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roohy / iLASH

iLASH - IBD Estimation Using Locality Sensitive Hashing
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No Output created #11

Open bassanio opened 8 months ago

bassanio commented 8 months ago

Hi ,

I was running through my data and I got the following stdout but I have got empty results

Map file address: ALL-phased_chr1_maf0nly.map
Loaded 56872 lines of SNP data.
Number of slices:1
Done with slicing.
The seed used for pseudo-random number generation is:1697441505944131589
Approximating for 0.7 for interest and 0.1 for Match
1/5: 0.447214
2/5: 0.632456
3/5: 0.774597
4/5: 0.894427
5/5: 1
Interest T:3
 Match T:1
The number of cores on the host: 64
Genotype file:ALL-phased_chr1_maf0nly.ped.
Threads started
Read everything from the file.
Waiting for threads for finish their jobs
Writing
---1653034
Starting Writer Threads...
All Threads Working
Everything done in the writer part

My Config file

map ALL-phased_chr1_maf0nly.map

ped ALL-phased_chr1_maf0nly.ped

output ALL-phased_chr1.match

slice_size 30

step_size 30

perm_count 10

shingle_size 10

shingle_overlap 0

bucket_count 5

max_thread 2

match_threshold 0.10

interest_threshold 0.70

min_length 0.6

auto_slice 1

slice_length 2.9

cm_overlap 0

minhash_threshold 5

Map File : I have kept the centimorgans in plink as 0 for every position

1   1_784860    0   784860
1   1_785739    0   785739
roohy commented 8 months ago

Hi, As a first step, you need correct genetic distance information in centimorgans in your map file.