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.
================================================================================================
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