Dear Working on a RHEL7 24cores I installed all and the ext/app's do work I edited opts.yaml (including creating .ooc 'rake' does not trigger anything! what did I miss? Thanks for help

drwxr-xr-x. 2 splaisan bits 4.0K Jun 12 11:09 data drwxr-xr-x. 5 splaisan bits 65 Jun 12 10:46 ext drwxr-xr-x. 8 splaisan bits 4.0K Jun 12 10:30 .git -rw-r--r--. 1 splaisan bits 1.5K Jun 12 10:30 opts_example.yaml -rw-r--r--. 1 splaisan bits 1.6K Jun 12 11:10 opts.yaml -rw-r--r--. 1 splaisan bits 7.9K Jun 12 10:30 Rakefile -rw-r--r--. 1 splaisan bits 6.0K Jun 12 10:30 README.md drwxr-xr-x. 2 splaisan bits 4.0K Jun 12 10:30 scripts

splaisan@NUC-SRV-01:/opt/biotools/flo$ ll data/ total 2.3G drwxr-xr-x. 2 splaisan bits 4.0K Jun 12 11:09 . drwxr-xr-x. 6 splaisan bits 4.0K Jun 12 11:14 .. -rw-r--r--. 1 splaisan bits 1.9M Jun 12 11:09 11.ooc -rw-r--r--. 1 splaisan bits 1.1G Jun 12 11:05 CA0.2_contigs.fasta -rw-r--r--. 1 splaisan bits 77M Jun 12 11:02 CA0.2_gene_models_noseq.gff3 -rw-r--r--. 1 splaisan bits 1.2G Jun 12 11:05 hybrid_CA0.2.fasta

splaisan@NUC-SRV-01:/opt/biotools/flo$ cat opts.yaml
# Location of binaries expected by flo.
#
# These will be added to PATH before the pipeline is run. The paths below
# are created by `scripts/install.sh`.Comment out or edit the paths based
# on how you installed UCSC-Kent toolkit, GNU Parallel and genometools.
:add_to_path:
- 'ext/kent/bin'
- 'ext/parallel-20150722/src'
- 'ext/genometools-1.5.6/bin'

Location of source and target assemblies.

If migrating annotations from assembly A to assembly B, A is the source

and B is the target. Source and target assemblies are specified as path

to the corresponding FASTA files (must end in .fa).

:source_fa: 'data/CA0.2_contigs.fasta' :target_fa: 'data/hybrid_CA0.2.fasta'

Number of processes that will be used to parallelise flo. Ideally, this

will be the number of CPU cores you have.

:processes: '24'

Parameters to run BLAT with.

In addition to the options specified here, -noHead option is set by flo.

-noHead simply causes the output BLAT output files to not have a header.

It doesn't impact accuracy of results.

Empty string is equivalent to:

-t=dna -q=dna -tileSize=11 -stepSize=11 -oneOff=0 -minMatch=2

-minScore=30 -minIdentity=90 -maxGap=2 -maxIntron=75000

The default string defined below is a suitable trade-off between running

time and sensitivity.

:blat_opts: '-fastMap -tileSize=12 -minIdentity=98'

:blat_opts: 'blat -noHead -fastMap -ooc=data/11.ooc -minScore=100 -minIdentity=98'

Path to the GFF files containing annotations on the source assembly that

will be lifted to the target assembly.

:lift:

'data/CA0.2_gene_models_noseq.gff3'

wurmlab / flo

running rake #10