trouble opening muse project

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ksaville
Posts: 45
Joined: Mon Aug 06, 2007 8:30 pm

trouble opening muse project

Post by ksaville » Thu Feb 07, 2008 8:44 pm

We tried downloading the mouse project

M_BB0112A10

after extracting the files then trying to open consed from within edit_dir we get the following error message

RT tag line should be:
<readname> <tag type> <tag source> <padded read pos start> <padded read pos end> <date YYMMDD:HH24MISS>
where the padded read pos's are from the left end and tag type must be recognized by consed but tag type is not recognized
ace file = M_BB0112A10.fasta.screen.ace.Bio4342
Version 15.0 (050831)
Linux@linux-raji:~/Desktop/M_BB0112A10/edit_dir> /usr/local/genome/bin/consed_linux2.6
no ~/.consedrc file so no user resources will be used--that's ok
couldn't open readOrder.txt--that's ok
Could not open consed.fileOfTagTypes: /usr/local/genome/lib/tagTypes.txt errno=2 No such file or directory
0% done. 50 reads read so far...
1% done. 100 reads read so far...
1% done. 150 reads read so far...
2% done. 200 reads read so far...
2% done. 250 reads read so far...
3% done. 300 reads read so far...
3% done. 350 reads read so far...
4% done. 400 reads read so far...
5% done. 450 reads read so far...
5% done. 500 reads read so far...
6% done. 550 reads read so far...
6% done. 600 reads read so far...
7% done. 650 reads read so far...
7% done. 700 reads read so far...
8% done. 750 reads read so far...
8% done. 800 reads read so far...
9% done. 850 reads read so far...
exception thrown: ace file error detected from source file parseAceFile.cpp at 1066
Error in file M_BB0112A10.fasta.screen.ace.Bio4342 at line 39990. Line:
ofl68h09.b1 nogrow tag_consed 1 784 031008:151609

RT tag line should be:
<readname> <tag type> <tag source> <padded read pos start> <padded read pos end> <date YYMMDD:HH24MISS>
where the padded read pos's are from the left end and tag type must be recognized by consed but tag type is not recognized

ace file: M_BB0112A10.fasta.screen.ace.Bio4342
Version 15.0 (050831)
ace file error detected from source file parseAceFile.cpp at 1066
Error in file M_BB0112A10.fasta.screen.ace.Bio4342 at line 39990. Line:
ofl68h09.b1 nogrow tag_consed 1 784 031008:151609

RT tag line should be:
<readname> <tag type> <tag source> <padded read pos start> <padded read pos end> <date YYMMDD:HH24MISS>
where the padded read pos's are from the left end and tag type must be recognized by consed but tag type is not recognized
ace file = M_BB0112A10.fasta.screen.ace.Bio4342
Version 15.0 (050831)

suggestions?
:?:

cshaffer
Posts: 211
Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
Contact:

Tag type issues with linux installation

Post by cshaffer » Thu Feb 07, 2008 10:09 pm

The mouse project is a project from the Genome Sequencing Center. The center has special tags that are not part of the default set that Consed recognizes. There is a file called tagTypes.txt that is used to describe these GSC specific tags. I believe your problem is missing file to add these GSC specific tag descriptions.

You can get the file here you should put it in /usr/local/genome/lib if you use the default.

See if that helps. If not I believe there is a way to edit the ace file to remove the offending tags, which we can go over if necessary.

Note there are other files that are project specific that are probably not installed if you are missing tagTypes.txt. Check the wiki for all the files. You should check to make sure you have the updated files posted on that wiki page in your installation:

http://gep.wustl.edu/wiki/index.php/GEP ... on_Package

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