Germline analysis

[tkcaccia]

The script for germline analysis produced:
*.gp.vcf.gz
*.phased.log
*chr22.phased.vcf.gz
for all chromosomes but in the command line the script seems suspended at chr20:

---

Command line: java -Xmx20480m -jar beagle.jar
gt=out/germline/chr20.germline.vcf
ref=/home/user/Documents/Data/BeeNetOutputs/1000G/CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.filtered.shapeit2-duohmm-phased.vcf.gz
chrom=chr20
out=out/germline/chr20.phased
impute=false
modelscale=2
nthreads=24
gprobs=true
niterations=0

No genetic map is specified: using 1 cM = 1 Mb

reference samples: 3202
target samples: 1

Window 1 [ chr20:94613-64283878 ]
reference markers: 14227
target markers: 14227

Starting burn-in iterations

Window=1 Iteration=1
Time for building model: 29 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 40 max edges/level: 102
mean edges/node: 1.292 mean count/edge: 160

Window=1 Iteration=2
Time for building model: 31 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 104
mean edges/node: 1.285 mean count/edge: 164

Window=1 Iteration=3
Time for building model: 29 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 96
mean edges/node: 1.283 mean count/edge: 164

Window=1 Iteration=4
Time for building model: 30 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 111
mean edges/node: 1.285 mean count/edge: 164

Window=1 Iteration=5
Time for building model: 30 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 102
mean edges/node: 1.283 mean count/edge: 164

Window=1 Iteration=6
Time for building model: 29 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 116
mean edges/node: 1.285 mean count/edge: 164

Window=1 Iteration=7
Time for building model: 29 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 100
mean edges/node: 1.282 mean count/edge: 164

Window=1 Iteration=8
Time for building model: 29 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 110
mean edges/node: 1.286 mean count/edge: 164

Window=1 Iteration=9
Time for building model: 28 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 105
mean edges/node: 1.283 mean count/edge: 164

Window=1 Iteration=10
Time for building model: 28 seconds
Time for sampling (singles): 0 seconds
DAG statistics
mean edges/level: 39 max edges/level: 102
mean edges/node: 1.283 mean count/edge: 164

Number of markers: 14227
Total time for building model: 4 minutes 51 seconds
Total time for sampling: 1 second
Total run time: 5 minutes 47 seconds

End time: 08:10 PM SAST on 10 Dec 2024
beagle.27Jul16.86a.jar (version 4.1) finished

[tkcaccia]

The issue could be produced because a vcf.gz file from 1000G dataset was not correctly downloaded. The python script did not recognize and the script not ends