Closed teepean closed 5 years ago
Hi,
Can you attach your '000_makefile.yaml' file? The error you're getting suggests that you have edited/entered the information in the wrong place, but it is impossible for me to tell what exactly has gone wrong from the error message itself.
Best regards, Mikkel
On Fri, Nov 30, 2018 at 3:47 PM teepean notifications@github.com wrote:
Hello,
I have been experimenting with PALEOMIX and have had success with BAM pipeline.
I decided to run phylogenetic pipeline but at the step $phylo_pipeline genotype+msa+phylogeny 000_makefile.yaml
I get an error message:
Reading makefile(s): Error reading makefiles: MakefileError: Makefile requirement not met at 'root:chimpanzee': Expected value(s): key in 'Project', 'PhylogeneticInference', 'Genotyping', 'PAML', or 'MultipleSequenceAlignment' Observed value(s): 'chimpanzee' Observed type: str
Has something changed since the example was made or what might be causing the issue?
Here's the produced Makefile:
`# -- mode: Yaml; -- Project: Title: ExampleProject List of samples to be included in the analytical steps, which may be grouped using any arbitrary number of (levels of) groups. (Sub)groups are not required, but may be used instead of listing individual samples in 'ExcludeSamples' and 'FilterSingletons'.
Samples: : bonobo: Sex: NA chimpanzee: Sex: NA gorilla: Sex: NA rCRS: Sex: NA GenotypingMethod: Reference Sequence sumatran_orangutan: Sex: NA white_handed_gibbon: Sex: NA Specifies a set of regions of interest, each representing one or more named regions in a reference sequence (e.g. genes) in BED format.
RegionsOfInterest: protein_coding.CDS:
Name of the prefix; is expected to correspond to the filename
of the FASTA file without the extension / the name of the
prefix used in the BAM pipeline.
Prefix: rCRS
If true, BAM files are expected to have the postfix ".realigned";
allows easier interopterability with the BAM pipeline.
Realigned: yes
Specifies whether or not the sequences are protein coding; if true
indels are only included in the final sequence if the length is
divisible by 3.
ProteinCoding: yes
Do not include indels in final sequence; note that indels are still
called, and used to filter SNPs. Requires that the option
'MultipleSequenceAlignment' is enabled
IncludeIndels: yes
List of contigs for which heterozygous SNPs should be filtered
(site set to 'N') based on sex; All sexes used in the 'Samples'
section must be listed:
HomozygousContigs: NA:
- NC_012920_1 Filter sites in a sample, replacing any nucleotide not observed in the specified list of samples or groups with 'N'. FilterSingletons: NAME_OF_SAMPLE: -
- NAME_OF_SAMPLE Genotyping: Default settings for all regions of interest
Defaults:
Regions of interest are expanded by this number of bases when calling
SNPs, in order to ensure that adjacent indels can be used during
filtering
(VCF_filter --min-distance-to-indels and --min-distance-between-indels).
The final sequences does not include the padding.
Padding: 10
By default, each set of regions of interest are genotyped seperately,
even if these overlap. By setting this option to true, the entire prefix
is genotyped once, and all regions of interest are extracted from this.
This can only be done for prefixes that only use genotyping defaults.
GenotypeEntirePrefix: no
Settings for genotyping by random sampling of nucletoides at each site
Random:
Min distance of variants to indels
--min-distance-to-indels: 2
MPileup: -E: # extended BAQ for higher sensitivity but lower specificity -A: # count anomalous read pairs
BCFTools: -g: # Call genotypes at variant sites
VCF_Filter:
Maximum coverage acceptable for genotyping calls; if set to zero, the
default vcf_filter value is used; if set to 'auto', the MaxDepth value
will be read from the depth histograms generated by the BAM pipeline.
MaxReadDepth: auto
Minimum coverage acceptable for genotyping calls
--min-read-depth: 6
Min RMS mapping quality
--min-mapping-quality: 10
Min QUAL score (Phred) for genotyping calls
--min-quality: 30
Min distance of variants to indels
--min-distance-to-indels: 2
Min distance between indels
--min-distance-between-indels: 10
Min P-value for strand bias (given PV4)
--min-strand-bias: 1.0e-4
Min P-value for baseQ bias (given PV4)
--min-baseq-bias: 1.0e-4
Min P-value for mapQ bias (given PV4)
--min-mapq-bias: 1.0e-4
Min P-value for end distance bias (given PV4)
--min-end-distance-bias: 1.0e-4
Max frequency of the major allele at heterozygous sites
--min-allele-frequency: 0.2
Minimum number of alternative bases observed for variants
--min-num-alt-bases: 2
Add / overwrite default settings for a set of regions NAME_OF_REGIONS: ...
MultipleSequenceAlignment: Default settings for all regions of interest
Defaults: Enabled: yes
Multiple sequence alignment using MAFFT
MAFFT:
Select alignment algorithm; valid values are 'mafft', 'auto', 'fft-ns-1',
'fft-ns-2', 'fft-ns-i', 'nw-ns-i', 'l-ins-i', 'e-ins-i', and 'g-ins-i'.
Algorithm: G-INS-i
Parameters for mafft algorithm; see above for example of how to specify
--maxiterate: 1000
Add / overwrite default settings for a set of regions NAME_OF_REGIONS: ...
PhylogeneticInference: ProteinCodingGenes:
Exclude (groups of) samples from this analytical step
ExcludeSamples: -
- NAME_OF_SAMPLE Root the final tree(s) on one or more samples; if no samples
are specified, the tree(s) will be rooted on the midpoint(s)
RootTreesOn: -
- NAME_OF_SAMPLE If 'yes', a tree is generated per named sequence in the areas of
interest; otherwise a super-matrix is created from the combined set
of regions specfied below.
PerGeneTrees: no
Which Regions Of Interest to build the phylogeny from.
RegionsOfInterest: protein_coding.CDS:
Partitioning scheme for sequences: Numbers specify which group a
# position belongs to, while 'X' excludes the position from the final # partioned sequence; thus "123" splits sequences by codon-positions, # while "111" produces a single partition per gene. If set to 'no', # a single partition is used for the entire set of regions. Partitions: "112" # Limit analysis to a subset of a RegionOfInterest; subsets are expected to be # located at <genome root>/<prefix>.<region name>.<subset name>.names, and # contain single name (corresponding to column 4 in the BED file) per line.
SubsetRegions: SUBSET_NAME
ExaML:
Number of times to perform full phylogenetic inference
Replicates: 1
Number of bootstraps to compute
Bootstraps: 100
Model of rate heterogeneity (GAMMA or PSR)
Model: GAMMA
`
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Hello,
I have been experimenting with PALEOMIX and have had success with BAM pipeline.
I decided to run phylogenetic pipeline but at the step $phylo_pipeline genotype+msa+phylogeny 000_makefile.yaml
I get an error message:
Reading makefile(s): Error reading makefiles: MakefileError: Makefile requirement not met at 'root:chimpanzee': Expected value(s): key in 'Project', 'PhylogeneticInference', 'Genotyping', 'PAML', or 'MultipleSequenceAlignment' Observed value(s): 'chimpanzee' Observed type: str
Has something changed since the example was made or what might be causing the issue?