a few more specific exceptions, increase Broad LSF9 latency wait for …

…Snakemake, remove some default snakemake targets

intrahost.py

@@ -758,6 +758,9 @@ def parse_eff(eff_field):
     (out['eff_type'], out['eff_codon_dna'], out['eff_aa'], out['eff_prot_len'], out['eff_gene'], out['eff_protein'], rank) = eff
     return out
 
+class SnpEffException(Exception):
+   pass
+
 def parse_ann(ann_field, alleles, transcript_blacklist=set(('GP.2','GP.3'))):
     ''' parse the new snpEff "ANN" INFO field '''
 
@@ -798,12 +801,12 @@ def parse_ann(ann_field, alleles, transcript_blacklist=set(('GP.2','GP.3'))):
     if not effs:
         return {}
     if len(effs) != len(effs_dict):
-        raise Exception("ANN field has non-unique alleles")
+        raise SnpEffException("ANN field has non-unique alleles")
     for a in alleles:
         if a not in effs_dict:
-           raise Exception("ANN field is missing ALT allele: " + a)
+           raise SnpEffException("ANN field is missing ALT allele: " + a)
     if len(effs) != len(set(alleles)):
-        raise Exception("ANN field has %s entries, but ALT field has %s unique alleles: %s" % (
+        raise SnpEffException("ANN field has %s entries, but ALT field has %s unique alleles: %s" % (
             len(effs), len(set(alleles)), ','.join(alleles)))
 
     out = {}

pipes/Broad_LSF/run-pipe.sh

@@ -17,6 +17,7 @@ source "$VENVDIR/bin/activate"
 # invoke Snakemake in cluster mode with custom wrapper scripts
 snakemake --timestamp --rerun-incomplete --keep-going --nolock \
 	--jobs 100000 --immediate-submit \
+        --latency-wait 20 \
 	--config mode=LSF job_profiler="$BINDIR/pipes/Broad_LSF/lsf-report.py" \
 	--directory . \
 	--jobscript "$BINDIR/pipes/Broad_LSF/jobscript.sh" \

pipes/Snakefile

@@ -36,9 +36,6 @@ rule all:
             sample=read_samples_file(config["samples_assembly"])),
         # intrahost variant calling
         config["dataDir"]+'/'+config["subdirs"]["intrahost"] +'/isnvs.vcf.gz',
-        # create reference-guided analyses of diversity (quick outputs)
-        os.path.join(config["dataDir"], config["subdirs"]["interhost"], 'ref_guided.fasta'),
-        os.path.join(config["dataDir"], config["subdirs"]["interhost"], 'ref_guided.vcf.gz'),
         # create summary reports
         config["reportsDir"]+'/summary.fastqc.txt',
         config["reportsDir"]+'/summary.spike_count.txt'