szpiech
commented
4 years ago Hi there,
I generated those example files several years ago, and since then the program defaults have slightly changed. If you are getting output, this means the program is functioning. Sorry for the confusion! I will have to update the example files to avoid this confusion in the future.
aastha-v
Hello!
I am running selscan on Ubuntu 18 LTS. I am unable to get the same iHS values as the example.ihs.out file here. My log looks like this:
../src/./selscan --ihs --hap example.hap --map example.map --out test.example --threads 10 v1.3.0 Calculating iHS. Input filename: example.hap Map filename: example.map Output file: test.example.ihs.out Threads: 10 Scale parameter: 20000 Max gap parameter: 200000 EHH cutoff value: 0.05 Alt flag set: no --skip-low-freq set. Removing all variants < 0.05. Removed 2750 low frequency variants. WARNING: Reached chromosome edge before EHH decayed below 0.05. Skipping calculation at Locus5 WARNING: Reached chromosome edge before EHH decayed below 0.05. Skipping calculation at Locus2 WARNING: Reached chromosome edge before EHH decayed below 0.05. Skipping calculation at Locus18 WARNING: Reached chromosome edge before EHH decayed below 0.05. Skipping calculation at Locus13 WARNING: Reached chromosome edge before EHH decayed below 0.05. Skipping calculation at Locus34 WARNING: Reached chromosome edge before EHH decayed below 0.05. Skipping calculation at Locus39 WARNING: Reached chromosome edge before EHH decayed below 0.05. Skipping calculation at Locus4
while the scores in both files look like this:
test.example.ihs.out:Locus188 108585 0.3 0.0263938 0.020108 0.118132 test.example.ihs.out:Locus1880 1168591 0.14 0.33279 0.0168633 1.29523 test.example.ihs.out:Locus1881 1169264 0.06 0.998161 0.0138525 1.85767 test.example.ihs.out:Locus1882 1170860 0.12 0.327554 0.0168659 1.28827 test.example.ihs.out:Locus1883 1172545 0.24 0.146858 0.0156062 0.9736 test.example.ihs.out:Locus1884 1173195 0.06 1.12876 0.0113121 1.99906 test.example.ihs.out:Locus1885 1173749 0.12 0.327569 0.0127553 1.40961 test.example.ihs.out:Locus1887 1174701 0.34 0.0489453 0.0206153 0.375522 test.example.ihs.out:Locus1888 1174777 0.34 0.0489453 0.0206153 0.375522 test.example.ihs.out:Locus1889 1175022 0.06 0.562215 0.00961574 1.76692
example.ihs.out:Locus188 108585 0.3 0.0173648 0.0150461 0.143324 example.ihs.out:Locus1880 1168591 0.14 0.157038 0.0110095 2.65773 example.ihs.out:Locus1881 1169264 0.06 0.573633 0.0092492 4.12745 example.ihs.out:Locus1882 1170860 0.12 0.20044 0.010789 2.92199 example.ihs.out:Locus1883 1172545 0.24 0.0475636 0.0105927 1.5019 example.ihs.out:Locus1884 1173195 0.06 0.498914 0.00738917 4.21242 example.ihs.out:Locus1885 1173749 0.12 0.200548 0.00833627 3.18044 example.ihs.out:Locus1887 1174701 0.34 0.029491 0.00829141 1.26886 example.ihs.out:Locus1888 1174777 0.34 0.029491 0.00829141 1.26886 example.ihs.out:Locus1889 1175022 0.06 0.123439 0.00563158 3.08735
The same applies to other scores like XP-EHH, though I'm primarily interested in iHS.
The hap and map files I have downloaded have the same number of lines as here.
How can I fix this?