Question: Problems Running Gkno Fastq-Tangram
0
gravatar for Masaki
5.3 years ago by
Masaki0
Masaki0 wrote:

Hello,

I'm trying to analyze mobile element insertion sites by gkno fastq-tangram pipeline. This pipeline looks very nice, but I'm stuck in running <gkno pipe="" fastq-tangram="">. I would like to ask what is wrong with my command and how to fix it.

I have downloaded gkno file sets with git and builded them according to the websites (http://blog.gkno.me/post/29962850248/getting-started-with-gkno). "gkno build" and "gkno run-test" seemed all right with the message, "gkno completed tasks successfully."

However, gkno pipe fastq-tangram did not run. I am wondering if something wrong happened in generating "generate-file-list.sh", although the message said "generate-file-list.json...done". Actually, "generate-file-list.sh" do not exist in my /PATH/TO/gkno_launcher/tools/scripts/ directory (The file "merge-vcf.sh" do exist in the same directory). The read data are derived from illumina-GAIIx exome sequencing on human sample. The reference is UCSC hg19.

Thanks in advance.

(edited on June 6. 2013)


My command was,

[nishioka@n000 gkno_launcher]$ ./gkno pipe fastq-tangram -r /home/nishioka/Data/hg19/hg19.fasta -mr /home/nishioka/Data/hg19_MEI/moblist_tangram.fa -q /media/molpsy/qf_read/s_5_1_sequence.fq -q2 /media/molpsy/qf_read/s_5_2_sequence.fq -srh 50 -sr moblist -rg chr1

===============================

Boston College gkno package

version: 0.72
date:    May 2013

===============================

Checking tool configuration files...

 concatenate-files.json...done.
 bamleftalign.json...done.
 vcflib.json...done.
 picard.json...done.
 tabix.json...done.
 bgzip.json...done.
 michigan-bam-utilities.json...done.
 bamtools.json...done.
 premo.json...done.
 freebayes.json...done.
 md5.json...done.
 gzip.json...done.
 merge-vcf-files.json...done.
 ogap.json...done.
 mosaik.json...done.
 gatk.json...done.
 tangram.json...done.
 samtools.json...done.
 generate-file-list.json...done.

Checking pipeline configuration file...done.
Reading in command line arguments...done.
Workflow:
 build-tangram-reference (tangram-index):                            Create an indexed reference
                                                                     file including the mobile
                                                                     elements
 merge-fasta (concatenate-files):                                    Join multiple files
 index-fasta (samtools-index-fasta):                                 Generate an index for a
                                                                     reference fasta file.
 create-sequence-dictionary (picard-create-sequence-dictionary):     Generate a dictionary
                                                                     containing all of the sequences
                                                                     in the input reference fasta.
 build-reference (mosaik-build-reference):                           Build the Mosaik reference
 build-jump-database (mosaik-jump):                                  Generate the jump database for
                                                                     a Mosaik reference
 generate-mosaik-parameters (premo):                                 Determine MosaikAligner
                                                                     parameters based on read and
                                                                     fragment length
 build-read-archive (mosaik-build-fastq):                            Build the Mosaik read archive
 align (mosaik-aligner):                                             Pairwise alignment of a read
                                                                     archive
 sort-primary-bam (bamtools-sort):                                   Sort a BAM file
 sort-multiple-bam (bamtools-sort):                                  Sort a BAM file
 index-primary-bam (bamtools-index):                                 Index a BAM file
 mark-duplicates (picard-mark-duplicates):                           Mark duplicate reads.
 index-final-bam (bamtools-index):                                   Index a BAM file
 generate-bam-list (generate-file-list):                             Generate a text file containing
                                                                     a list of files
 scan-bam-files (tangram-scan):                                      Generate a histogram of the
                                                                     fragment length distributions
                                                                     of the input libraries.
 detect-mei (tangram-detect):                                        Detect and genotype structural
                                                                     variation events.

Assigning command line arguments to tasks...done.
Checking the command line arguments...done.
Checking instance information...done.
Checking multiple runs information...done.

ERROR:   Missing executable files
DETAILS: The following executable files are not available, but are required:

     /home/nishioka/gkno_launcher/tools/scripts/generate-file-list.sh

================================================================================================

TERMINATED: Errors found in running gkno.  See specific error messages above for resolution.

================================================================================================
• 1.7k views
ADD COMMENTlink modified 5.3 years ago by Malachi Griffith16k • written 5.3 years ago by Masaki0

Thanks for editing the question. In future, please post comments under the original answer, rather than as a new answer.

ADD REPLYlink written 5.3 years ago by Neilfws48k
1
gravatar for Neilfws
5.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

EDIT: question has been edited to reflect the problems outlined in my answer, so answer no longer relevant.

Is this a faithful rendering of the error message and does it really say, for example:

/Path/to/gkno_launcher/tools/scripts/generate-file-list.sh

If so, I doubt that the directory gkno_launcher is located under directories named /Path/to on your machine. It looks like you have just copied and pasted this command without understanding what it means.

You need to substitute /Path/to with the real path to your directory. For example, if the file hg19.fasta is located in /home/masaki/Documents, then you would use

/home/masaki/Documents/hg19.fasta

not

/Path/to/hg19.fasta

And so on for the other files in the command.

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Neilfws48k
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