omega plus does not work on macs simulated data

[Li Wang]

Dear Authors and Users

I was trying to identify omegaPlus and SweeD outlier based on the simulation data. As I simulated around one chromosome size sequence length 200Mb, I used macs, which is pretty faster than ms. Macs works perfectly. But the problem is that either SweeD and OmegaPlus cannot run on this simulated data. 

My simulation command:

macs 6 200000000 -t 0.12 -r 0.12 -h 1e2 -G 12280.45382930157698141330 -eG .000375 0 -eN .0025 1

The error i got from SweeD  and OmegaPlus is as follows:

> commandOmega

[1] "OmegaPlus-M -name macsNeutral -grid 40000 -length 200000000 -input macsNeutral.out -minwin 5000 -noSeparator -b 10  -minsnps 5 -seed 123456789 -threads 6 -maxwin 100000"

> commandSweeD

[1] "SweeD-P -name msNeutral -grid 40000 -length 200000000 -noSeparator -threads 6 -input macsNeutral.out"

> 

> system(commandOmega)

 ERROR: Empty alignment? ( no states found ).

                                      _______________

                                         OmegaPlus

                                      _______________

 OmegaPlus version 3.0.0 released by Nikolaos Alachiotis and Pavlos Pavlidis in December 2014.

 Command:

OmegaPlus-M -name macsNeutral -grid 40000 -length 200000000 -input macsNeutral.out -minwin 5000 -noSeparator -b 10 -minsnps 5 -seed 123456789 -threads 6 -maxwin 100000

 Input file format (0:ms, 1:fasta, 2:macs, 3:vcf, 4:sf): 2

 Gap (-) imputation: OFF

 Ambiguous character (N) imputation: OFF

 Omega search strategy: #SNPsLeft - 10 < #SNPsRight < #SNPsLeft + 10

 Alignment 1

Sequences: 17

Sites: 2> system(commandSweeD)

                                      _______________

                                           SweeD

                                      _______________

 SweeD version 3.3.1 released by Nikolaos Alachiotis and Pavlos Pavlidis in January 2015.

 Command:

SweeD-P -name msNeutral -grid 40000 -length 200000000 -noSeparator -threads 6 -input macsNeutral.out

 Input file format (0:ms, 1:fasta, 2:macs, 3:vcf, 4:sf): 2

 Alignment 1

Sequences: 17

Sites: 2

Discarded sites: 0

Processing ... NOT POSSIBLE (too few SNPs after removing monomorphic)

 Total elapsed time 32.19 seconds.

i also attached part of my macs simulation results here (tried to upload the whole file, but has an upload error). If anyone has any suggestions/comments, you will be very appreciated.

Best

Li

[Pavlos Pavlidis]

Hi Li,

it seems that the output of macs has been changed since we developed macs. THanks for posting this error.

could you please try to replace your SweeD_Input.c file with the attached? If this will work, then we will release an update for the SweeD and OmegaPlus. Also please use the whole macs file and not just a small subset.

best

pavlos

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Pavlos Pavlidis, PhD

Research C

Foundation for Research and Technology - Hellas

Institute of Computer Science
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[Pavlos Pavlidis]

... I meant "since we developed SweeD"... sorry