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xiaoming-liu / stairway-plot-v2

The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data.
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nseq/2 number error #13

Open lpabonv opened 1 year ago

lpabonv commented 1 year ago

Hi, I'm trying to run the Stairbuilder wiht the blueprint file for my data with 9 sequences. I've produced the FSF file with angsd just filtering the Q values of the bam files. When I try to run the command java -cp /stairway_plot_es Stairbuilder atsc.blueprint I keep getting this error: SFS error: shall have nseq/2 numbers but I'm not quite sure why it can be.

Here is the inpurts of the blueprint file I'm trying to run

atsc blueprint file

input setting

popid: atsc #id of the population (no white space)

nseq: 9 # number of sequences

L: 926917453 # total number of observed nucleic sites, including polymorphic and monomorphic

whether_folded: true # whethr the SFS is folded (true or false)

SFS: 849918911.235305 5533172.340831 3585877.498525 2394020.608020 1735951.167280 1126263.513418 951597.499224 824435.697279 630408.337808 1304744.999719 329435.952282 433277.195734 430147.468001 463207.276422 659667.877063 811322.643672 1268956.11 1421 2758312.563082 65349606.014913 #snp frequency spectrum: number of singleton, number of doubleton, etc. (separated by wh ite space)

smallest_size_of_SFS_bin_used_for_estimation: 1 #default is 1; to ignore singletons, uncomment this line and change this num ber to 2

largest_size_of_SFS_bin_used_for_estimation: 4 #default is n-1; to ignore singletons, uncomment this line and change this nu mber to nseq-2

pct_training: 0.67 #percentage of sites for training

nrand: 1 3 5 7 #number of random break points for each try (separated by white space)

project_dir:/hpcfs/home/ciencias_biologicas/l.pabonv/Secuencias/Secuencias_raw/raw_seqs_Cund/a_schistaceus_raw_seq # projec t directory

stairway_plot_dir: /hpcfs/home/ciencias_biologicas/l.pabonv/stairway-plot-v2/stairway_plot_v2.1.2/stairway_plot_es # directo ry to the stairway plot files

ninput: 200 # number of input files to be created for each estimation

random_seed: 6

output setting

mu: 1.9e-3 # assumed mutation rate per site per generation year_per_generation: 5 # assumed generation time (in years)

plot setting

plot_title: Atlapetes schistaceus # title of the plot xrange: 0.1,10000 # Time (1k year) range; format: xmin,xmax; "0,0" for default yrange: 0,0 # Ne (1k individual) range; format: xmin,xmax; "0,0" for default xspacing: 2 # X axis spacing yspacing: 2 # Y axis spacing fontsize: 12 # Font size

Erythroxylum commented 1 year ago

Hello Ipabonv, Since you have 9 sequences, you need to have 4 or five floating point numbers in your SFS line.