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inti / bcbio-nextgen-debug.log
Created December 23, 2014 17:13
[ipedroso@jimi log]$ cat bcbio-nextgen-debug.log
[2014-12-17T14:05Z] Resource requests: bwa, sambamba, samtools; memory: 2.00; cores: 16, 1, 16
[2014-12-17T14:05Z] Configuring 3 jobs to run, using 16 cores each with 32.1g of memory reserved for each job
[2014-12-17T14:05Z] Timing: organize samples
[2014-12-17T14:05Z] multiprocessing: organize_samples
[2014-12-17T14:05Z] Using input YAML configuration: /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/config/populus_trichocarpa_diversity_1.yaml
[2014-12-17T14:05Z] Checking sample YAML configuration: /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/config/populus_trichocarpa_diversity_1.yaml
[2014-12-17T14:05Z] Testing minimum versions of installed programs
[2014-12-17T14:05Z] Timing: alignment preparation
[2014-12-17T14:05Z] multiprocessing: prep_align_inputs
@inti
inti / bcf_call_output.vcf
Created October 14, 2014 13:37
example output generating error on BCF and VT normalise. command used was the following using an mpileup as piped output: /home/ipedroso/APP/bcbio-nextgen/bin/bcftools call -v -m -
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.0+htslib-1.0
##samtoolsCommand=samtools mpileup -f /home/ipedroso/APP/bcbio-nextgen/genomes/populus_trichicarpa/ptri_v3/seq/ptri_v3.fa -t DP -u -g -l /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/work/samtools/scaffold_2499/GW-10958-scaffold_2499_0_3827-raw-regions.bed /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/work/align/GW-10958/14_2014-09-26_populus_trichocarpa_diversity_1-sort.bam
##reference=file:///home/ipedroso/APP/bcbio-nextgen/genomes/populus_trichicarpa/ptri_v3/seq/ptri_v3.fa
##contig=<ID=Chr01,length=50495391>
##contig=<ID=Chr02,length=25263035>
##contig=<ID=Chr03,length=21816808>
##contig=<ID=Chr04,length=24267051>
##contig=<ID=Chr05,length=25890704>
@inti
inti / example_theano_scan.py
Last active January 2, 2016 10:49
Example of using theano scan to update two variables on a loop
import theano
import theano.tensor as T
theano.config.compute_test_value = 'off'
import numpy as np
# routine to make some data up
def makeup_data(n,p):
X = np.memmap('test.memmap', dtype='float64', mode='w+', shape=(n,p))
@inti
inti / test_step_method.py
Last active January 1, 2016 23:49
Example using custom step method on PyMC: - generate samples for a sum of gaussian variables with mean 0 and std 1. - build a pymc model to fit a generative model to this set of observations. First declare all variables within the model context. The std of the (s variable) should be 1.4 as expected. Second try to update the variable p using a cu…
import pymc as mc
import numpy as np
import time
import theano.tensor as T
import theano
theano.config.compute_test_value = 'off'
## generate some data
N = 10000
@inti
inti / gist:450303
Created June 23, 2010 18:10
structure(list(ensembl = structure(c(11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 28L, 28L,
28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,