def start_ab(args, logger):
'''Perform alignment and bam processing'''
import os
import subprocess
final_bam = args.outbam
# initialize library file from given arguments
library = genobox_modules.initialize_library(args.libfile, args.se, args.pe1, args.pe2, args.sample, args.mapq, args.libs, args.pl)
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
print "Starting alignment"
(bamfiles, library) = start_alignment(args, logger)
print "Starting bam processing"
final_bam = start_bamprocess(library, genobox_modules.unique(bamfiles.values()), args.mapq, args.libs, args.tmpdir, args.queue, final_bam, args.realignment, args.known, args.fa, args.sample, args.partition, logger)
# remove queuing system outfiles
genobox_modules.rm_files(['run_genobox_*', 'semaphores.*'])
print "Done"
print "--------------------------------------"
def start_ab(args, logger):
'''Perform alignment and bam processing'''
import os
import subprocess
final_bam = args.outbam
# initialize library file from given arguments
library = genobox_modules.initialize_library(args.libfile, args.se,
args.pe1, args.pe2,
args.sample, args.mapq,
args.libs, args.pl)
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
print "Starting alignment"
(bamfiles, library) = start_alignment(args, logger)
print "Starting bam processing"
final_bam = start_bamprocess(library,
genobox_modules.unique(bamfiles.values()),
args.mapq, args.libs, args.tmpdir, args.queue,
final_bam, args.realignment, args.known,
args.fa, args.sample, args.partition, logger)
# remove queuing system outfiles
genobox_modules.rm_files(['run_genobox_*', 'semaphores.*'])
print "Done"
print "--------------------------------------"
def clean(f):
'''Clean up tmp and raw files'''
import genobox_modules
import os
# finding files to delete
f_base = os.path.split(f)[1]
f_base = f_base.replace('.raw.vcf.gz', '')
f_base = 'tmp/tmp.' + f_base
files_to_delete = []
files_to_delete.append(f_base+'.header.vcf')
files_to_delete.append(f_base+'.indels.pass.vcf')
files_to_delete.append(f_base+'.indels.pass.vcf.idx')
files_to_delete.append(f_base+'.raw.vcf.gz.indels.vcf')
files_to_delete.append(f_base+'.raw.vcf.gz.indels.vcf.idx')
files_to_delete.append(f_base+'.raw.vcf.gz.ref.vcf')
files_to_delete.append(f_base+'.raw.vcf.gz.ref.vcf.idx')
files_to_delete.append(f_base+'.raw.vcf.gz.snps.vcf')
files_to_delete.append(f_base+'.raw.vcf.gz.snps.vcf.idx')
files_to_delete.append(f_base+'.ref.pass.vcf')
files_to_delete.append(f_base+'.ref.pass.vcf.idx')
files_to_delete.append(f_base+'.snps.pass.vcf')
files_to_delete.append(f_base+'.snps.pass.vcf.idx')
# deleting files
genobox_modules.rm_files(files_to_delete)
def start_gv(args, logger):
'''Perform alignment and bam processing'''
import os
import subprocess
genobox_modules.check_genome(args.genome)
final_bcf = 'genotyping/%s.all.bcf' % args.sample
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
if args.caller == 'samtools':
print "Starting genotyping (samtools)"
final_bcf = start_genotyping(args.bam, args.genome, args.fa,
args.prior, args.pp, args.queue,
final_bcf, args.sample, args.partition,
logger)
print "Starting vcffiltering"
final_vcf = start_vcffilter(final_bcf, args.genome, args.caller,
args.Q, args.ex, args.rmsk, args.ab,
args.prune, args.ovar, args.queue,
args.sample, args.partition, logger)
print "Start dbsnp"
final_dbsnp_vcf = start_dbsnp(final_vcf, args.ex, args.dbsnp,
args.ovar, args.queue, args.partition,
logger)
print "Start bcf2ref"
start_bcf2ref(final_bcf, args.genome, args.Q, args.ex, args.dbsnp,
args.rmsk, 'genotyping/indels_for_filtering.vcf',
args.oref, args.queue, args.sample, args.partition,
logger)
elif args.caller == 'gatk':
print "Start genotyping (gatk)"
vcffiles = start_genotyping_gatk(args.bam, args.genome, args.fa,
args.dbsnp, args.call_conf,
args.call_emit, args.output_mode,
args.queue, args.sample,
args.partition, logger)
print "Start vcffiltering (gatk)"
final_vcfs = start_vcffilter_gatk(vcffiles, args.genome, args.fa,
args.Q, args.rmsk, args.ab,
args.prune, args.queue, args.sample,
args.partition, logger)
# remove queuing system outfiles
genobox_modules.rm_files(['run_genobox_*', 'semaphores.*'])
print "Done"
print "--------------------------------------"
def start_genotyping(bam, chr, fa, prior, pp, queue, o, sample, partition, logger):
'''Starts genotyping using samtools of input bam file'''
import subprocess
import genobox_modules
from genobox_classes import Moab
from genobox_classes import Semaphore
import os
if not os.path.exists('genotyping'):
os.makedirs('genotyping')
# set queueing
paths = genobox_modules.setSystem()
home = os.getcwd()
cpuA = 'nodes=1:ppn=1,mem=512mb,walltime=172800'
cpuC = 'nodes=1:ppn=1,mem=2gb,walltime=172800'
cpuE = 'nodes=1:ppn=1,mem=5gb,walltime=172800'
cpuF = 'nodes=1:ppn=2,mem=2gb,walltime=172800'
cpuB = 'nodes=1:ppn=16,mem=10gb,walltime=172800'
# create calls
bamindex_calls = bam_index(bam)
(mpileup_calls, bcffiles) = mpileup(bam, chr, fa, prior, pp)
bcfcombine_calls = bcf_combine(bcffiles, o)
bcfindex_calls = bcf_index(o)
consensus_calls = consensus(o, sample)
# submit jobs #
print "Submitting jobs"
bamindex_moab = Moab(bamindex_calls, logfile=logger, runname='run_genobox_bamindex', queue=queue, cpu=cpuC, partition=partition)
mpileup_moab = Moab(mpileup_calls, logfile=logger, runname='run_genobox_mpileup', queue=queue, cpu=cpuF, depend=True, depend_type='expand', depend_val=[len(mpileup_calls)], depend_ids=bamindex_moab.ids, partition=partition)
bcfcombine_moab = Moab(bcfcombine_calls, logfile=logger, runname='run_genobox_bcfcombine', queue=queue, cpu=cpuC, depend=True, depend_type='conc', depend_val=[len(mpileup_calls)], depend_ids=mpileup_moab.ids, partition=partition)
bcfindex_moab = Moab(bcfindex_calls, logfile=logger, runname='run_genobox_bcfindex', queue=queue, cpu=cpuC, depend=True, depend_type='one2one', depend_val=[1], depend_ids=bcfcombine_moab.ids, partition=partition)
#consensus_moab = Moab(consensus_calls, logfile=logger, runname='run_genobox_consensus', queue=queue, cpu=cpuA, depend=True, depend_type='one2one', depend_val=[1], depend_ids=bcfcombine_moab.ids, partition=partition)
# release jobs #
print "Releasing jobs"
#bamindex_moab.release()
#mpileup_moab.release()
#bcfcombine_moab.release()
#bcfindex_moab.release()
#consensus_moab.release()
# semaphore (consensus is currently not waited for)
print "Waiting for jobs to finish ..."
s = Semaphore(bcfindex_moab.ids, home, 'genotyping', queue, 20, 2*86400)
s.wait()
print "--------------------------------------"
# remove temporary files
genobox_modules.rm_files(bcffiles)
# return output bcf
return o
def start_gv(args, logger):
'''Perform alignment and bam processing'''
import os
import subprocess
genobox_modules.check_genome(args.genome)
final_bcf = 'genotyping/%s.all.bcf' % args.sample
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
if args.caller == 'samtools':
print "Starting genotyping (samtools)"
final_bcf = start_genotyping(args.bam, args.genome, args.fa, args.prior, args.pp, args.queue, final_bcf, args.sample, args.partition, logger)
print "Starting vcffiltering"
final_vcf = start_vcffilter(final_bcf, args.genome, args.caller, args.Q, args.ex, args.rmsk, args.ab, args.prune, args.ovar, args.queue, args.sample, args.partition, logger)
print "Start dbsnp"
final_dbsnp_vcf = start_dbsnp(final_vcf, args.ex, args.dbsnp, args.ovar, args.queue, args.partition, logger)
print "Start bcf2ref"
start_bcf2ref(final_bcf, args.genome, args.Q, args.ex, args.dbsnp, args.rmsk, 'genotyping/indels_for_filtering.vcf', args.oref, args.queue, args.sample, args.partition, logger)
elif args.caller == 'gatk':
print "Start genotyping (gatk)"
vcffiles = start_genotyping_gatk(args.bam, args.genome, args.fa, args.dbsnp, args.call_conf, args.call_emit, args.output_mode, args.queue, args.sample, args.partition, logger)
print "Start vcffiltering (gatk)"
final_vcfs = start_vcffilter_gatk(vcffiles, args.genome, args.fa, args.Q, args.rmsk, args.ab, args.prune, args.queue, args.sample, args.partition, logger)
# remove queuing system outfiles
genobox_modules.rm_files(['run_genobox_*', 'semaphores.*'])
print "Done"
print "--------------------------------------"
files['filterAll'] = 'genotyping/tmp.all.bcf.%s.flt.vcf.gz' % args.chr
files['filterAll_tbi'] = 'genotyping/tmp.all.bcf.%s.flt.vcf.gz.tbi' % args.chr
files['dbsnp_ann'] = 'genotyping/tmp.all.bcf.%s.flt.ann.vcf.gz' % args.chr
files['rmsk'] = 'genotyping/tmp.all.bcf.%s.flt.ann.nr.vcf.gz' % args.chr
files['indel_filt'] = 'genotyping/tmp.indel_filtered.%s.vcf' % args.chr
# vcf_filter_All
vcf_filterAll(args.bcf, args.chr_id, args.d, args.D, args.Q, args.ex, files['filterAll'])
# tabix
vcf_tabix(files['filterAll'])
# dbsnp
vcf_annotate_dbsnp(files['filterAll'], args.dbsnp, files['dbsnp_ann'])
# rmsk filtering
if args.chr.find('MT') > -1:
# if chromosome short name is chrMT or MT run manual filtering for MT only
manual_rmsk_filter(files['dbsnp_ann'], args.chr, args.rmsk, files['rmsk'])
else:
# filter for rmsk using BEDtools
vcf_filter_rmsk(files['dbsnp_ann'], args.rmsk, files['rmsk'])
# indel filter
vcf_filter_indels(files['rmsk'], args.chr, args.indels, files['indel_filt'], args.o)
# remove tmp files
genobox_modules.rm_files(files.values())
def start_abgv(args, logger):
'''Start alignment, bam processing, genotyping, vcffiltering, dbsnp annotation, bcf2ref'''
import os
import subprocess
# check genome file
genobox_modules.check_genome(args.genome)
final_bam = 'alignment/%s.flt.sort.rmdup.bam' % args.sample
final_bcf = 'genotyping/%s.all.bcf' % args.sample
# initialize library file from given arguments
library = genobox_modules.initialize_library(args.libfile, args.se,
args.pe1, args.pe2,
args.sample, args.mapq,
args.libs, args.pl)
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
# toggle start trimming
#if args.no_trim == False:
# print "Starting trimming"
# (se_files, pe1_files, pe2_files) = start_trim(args, logger)
# library.update(Trim=se_files+pe1_files+pe2_files)
print "Starting alignment"
(bamfiles, library) = start_alignment(args, logger)
print "Starting bam processing"
final_bam = start_bamprocess(library,
genobox_modules.unique(bamfiles.values()),
args.mapq, args.libs, args.tmpdir, args.queue,
final_bam, args.realignment, args.known,
args.fa, args.sample, args.partition, logger)
print "Starting bam stats"
start_bamstats(args, final_bam, args.partition, logger, wait=False)
print "Starting genotyping"
if args.caller == 'samtools':
final_bcf = start_genotyping(final_bam, args.genome, args.fa,
args.prior, args.pp, args.queue,
final_bcf, args.sample, args.partition,
logger)
print "Starting vcffiltering"
final_vcf = start_vcffilter(final_bcf, args.genome, args.caller,
args.Q, args.ex, args.rmsk, args.ab,
args.prune, args.ovar, args.queue,
args.sample, args.partition, logger)
print "Start dbsnp"
final_dbsnp_vcf = start_dbsnp(final_vcf, args.ex, args.dbsnp,
args.ovar, args.queue, args.partition,
logger)
print "Start bcf2ref"
start_bcf2ref(final_bcf, args.genome, args.Q, args.ex, args.dbsnp,
args.rmsk, 'genotyping/indels_for_filtering.vcf',
args.oref, args.queue, args.sample, args.partition,
logger)
elif args.caller == 'gatk':
print "Start genotyping (gatk)"
vcffiles = start_genotyping_gatk(final_bam, args.genome, args.fa,
args.dbsnp, args.call_conf,
args.args.call_emit, args.output_mode,
args.queue, args.sample,
args.partition, logger)
print "Start vcffiltering (gatk)"
final_vcfs = start_vcffilter_gatk(vcffiles, args.genome, args.fa,
args.Q, args.rmsk, args.ab,
args.prune, args.queue, args.sample,
args.partition, args.logger)
# remove queuing system outfiles
genobox_modules.rm_files(['run_genobox_*', 'semaphores.*'])
print "Done"
print "--------------------------------------"
print "Raw genotyping is written in genotyping/all.bcf"
print "High confidence variants: %s" % args.ovar
print "High confidence reference: %s" % args.oref
print "--------------------------------------"
def start_abgv(args, logger):
"""Start alignment, bam processing, genotyping, vcffiltering, dbsnp annotation, bcf2ref"""
import os
import subprocess
# check genome file
genobox_modules.check_genome(args.genome)
final_bam = "alignment/%s.flt.sort.rmdup.bam" % args.sample
final_bcf = "genotyping/%s.all.bcf" % args.sample
# initialize library file from given arguments
library = genobox_modules.initialize_library(
args.libfile, args.se, args.pe1, args.pe2, args.sample, args.mapq, args.libs, args.pl
)
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
# toggle start trimming
# if args.no_trim == False:
# print "Starting trimming"
# (se_files, pe1_files, pe2_files) = start_trim(args, logger)
# library.update(Trim=se_files+pe1_files+pe2_files)
print "Starting alignment"
(bamfiles, library) = start_alignment(args, logger)
print "Starting bam processing"
final_bam = start_bamprocess(
library,
genobox_modules.unique(bamfiles.values()),
args.mapq,
args.libs,
args.tmpdir,
args.queue,
final_bam,
args.realignment,
args.known,
args.fa,
args.sample,
args.partition,
logger,
)
print "Starting bam stats"
start_bamstats(args, final_bam, args.partition, logger, wait=False)
print "Starting genotyping"
if args.caller == "samtools":
final_bcf = start_genotyping(
final_bam,
args.genome,
args.fa,
args.prior,
args.pp,
args.queue,
final_bcf,
args.sample,
args.partition,
logger,
)
print "Starting vcffiltering"
final_vcf = start_vcffilter(
final_bcf,
args.genome,
args.caller,
args.Q,
args.ex,
args.rmsk,
args.ab,
args.prune,
args.ovar,
args.queue,
args.sample,
args.partition,
logger,
)
print "Start dbsnp"
final_dbsnp_vcf = start_dbsnp(final_vcf, args.ex, args.dbsnp, args.ovar, args.queue, args.partition, logger)
print "Start bcf2ref"
start_bcf2ref(
final_bcf,
args.genome,
args.Q,
args.ex,
args.dbsnp,
args.rmsk,
"genotyping/indels_for_filtering.vcf",
args.oref,
args.queue,
args.sample,
args.partition,
logger,
)
elif args.caller == "gatk":
print "Start genotyping (gatk)"
vcffiles = start_genotyping_gatk(
final_bam,
args.genome,
args.fa,
args.dbsnp,
args.call_conf,
args.args.call_emit,
args.output_mode,
args.queue,
args.sample,
args.partition,
logger,
)
print "Start vcffiltering (gatk)"
final_vcfs = start_vcffilter_gatk(
vcffiles,
args.genome,
args.fa,
args.Q,
args.rmsk,
args.ab,
args.prune,
args.queue,
args.sample,
args.partition,
args.logger,
)
# remove queuing system outfiles
genobox_modules.rm_files(["run_genobox_*", "semaphores.*"])
print "Done"
print "--------------------------------------"
print "Raw genotyping is written in genotyping/all.bcf"
print "High confidence variants: %s" % args.ovar
print "High confidence reference: %s" % args.oref
print "--------------------------------------"
paths = genobox_modules.setSystem()
home = os.getcwd()
# get genome file
genome = get_genome(args.genome)
# perform varfilter to get filtered vcf
vcf_files = bcf2varfilter(args.bcf, genome, args.Q, 'genotyping/tmp.flt.')
# combine to one file
cat_vcfs(vcf_files, 'genotyping/tmp.flt.all.vcf')
# remove in annotated repeat (rmsk)
vcf_filter_rmsk('genotyping/tmp.flt.all.vcf', args.rmsk, 'genotyping/tmp.flt.all.rmsk.vcf')
# filter haploid chromosomes for heterozygote calls
vcf_filter_haploid('genotyping/tmp.flt.all.rmsk.vcf', genome, 'genotyping/tmp.flt.all.rmsk.hetfilt.vcf')
# filter for allelic balance
vcf_filter_allelic_balance('genotyping/tmp.flt.all.rmsk.hetfilt.vcf', args.ab, args.caller, 'genotyping/tmp.flt.all.rmsk.hetfilt.abfilt.vcf')
# pruning of nearby calls
vcf_filter_prune('genotyping/tmp.flt.all.rmsk.hetfilt.abfilt.vcf', args.prune, args.o)
# write indels for filtering of reference calls
write_indels_for_filtering(args.o, args.ex)
# remove temporary files
genobox_modules.rm_files(['genotyping/tmp.flt*'])
files = {}
files["filterAll"] = "genotyping/tmp.all.bcf.%s.flt.vcf.gz" % args.chr
files["filterAll_tbi"] = "genotyping/tmp.all.bcf.%s.flt.vcf.gz.tbi" % args.chr
files["dbsnp_ann"] = "genotyping/tmp.all.bcf.%s.flt.ann.vcf.gz" % args.chr
files["rmsk"] = "genotyping/tmp.all.bcf.%s.flt.ann.nr.vcf.gz" % args.chr
files["indel_filt"] = "genotyping/tmp.indel_filtered.%s.vcf" % args.chr
# vcf_filter_All
vcf_filterAll(args.bcf, args.chr_id, args.d, args.D, args.Q, args.ex, files["filterAll"])
# tabix
vcf_tabix(files["filterAll"])
# dbsnp
vcf_annotate_dbsnp(files["filterAll"], args.dbsnp, files["dbsnp_ann"])
# rmsk filtering
if args.chr.find("MT") > -1:
# if chromosome short name is chrMT or MT run manual filtering for MT only
manual_rmsk_filter(files["dbsnp_ann"], args.chr, args.rmsk, files["rmsk"])
else:
# filter for rmsk using BEDtools
vcf_filter_rmsk(files["dbsnp_ann"], args.rmsk, files["rmsk"])
# indel filter
vcf_filter_indels(files["rmsk"], args.chr, args.indels, files["indel_filt"], args.o)
# remove tmp files
genobox_modules.rm_files(files.values())
genome = get_genome(args.genome)
# perform varfilter to get filtered vcf
vcf_files = bcf2varfilter(args.bcf, genome, args.Q, 'genotyping/tmp.flt.')
# combine to one file
cat_vcfs(vcf_files, 'genotyping/tmp.flt.all.vcf')
# remove in annotated repeat (rmsk)
vcf_filter_rmsk('genotyping/tmp.flt.all.vcf', args.rmsk,
'genotyping/tmp.flt.all.rmsk.vcf')
# filter haploid chromosomes for heterozygote calls
vcf_filter_haploid('genotyping/tmp.flt.all.rmsk.vcf', genome,
'genotyping/tmp.flt.all.rmsk.hetfilt.vcf')
# filter for allelic balance
vcf_filter_allelic_balance('genotyping/tmp.flt.all.rmsk.hetfilt.vcf', args.ab,
args.caller,
'genotyping/tmp.flt.all.rmsk.hetfilt.abfilt.vcf')
# pruning of nearby calls
vcf_filter_prune('genotyping/tmp.flt.all.rmsk.hetfilt.abfilt.vcf', args.prune,
args.o)
# write indels for filtering of reference calls
write_indels_for_filtering(args.o, args.ex)
# remove temporary files
genobox_modules.rm_files(['genotyping/tmp.flt*'])
#!/panvol1/simon/bin/python2.7
from genobox_modules import rm_files
import subprocess
import os
rm_files([
'run_genobox_velveth.*', 'run_genobox_velvetg.*',
'run_genobox_interleave.*', '*.interleaved', 'pbsjob.tmp*',
'run_genobox_velvetaccept.*', 'run_mlst_trim.*'
])
if os.path.exists('trimmed'):
subprocess.call('rm -r trimmed/', shell=True)
#!/panvol1/simon/bin/python2.7
from genobox_modules import rm_files
import subprocess
import os
rm_files(['run_genobox_velveth.*', 'run_genobox_velvetg.*', 'run_genobox_interleave.*', '*.interleaved', 'pbsjob.tmp*', 'run_genobox_velvetaccept.*', 'run_mlst_trim.*'])
if os.path.exists('trimmed'):
subprocess.call('rm -r trimmed/', shell=True)
def start_genotyping(bam, chr, fa, prior, pp, queue, o, sample, partition,
logger):
'''Starts genotyping using samtools of input bam file'''
import subprocess
import genobox_modules
from genobox_classes import Moab
from genobox_classes import Semaphore
import os
if not os.path.exists('genotyping'):
os.makedirs('genotyping')
# set queueing
paths = genobox_modules.setSystem()
home = os.getcwd()
cpuA = 'nodes=1:ppn=1,mem=512mb,walltime=172800'
cpuC = 'nodes=1:ppn=1,mem=2gb,walltime=172800'
cpuE = 'nodes=1:ppn=1,mem=5gb,walltime=172800'
cpuF = 'nodes=1:ppn=2,mem=2gb,walltime=172800'
cpuB = 'nodes=1:ppn=16,mem=10gb,walltime=172800'
# create calls
bamindex_calls = bam_index(bam)
(mpileup_calls, bcffiles) = mpileup(bam, chr, fa, prior, pp)
bcfcombine_calls = bcf_combine(bcffiles, o)
bcfindex_calls = bcf_index(o)
consensus_calls = consensus(o, sample)
# submit jobs #
print "Submitting jobs"
bamindex_moab = Moab(bamindex_calls,
logfile=logger,
runname='run_genobox_bamindex',
queue=queue,
cpu=cpuC,
partition=partition)
mpileup_moab = Moab(mpileup_calls,
logfile=logger,
runname='run_genobox_mpileup',
queue=queue,
cpu=cpuF,
depend=True,
depend_type='expand',
depend_val=[len(mpileup_calls)],
depend_ids=bamindex_moab.ids,
partition=partition)
bcfcombine_moab = Moab(bcfcombine_calls,
logfile=logger,
runname='run_genobox_bcfcombine',
queue=queue,
cpu=cpuC,
depend=True,
depend_type='conc',
depend_val=[len(mpileup_calls)],
depend_ids=mpileup_moab.ids,
partition=partition)
bcfindex_moab = Moab(bcfindex_calls,
logfile=logger,
runname='run_genobox_bcfindex',
queue=queue,
cpu=cpuC,
depend=True,
depend_type='one2one',
depend_val=[1],
depend_ids=bcfcombine_moab.ids,
partition=partition)
#consensus_moab = Moab(consensus_calls, logfile=logger, runname='run_genobox_consensus', queue=queue, cpu=cpuA, depend=True, depend_type='one2one', depend_val=[1], depend_ids=bcfcombine_moab.ids, partition=partition)
# release jobs #
print "Releasing jobs"
#bamindex_moab.release()
#mpileup_moab.release()
#bcfcombine_moab.release()
#bcfindex_moab.release()
#consensus_moab.release()
# semaphore (consensus is currently not waited for)
print "Waiting for jobs to finish ..."
s = Semaphore(bcfindex_moab.ids, home, 'genotyping', queue, 20, 2 * 86400)
s.wait()
print "--------------------------------------"
# remove temporary files
genobox_modules.rm_files(bcffiles)
# return output bcf
return o
