Further enquiry on constructing DIYA pipeline (Luqman@MKLMS) (20100612)

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Further enquiry on constructing DIYA pipeline (Luqman@MKLMS) (20100612)

Muhd Khairul Luqman Muhd Sakaff
Dear all,

Greetings and good day. I am Luqman, a Msc student in enviromental microbiology from Centre for Chemical Biology (CCB@USM), Universiti Sains Malaysia (USM), Malaysia.

I am currently working on a genome assembly and annotation project of a bacteria, and are interested in using DIYA for the project. I am using the genome-annotater-fasta-test.cofg as my foundation. I have question on the type of error encountered during the run and would like to ask for help and guidance on correcting the obstacle. Please refer below for the error message...

************************************************
[root@linuxtest01 diya-1.0-rc4]# ./diya.pl --conf genome-annotator-fasta-test-SG.conf S.grandis-ace10.fasta

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/'
Using 'genome-annotator-fasta-test-SG.conf'
Reading 'genome-annotator-fasta-test-SG.conf'
File count is 1
Next input file is 'S.grandis-ace10.fasta'
The diya home directory is '/opt/diya-1.0-rc4/'
No output directory defined, will use '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya'
<mode> for the pipeline is 'serial'
Directory '/opt/diya-1.0-rc4/2010_06_15_14_39_43_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 'S.grandis-ace10.fasta' is 'fasta'
No <inputformat> found for step 'assemble_pseudocontig', no conversion needed
No <inputfrom> found for 'assemble_pseudocontig'
'S.grandis-ace10.fasta' will be used as input file for 'assemble_pseudocontig'
Using '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/' as output directory
Copying 'S.grandis-ace10.fasta' to '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/'
'/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/S.grandis-ace10.fasta' 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 'genome-annotator-fasta-test-SG.conf'
Using '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/' as output directory
Output file name for 'assemble_pseudocontig' is '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/2010_06_15_14_39_43-assemble_pseudocontig.out'
Found <home> '/opt/diya-1.0-rc4/scripts/' for 'assemble_pseudocontig'
Found <executable> 'diya-assemble_pseudocontig.pl' for 'assemble_pseudocontig' in 'genome-annotator-fasta-test-SG.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_15_14_39_43_diya/S.grandis-ace10.fasta'
'OUTPUTFILE' will be substituted with '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/2010_06_15_14_39_43-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_15_14_39_43_diya/S.grandis-ace10.fasta -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID'
Using '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/' as output directory
'OUTPUTDIR' will be substituted with '/opt/diya-1.0-rc4/2010_06_15_14_39_43_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_15_14_39_43_diya/S.grandis-ace10.fasta -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_15_14_39_43_diya/S.grandis-ace10.fasta -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 = 4345237
Contigs tiled  = 0
Total length of tiled contigs =
Untiled contigs = 1
Total length of untiled contigs = 4345237
Number of excluded contigs =
Total length of excluded contigs = 0

Preparing to run 'make-single-fa', step count of 2
'make-single-fa' is a 'script'
'make-single-fa' is a 'script'
Format of 'S.grandis-ace10.fasta' is 'fasta'
No <inputformat> found for step 'make-single-fa', no conversion needed
No <inputfrom> found for 'make-single-fa'
'S.grandis-ace10.fasta' will be used as input file for 'make-single-fa'
Using '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/' as output directory
'/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/S.grandis-ace10.fasta' will be used as input file for 'make-single-fa'
Found <home> '/opt/diya-1.0-rc4/scripts/' for 'make-single-fa'
Found <executable> 'make-single-fa.pl' for 'make-single-fa' in 'genome-annotator-fasta-test-SG.conf'
Using '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/' as output directory
Output file name for 'make-single-fa' is '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/2010_06_15_14_39_45-make-single-fa.out'
Found <home> '/opt/diya-1.0-rc4/scripts/' for 'make-single-fa'
Found <executable> 'make-single-fa.pl' for 'make-single-fa' in 'genome-annotator-fasta-test-SG.conf'
Found <command> 'MYSEQID.gbk' for 'make-single-fa'
Found <command> 'MYSEQID.gbk' for 'make-single-fa'
'make-single-fa' command before substitution is '/opt/diya-1.0-rc4/scripts/make-single-fa.pl MYSEQID.gbk'
'INPUTFILE' will be substituted with '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/S.grandis-ace10.fasta'
'OUTPUTFILE' will be substituted with '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/2010_06_15_14_39_45-make-single-fa.out'
'make-single-fa' command after parser-specific substitution is '/opt/diya-1.0-rc4/scripts/make-single-fa.pl MYSEQID.gbk'
Using '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/' as output directory
'OUTPUTDIR' will be substituted with '/opt/diya-1.0-rc4/2010_06_15_14_39_43_diya/'
'make-single-fa' command after global substitution is '/opt/diya-1.0-rc4/scripts/make-single-fa.pl MYSEQID.gbk'
'make-single-fa' command after variable substitution is '/opt/diya-1.0-rc4/scripts/make-single-fa.pl MYSEQID.gbk'
<mode> for the pipeline is 'serial'
<mode> for the pipeline is 'serial'
No directory given at /opt/diya-1.0-rc4/scripts/make-single-fa.pl line 11.
<mode> for the pipeline is 'serial'
Child error: 65280

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

What does it mean by No directory given at /opt/diya-1.0-rc4/scripts/make-single-fa.pl line 11.

And second is that is the  assemble_pseudocontig. Did it run correctly as I did not found 2010_06_15_14_39_43-assemble_pseudocontig.out after the aborted run.

Thank you.

Best regard,
-Luqman@MKLMS-



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