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