Hi Drew,
The .ntm files are temporary files that the NCBI library uses when
constructing the database indices.
This seems to be the relevant error message:
NOTE: CoreLib [002.003]
FileOpen("/opt/blast/newdb/vertebrate_mammalian.002.ntm"
,"r") failed
ERROR: [000.000] SORTFiles failed, change TMPDIR to a partition with more
free s
pace or use -s option
Is it true that the machine is running out of space in
/opt/blast/newdb? It's possible to check drive space on many unix
machines with the `df` command.
-Aaron
Drew Bullard wrote:
Hi all,
Has anyone successfully formatted the vertebrate_mammalian NCBI database
using mpiformatdb. I have tried several iterations to format the data into 5
chunks.
Here's my latest:
$ echo $TMPDIR
/opt/blast/tmpdir
$ df -h /opt/blast
Filesystem Size Used Avail Use% Mounted on
api-lcbkup-1:/blast 545G 374G 172G 69% /opt/blast
$ cat .ncbirc
[NCBI]
Data=/opt/blast/data
[BLAST]
BLASTDB=/opt/blast/newdb
BLASTMAT=/opt/blast/data
[mpiBLAST]
Shared=/opt/blast/newdb
Local=/opt/blast/tmpdir
Here's the database:
$ ls -lh /opt/blast/download/vertebrate_mammalian
-rw-r--r-- 1 dbullard ri 34G Dec 17 05:04
/opt/blast/download/vertebrate_mammalian
Here's the command:
mpiformatdb -N 5 -i /opt/blast/download/vertebrate_mammalian -p
F --skip-reorder
Here's the log:
========================[ Jan 24, 2006 7:03 AM ]========================
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Closing volume /opt/blast/newdb/vertebrate_mammalian.001 with 10402
sequences, 3
,873,748,360 letters(.nsq file = 1006885366 bytes; .nhr file = 1401461
bytes)
Formatted 10402 sequences in volume 1
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Closing volume /opt/blast/newdb/vertebrate_mammalian.002 with 10894
sequences, 3
,880,693,254 letters(.nsq file = 1002450993 bytes; .nhr file = 1467235
bytes)
Formatted 10894 sequences in volume 2
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Closing volume /opt/blast/newdb/vertebrate_mammalian.003 with 8985
sequences, 3,
912,490,460 letters(.nsq file = 1011952328 bytes; .nhr file = 1212563 bytes)
Formatted 8985 sequences in volume 3
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Closing volume /opt/blast/newdb/vertebrate_mammalian.000 with 9760
sequences, 3,
914,162,677 letters(.nsq file = 1002394425 bytes; .nhr file = 1319243 bytes)
Formatted 9760 sequences in volume 0
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Closing volume /opt/blast/newdb/vertebrate_mammalian.004 with 8487
sequences, 3,
925,218,720 letters(.nsq file = 1000860920 bytes; .nhr file = 1145719 bytes)
Formatted 8487 sequences in volume 4
Version 2.2.10 [Oct-19-2004]
Started database file "/opt/blast/download/vertebrate_mammalian"
Formatted 31345 sequences in volume 1
NOTE: CoreLib [002.003]
FileOpen("/opt/blast/newdb/vertebrate_mammalian.002.ntm"
,"r") failed
ERROR: [000.000] SORTFiles failed, change TMPDIR to a partition with more
free s
pace or use -s option
Here's a listing of the final directory, NOTE the 005.ntm file? What is
that?
$ ls -l /opt/blast/newdb/
total 6611631
-rw-r--r-- 1 dbullard ri 1319243 Jan 24 08:05
vertebrate_mammalian.000.00.nhr
-rw-r--r-- 1 dbullard ri 117228 Jan 24 08:05
vertebrate_mammalian.000.00.nin
-rw-r--r-- 1 dbullard ri 78080 Jan 24 08:05
vertebrate_mammalian.000.00.nnd
-rw-r--r-- 1 dbullard ri 356 Jan 24 08:05
vertebrate_mammalian.000.00.nni
-rw-r--r-- 1 dbullard ri 1955463 Jan 24 08:05
vertebrate_mammalian.000.00.nsd
-rw-r--r-- 1 dbullard ri 45207 Jan 24 08:05
vertebrate_mammalian.000.00.nsi
-rw-r--r-- 1 dbullard ri 997954313 Jan 24 08:05
vertebrate_mammalian.000.00.nsq
-rw-r--r-- 1 dbullard ri 4131317 Jan 24 08:51
vertebrate_mammalian.000.01.nhr
-rw-r--r-- 1 dbullard ri 376248 Jan 24 08:51
vertebrate_mammalian.000.01.nin
-rw-r--r-- 1 dbullard ri 250760 Jan 24 08:51
vertebrate_mammalian.000.01.nnd
-rw-r--r-- 1 dbullard ri 1028 Jan 24 08:51
vertebrate_mammalian.000.01.nni
-rw-r--r-- 1 dbullard ri 6720507 Jan 24 08:51
vertebrate_mammalian.000.01.nsd
-rw-r--r-- 1 dbullard ri 156680 Jan 24 08:51
vertebrate_mammalian.000.01.nsi
-rw-r--r-- 1 dbullard ri 875184322 Jan 24 08:51
vertebrate_mammalian.000.01.nsq
-rw-r--r-- 1 dbullard ri 1401461 Jan 24 08:04
vertebrate_mammalian.001.nhr
-rw-r--r-- 1 dbullard ri 124932 Jan 24 08:04
vertebrate_mammalian.001.nin
-rw-r--r-- 1 dbullard ri 83216 Jan 24 08:04
vertebrate_mammalian.001.nnd
-rw-r--r-- 1 dbullard ri 372 Jan 24 08:04
vertebrate_mammalian.001.nni
-rw-r--r-- 1 dbullard ri 2122526 Jan 24 08:04
vertebrate_mammalian.001.nsd
-rw-r--r-- 1 dbullard ri 49005 Jan 24 08:04
vertebrate_mammalian.001.nsi
-rw-r--r-- 1 dbullard ri 989185886 Jan 24 08:04
vertebrate_mammalian.001.nsq
-rw-r--r-- 1 dbullard ri 3618358 Jan 24 08:51
vertebrate_mammalian.002.nhr
-rw-r--r-- 1 dbullard ri 330624 Jan 24 08:52
vertebrate_mammalian.002.nin
-rw-r--r-- 1 dbullard ri 220344 Jan 24 08:51
vertebrate_mammalian.002.nnd
-rw-r--r-- 1 dbullard ri 908 Jan 24 08:51
vertebrate_mammalian.002.nni
-rw-r--r-- 1 dbullard ri 0 Jan 24 08:51
vertebrate_mammalian.002.nsd
-rw-r--r-- 1 dbullard ri 648 Jan 24 08:04
vertebrate_mammalian.002.nsi
-rw-r--r-- 1 dbullard ri 994808643 Jan 24 08:51
vertebrate_mammalian.002.nsq
-rw-r--r-- 1 dbullard ri 3408746 Jan 24 08:51
vertebrate_mammalian.003.nhr
-rw-r--r-- 1 dbullard ri 107928 Jan 24 08:05
vertebrate_mammalian.003.nin
-rw-r--r-- 1 dbullard ri 71880 Jan 24 08:05
vertebrate_mammalian.003.nnd
-rw-r--r-- 1 dbullard ri 332 Jan 24 08:05
vertebrate_mammalian.003.nni
-rw-r--r-- 1 dbullard ri 1815511 Jan 24 08:05
vertebrate_mammalian.003.nsd
-rw-r--r-- 1 dbullard ri 161 Jan 24 08:05
vertebrate_mammalian.003.nsi
-rw-r--r-- 1 dbullard ri 998850878 Jan 24 08:52
vertebrate_mammalian.003.nsq
-rw-r--r-- 1 dbullard ri 3653467 Jan 24 08:51
vertebrate_mammalian.004.nhr
-rw-r--r-- 1 dbullard ri 101952 Jan 24 08:06
vertebrate_mammalian.004.nin
-rw-r--r-- 1 dbullard ri 67896 Jan 24 08:06
vertebrate_mammalian.004.nnd
-rw-r--r-- 1 dbullard ri 316 Jan 24 08:06
vertebrate_mammalian.004.nni
-rw-r--r-- 1 dbullard ri 1705972 Jan 24 08:06
vertebrate_mammalian.004.nsd
-rw-r--r-- 1 dbullard ri 388 Jan 24 08:06
vertebrate_mammalian.004.nsi
-rw-r--r-- 1 dbullard ri 999163733 Jan 24 08:51
vertebrate_mammalian.004.nsq
-rw-r--r-- 1 dbullard ri 3611609 Jan 24 08:51
vertebrate_mammalian.005.nhr
-rw-r--r-- 1 dbullard ri 0 Jan 24 08:06
vertebrate_mammalian.005.nin
-rw-r--r-- 1 dbullard ri 871563163 Jan 24 08:52
vertebrate_mammalian.005.nsq
-rw-r--r-- 1 dbullard ri 5937997 Jan 24 08:52
vertebrate_mammalian.005.ntm
-rw-r--r-- 1 dbullard ri 339 Jan 24 08:51
vertebrate_mammalian.nal
Here's the nal file:
$ cat /opt/blast/newdb/*.nal
#
# Alias file created Tue Jan 24 08:51:22 2006
#
#
TITLE /opt/blast/newdb/vertebrate_mammalian
#
DBLIST /opt/blast/newdb/vertebrate_mammalian.000
/opt/blast/newdb/vertebrate_mammalian.001
/opt/blast/newdb/vertebrate_mammalian.002
/opt/blast/newdb/vertebrate_mammalian.003
/opt/blast/newdb/vertebrate_mammalian.004
#
#GILIST
#
#OIDLIST
#
thanks,
-- Drew
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