Enquiry on DIYA output 20100607 (Luqman@MKLMS-CCB@USM)

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Enquiry on DIYA output 20100607 (Luqman@MKLMS-CCB@USM)

Muhd Khairul Luqman Muhd Sakaff
Greetings and good day to everyone,

I am Luqman from CCB@USM, Malaysia. I am interested in using DIYA for annotating the assembled genome data of the bacteria that I am working on. After setting up  DIYA I and my colleagues tried to run it and actually get the below feed back...

***********************************************

[root@linuxtest01 diya-1.0-rc4]# ./diya.pl -genome-annotator-fasta-test.conf Luqman.fa

 

Do It Yourself Annotator (diya) v. 1.0;

        --help for usage

        --license for copyright information

 

The diya home directory is '/opt/diya-1.0-rc4/'

Unknown option: genome-annotator-fasta-test.conf

The diya home directory is '/opt/diya-1.0-rc4/'

Will use '/opt/diya-1.0-rc4/diya.conf'

Using '/opt/diya-1.0-rc4/diya.conf'

Reading '/opt/diya-1.0-rc4/diya.conf'

File count is 1

Next input file is 'Luqman.fa'

The diya home directory is '/opt/diya-1.0-rc4/'

No output directory defined, will use '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya'

<mode> for the pipeline is 'serial'

Directory '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya' does not exist, will create it

Current <order> is 'assemble_pseudocontig make-single-fa PipeLineOne::glimmer3 extractCDS PipeLineOne::blastpCDS PipeLineOne::rpsblastCDS PipeLineOne::tRNAscanSE PipeLineOne::rnammer cleanup'

 

Preparing to run 'assemble_pseudocontig', step count of 1

'assemble_pseudocontig' is a 'script'

'assemble_pseudocontig' is a 'script'

Format of 'Luqman.fa' is 'fasta'

No <inputformat> found for step 'assemble_pseudocontig', no conversion needed

No <inputfrom> found for 'assemble_pseudocontig'

'Luqman.fa' will be used as input file for 'assemble_pseudocontig'

Using '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/' as output directory

Copying 'Luqman.fa' to '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/'

'/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/Luqman.fa' will be used as input file for 'assemble_pseudocontig'

Found <home> '/opt/diya-1.0-rc4/scripts/' for 'assemble_pseudocontig'

Found <executable> 'diya-assemble_pseudocontig.pl' for 'assemble_pseudocontig' in '/opt/diya-1.0-rc4/diya.conf'

Using '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/' as output directory

Output file name for 'assemble_pseudocontig' is '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/2010_06_02_17_12_07-assemble_pseudocontig.out'

Found <home> '/opt/diya-1.0-rc4/scripts/' for 'assemble_pseudocontig'

Found <executable> 'diya-assemble_pseudocontig.pl' for 'assemble_pseudocontig' in '/opt/diya-1.0-rc4/diya.conf'

Found <command> '-bin /arch/bin -infile INPUTFILE -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID' for 'assemble_pseudocontig'

Found <command> '-bin /arch/bin -infile INPUTFILE -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID' for 'assemble_pseudocontig'

'assemble_pseudocontig' command before substitution is '/opt/diya-1.0-rc4/scripts/diya-assemble_pseudocontig.pl -bin /arch/bin -infile INPUTFILE -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID'

'INPUTFILE' will be substituted with '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/Luqman.fa'

'OUTPUTFILE' will be substituted with '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/2010_06_02_17_12_07-assemble_pseudocontig.out'

'assemble_pseudocontig' command after parser-specific substitution is '/opt/diya-1.0-rc4/scripts/diya-assemble_pseudocontig.pl -bin /arch/bin -infile /opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/Luqman.fa -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID'

Using '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/' as output directory

'OUTPUTDIR' will be substituted with '/opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/'

'assemble_pseudocontig' command after global substitution is '/opt/diya-1.0-rc4/scripts/diya-assemble_pseudocontig.pl -bin /arch/bin -infile /opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/Luqman.fa -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID'

'assemble_pseudocontig' command after variable substitution is '/opt/diya-1.0-rc4/scripts/diya-assemble_pseudocontig.pl -bin /arch/bin -infile /opt/diya-1.0-rc4/2010_06_02_17_12_07_diya/Luqman.fa -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID'

<mode> for the pipeline is 'serial'

<mode> for the pipeline is 'serial'

<mode> for the pipeline is 'serial'

Scaffold file appears not to exist at MYSEQID.scaff. Carrying on without scaffolding

 

Total size of pseudocontig = 3064

Contigs tiled  = 0

Total length of tiled contigs =

Untiled contigs = 1

Total length of untiled contigs = 3064

Number of excluded contigs =

Total length of excluded contigs = 0

 

Preparing to run 'make-single-fa', step count of 2

No type found for 'make-single-fa' in /opt/diya-1.0-rc4/diya.conf at /usr/lib/perl5/site_perl/5.8.5/diya.pm line 1958.

[root@linuxtest01 diya-1.0-rc4]#

****************************************

I am currently stuck at the above process. I have several question. 1st is that I did not have the make-single-fa scripts. Is there any database available on the internet that I could access to get the scripts or any reference on how to write the scripts?

Second, is there any error or mistake that I miss in the output?

Thank you.

Best regard,
-Luqman@MKLMS-

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Diyg-pub-l mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/diyg-pub-l