#60 Pregap4 exercise open_db invalid command

v1.6.0
closed
nobody
Gap4 (50)
5
2006-05-18
2006-05-18
Jin Kee
No

I'm running Staden-linux-1.6.0 on Fedora core 4

2.6.16-1.2108_FC4 #1 Thu May 4 23:52:01 EDT 2006 i686
i686 i386 GNU/Linux

set up as described here
http://thekit.livejournal.com/548526.html

I'm working through the staden course "Sequencing
Project Management Using The Staden Package" Last
update 24 Feb 2005 By DP Judge, JK Bonfield and R Staden.

On chapter 2, I get the following error message.

- Report from 'Gap4 shotgun assembly' -
ERR: Failed to open database testdb.0.
ERR: "invalid command name "open_db""
ERR: Aborting.
invalid command name "open_db"

There were no failed files or failed files in the history.

I'm having trouble uploading my tarball of directory
contents to sourceforge, so I'll just paste the
pregap4.config here

# Config file format version 1.0
[global_variables]
set CF
/home/jinkee/jinsdocuments/PhD_work/trunk/staden_exercises/exercise2/lorist6.vector
proc CH_com {} { global lines
if {[regexp {([^.]*)\.(.[0-9]+)(.)?.*}
$lines(ID) matched 1 2 3] == 0} {
return ""
}
if {[string match t $3]} {return 1}
return 0
}
proc PR_com {} { global lines
if {[regexp {([^.]*)\.(.[0-9]+)(.)?.*}
$lines(ID) matched 1 2 3] == 0} {
return ""
}
if {[string match {[spf]1} $2]} {return 1}
if {[string match {[qr]1} $2]} {return 2}
if {[string match {[spf]*} $2]} {return 3}
if {[string match {[qr]*} $2]} {return 4}
return 0
}
set SI 1400..2000
proc TN_com {} { global lines
if {[regexp {([^.]*)\.(.[0-9]+)(.)?.*}
$lines(ID) matched 1 2 3] == 0} {
return ""
}
return $1
}
set SF {}
set SC {}
set SP {}

[::gap4_assemble]
set database_name testdb
set database_version 0
set create 1
set min_match 15
set max_pads 25
set max_pmismatch 5.0
set enter_all 0
set gap4_maxseq 100000
set gap4_maxdb 8000
set enabled 1

[::quality_clip]
set clip_mode confidence
set offset 70
set min_extent 0
set max_extent 999999
set min_length 0
set window_length 50
set conf_val 15
set right_win_length 100
set right_num_uncalled 5
set left_win_length 25
set left_num_uncalled 3
set enabled 1

[::init]
set use_sample_name 0
set enabled 1

[::sequence_vector_clip]
set use_vp_file 1
set vp_file
/bin/staden/staden-linux-1-6-0/tables/vector_primer
set vector_list m13mp18/SmaI
set vp_length 40
set min_5_match 60
set min_3_match 80
set def_5_pos -1
set enabled 1

[::screen_vector]
set min_match 30
set enabled 1

[::cloning_vector_clip]
set word_length 4
set probability 1e-12
set enabled 1

[naming_scheme]
#
# This matches the old-style Sanger Centre naming scheme.
#
set ns_name "Old style Sanger Centre naming scheme"
set ns_regexp {([^.]*)\.(.[0-9]+)(.)?.*}
set ns_lt(TN) {$1}
set ns_lt(PR) {subst {$2 {[spf]1 1} {[qr]1 2} {[spf]*
3} {[qr]* 4} 0}}
set ns_lt(CH) {subst {$3 {t 1} 0}}
set_name_scheme

[module_list]
set MODULE_PATH {$env(STADLIB)/pregap4/modules }
set MODULES {
phred
atqa
eba
convert_trace
compress_trace
init_exp
augment_exp
quality_clip
sequence_vector_clip
cross_match_svec
screen_vector
polyA
cloning_vector_clip
screen_seq
blast
interactive_clip
repeat_masker
hetins
reference
mutscan
gap4_assemble
cap3_assemble
fakii_assemble
phrap_assemble
enter_assembly
email
}

[::phred]
set enabled 0

[::atqa]
set enabled 0

[::eba]
set enabled 0

[::convert_trace]
set enabled 0

[::compress_trace]
set enabled 0

[::init_exp]
set enabled 1

[::augment_exp]
set enabled 1

[::cross_match_svec]
set enabled 0

[::polyA]
set enabled 0

[::screen_seq]
set enabled 0

[::blast]
set enabled 0

[::interactive_clip]
set enabled 0

[::repeat_masker]
set enabled 0

[::hetins]
set enabled 0

[::reference]
set enabled 0

[::mutscan]
set enabled 0

[::cap3_assemble]
set enabled 0

[::fakii_assemble]
set enabled 0

[::phrap_assemble]
set enabled 0

[::enter_assembly]
set enabled 0

[::email]
set enabled 0

[::shutdown]
set enabled 1

Discussion

  • Jin Kee

    Jin Kee - 2006-05-18
    • status: open --> closed
     

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