Fixed - Low MQ and Low FQ Positions masking issue

config_ali

@@ -11,24 +11,24 @@ binbase: /nfs/esnitkin/bin_group/variant_calling_bin/
 
 #resources: nodes=1:ppn=12,mem=47gb,walltime=250:00:00
 [scheduler]
-resources: nodes=1:ppn=4,pmem=4000mb,walltime=250:00:00
-large_resources: nodes=1:ppn=12,mem=47gb,walltime=250:00:00
+resources: nodes=1:ppn=4,pmem=4000mb,walltime=50:00:00
+large_resources: nodes=1:ppn=12,mem=47gb,walltime=50:00:00
 email: [email protected]
 queue: flux
 flux_account: esnitkin_flux
 notification: a
 
 [flux]
-resources: nodes=1:ppn=4,pmem=4000mb,walltime=250:00:00
-large_resources: nodes=1:ppn=12,mem=47gb,walltime=250:00:00
+resources: nodes=1:ppn=4,pmem=4000mb,walltime=50:00:00
+large_resources: nodes=1:ppn=12,mem=47gb,walltime=50:00:00
 email: [email protected]
 queue: flux
 flux_account: esnitkin_flux
 notification: a
 
 [slurm]
-resources: nodes=1:ppn=4,pmem=4000mb,walltime=250:00:00
-large_resources: nodes=1:ppn=12,mem=47gb,walltime=250:00:00
+resources: nodes=1:ppn=4,pmem=4000mb,walltime=50:00:00
+large_resources: nodes=1:ppn=12,mem=47gb,walltime=50:00:00
 email: [email protected]
 queue: flux
 flux_account: esnitkin_flux
@@ -1070,3 +1070,9 @@ Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/Pt0_Chromosome_O
 Ref_Name: NTHi_86-028NP.fasta
 # path to the reference genome fasta file.
 Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/NTHi_86-028NP/
+
+[Legionella_SG6_Thunder_Bay]
+# Name of reference genome fasta file.
+Ref_Name: Legionella_SG6_Thunder_Bay.fasta
+# path to the reference genome fasta file.
+Ref_Path: /nfs/esnitkin/bin_group/variant_calling_bin/reference/Legionella_SG6_Thunder_Bay/

modules/picard.py

@@ -7,7 +7,7 @@
 def markduplicates(out_sorted_bam, out_path, analysis, files_to_delete, logger, Config):
     base_cmd = ConfigSectionMap("bin_path", Config)['binbase'] + "/" + ConfigSectionMap("picard", Config)['picard_bin'] + "/" + ConfigSectionMap("picard", Config)['base_cmd']
     keep_logging('Removing PCR duplicates using PICARD', 'Removing PCR duplicates using PICARD', logger, 'info')
-    cmd = "java -jar %s MarkDuplicates REMOVE_DUPLICATES=true INPUT=%s OUTPUT=%s/%s_aln_marked.bam METRICS_FILE=%s/%s_markduplicates_metrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT" % (base_cmd, out_sorted_bam, out_path, analysis, out_path, analysis)
+    cmd = "java -jar %s MarkDuplicates REMOVE_DUPLICATES=true INPUT=%s OUTPUT=%s/%s_aln_marked.bam METRICS_FILE=%s/%s_markduplicates_metrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT MAX_FILE_HANDLES=500" % (base_cmd, out_sorted_bam, out_path, analysis, out_path, analysis)
     keep_logging(cmd, cmd, logger, 'debug')
     try:
         call(cmd, logger)
@@ -62,4 +62,4 @@ def picardstats(out_sorted_bam, out_path, analysis, reference, logger, Config):
     except sp.CalledProcessError:
         keep_logging('Error in Picard CollectWgsMetrics step. Exiting.',
                      'Error in Picard CollectWgsMetrics step. Exiting.', logger, 'exception')
-        sys.exit(1)
+        sys.exit(1)