pid index files

Morten Stig Andersen mosa at novo.dk
Tue Feb 9 08:47:11 EST 1999


Has anyone got a solution to this:


The "PID" field of coding sequences in EMBL cannot be indexed in SRS.
The srsupdate script can generate and compress the individual index
files, but it dumps core when it tries to merge them. There are no
problems in EMBLNEW, or with generation with any of the other EMBL
indices. My SRS server runs on a SGI IRIX64, v. 6.4.

An extract from the log file is given below.


+ srsbuild EMBL -f  pid -xdir SRSINX: -odir SRSINX: -s unix -nn
...processing EMBL
...processing /usr/databases/embl/est1.dat
...processing /usr/databases/embl/est1.dat

...wrote index file "/z/monet/appl/srs51/index/embl_pid_1.inx"
         size: 0 kbytes, bucket size: 1, records: 0
...wrote IDs file "/z/monet/appl/srs51/index/embl_pid_1.ids"
         size: 1 kbytes, IDs: 0
...processing /usr/databases/embl/est10.dat
...processing /usr/databases/embl/est10.dat

...wrote index file "/z/monet/appl/srs51/index/embl_pid_2.inx"
         size: 1 kbytes, bucket size: 2, records: 3

(... output truncated here)

...processing /usr/databases/embl/vrt.dat
...processing /usr/databases/embl/vrt.dat

...wrote index file "/z/monet/appl/srs51/index/embl_pid_31.inx"
         size: 892 kbytes, bucket size: 40, records: 42034
...wrote IDs file "/z/monet/appl/srs51/index/embl_pid_31.ids"
         size: 421 kbytes, IDs: 42043
...program "srsbuild" completed successfully.

real 5h58m29.60s
user 5h25m14.96s
sys 17m58.02s
+ srsbuild EMBL -c -f  pid -xdir SRSINX: -odir SRSINX: -s unix
...wrote IDs file "/z/monet/appl/srs51/index/embl_pid_1.ids"
         size: 1 kbytes, IDs: 0
...wrote IDs file "/z/monet/appl/srs51/index/embl_pid_2.ids"
         size: 1 kbytes, IDs: 3

(... output truncated here)


...wrote IDs file "/z/monet/appl/srs51/index/embl_pid_31.ids"
         size: 253 kbytes, IDs: 42043
...program "srsbuild" completed successfully.

real 0m3.54s
user 0m1.01s
sys 0m0.87s
+ srsbuild EMBL -m -f  pid -xdir SRSINX: -odir SRSINX: -s unix
./embl_pid[17]: 8624 Bus error(coredump)

real 1m0.01s
user 0m33.25s
sys 0m25.54s


--
=-=-=-=-=-=-=-=-=-=-=-=  \,`/ /  -=-=-=-=-=-=-=-=-=-=-=-=-=
 Morten Stig Andersen   _)..  `_     9M1.83
                       ( __  -\      Scientific Computing
 Tel: +45 444 26959        '`.       Novo Nordisk A/S
 Fax: +45 444 26003       ( \>_-_,   DK-2880 Bagsvaerd
 MoSA at novo.dk             _||_ ~-/   Denmark







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