mutations_caller_pipeline_aws 0.0.17 → 0.0.18

data/lib/mutations_caller_pipeline_aws/gatk_caller.rb

@@ -15,7 +15,7 @@ class GatkCaller
   # Coverage Summary
   # parallel not possible yet (1.6-13-g91f02df)
   def self.coverage(log_dir, gatk, index_fa, read_bam, outfile_prefix, job_prefix, account, debug)
-    cmd = "qsub -o #{log_dir} -e #{log_dir}_coverage_errors -V -cwd -b y -N coverage_#{job_prefix} -l h_vmem=7G -hold_jid recalibration_#{job_prefix} #{account}\
+    cmd = "qsub -o #{log_dir} -e #{log_dir}_coverage_errors -V -cwd -b y -N coverage_#{job_prefix} -l h_vmem=14G -hold_jid recalibration_#{job_prefix} #{account}\
       java -Xmx6g -jar #{gatk} -R #{index_fa} -T DepthOfCoverage \
       -I #{read_bam} --omitDepthOutputAtEachBase \
       -o #{outfile_prefix} --omitIntervalStatistics --omitLocusTable"
@@ -25,7 +25,7 @@ class GatkCaller
 
   # Making recalibration table
   def self.recalibrate_bam(log_dir ,gatk, index_fa, read_bam, recal_file, job_prefix, account, dbsnp_file, debug )
-    cmd = "qsub -o #{log_dir} -e #{log_dir}_recalibrate_errors -V -cwd -b y -N recalibration_table_#{job_prefix} -l h_vmem=7G  -hold_jid realignment_#{job_prefix} #{account} \
+    cmd = "qsub -o #{log_dir} -e #{log_dir}_recalibrate_errors -V -cwd -b y -N recalibration_table_#{job_prefix} -l h_vmem=14G  -hold_jid realignment_#{job_prefix} #{account} \
       java -Xmx6g -jar #{gatk} -knownSites #{dbsnp_file} -I #{read_bam} \
       -R #{index_fa} -T BaseRecalibrator  \
       -o #{recal_file}"
@@ -36,7 +36,7 @@ class GatkCaller
   # Using recalibration table
   # parallel not possible yet (1.6-13-g91f02df)
   def self.table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file, job_prefix, account, debug)
-    cmd = "qsub -V -o #{log_dir} -e #{log_dir}_prep_recal_errors -cwd -b y -N recalibration_#{job_prefix} -l h_vmem=7G -hold_jid recalibration_table_#{job_prefix} #{account} \
+    cmd = "qsub -V -o #{log_dir} -e #{log_dir}_prep_recal_errors -cwd -b y -N recalibration_#{job_prefix} -l h_vmem=14G -hold_jid recalibration_table_#{job_prefix} #{account} \
       java -Xmx6g -jar #{gatk} \
       -R #{index_fa} \
       -I #{read_bam} \
@@ -63,7 +63,7 @@ class GatkCaller
   # Realignment
   # parallel not possible yet (1.6-13-g91f02df)
   def self.realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam, job_prefix, account, debug)
-    cmd = "qsub -o #{log_dir} -e #{log_dir}_realign_errors -V -cwd -b y -N realignment_#{job_prefix} -l h_vmem=7G -hold_jid prep_realignment_#{job_prefix} #{account} \
+    cmd = "qsub -o #{log_dir} -e #{log_dir}_realign_errors -V -cwd -b y -N realignment_#{job_prefix} -l h_vmem=14G -hold_jid prep_realignment_#{job_prefix} #{account} \
       java -Xmx6g -jar #{gatk} \
       -I #{read_bam} \
       -R #{index_fa} \

data/lib/mutations_caller_pipeline_aws/picard_caller.rb

@@ -1,13 +1,13 @@
 class PicardCaller
   #converter = "java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/SamFormatConverter.jar I=WT_aligned_sorted_rg.bam O=tmp.sam VALIDATION_STRINGENCY=LENIENT"
   def self.convert(sam_file, bam_file, picard_tools, log_file, job_prefix, account)
-    cmd = "qsub -o #{log_file} -e #{log_file}_conversion_errors -V -cwd -b y -hold_jid bwa_#{job_prefix} -N convert_#{job_prefix} -l h_vmem=7G #{account} \
+    cmd = "qsub -o #{log_file} -e #{log_file}_conversion_errors -V -cwd -b y -hold_jid bwa_#{job_prefix} -N convert_#{job_prefix} -l h_vmem=14G #{account} \
       java -Xmx6g -jar  #{picard_tools}/SamFormatConverter.jar I=#{sam_file} O=#{bam_file} VALIDATION_STRINGENCY=LENIENT "
   end
 
   #rg_and_sorting = "java -jar -Xmx3g ~/Downloads/picard-tools-1.56/picard-tools-1.56/AddOrReplaceReadGroups.jar I=WT_aligned.bam O=WT_aligned_sorted_rg.bam SO=coordinate ID=15 LB=nina_library PL=Illumina PU=ATCATC SM=My_test VALIDATION_STRINGENCY=LENIENT"
   def self.rg_and_sorting(bam_file, bam_file_sorted, picard_tools, library, index, sample_name, log_file, id, job_prefix, account)
-    cmd = "qsub -o #{log_file} -e #{log_file}_rg_sorting_errors -V -cwd -b y -hold_jid convert_#{job_prefix} -N sort_#{job_prefix} -l h_vmem=7G #{account} \
+    cmd = "qsub -o #{log_file} -e #{log_file}_rg_sorting_errors -V -cwd -b y -hold_jid convert_#{job_prefix} -N sort_#{job_prefix} -l h_vmem=14G #{account} \
       java -Xmx6g -jar  #{picard_tools}/AddOrReplaceReadGroups.jar I=#{bam_file} O=#{bam_file_sorted} SO=coordinate ID=#{id} \
       LB=#{library} PL=Illumina PU=#{index} SM=#{sample_name} VALIDATION_STRINGENCY=LENIENT MAX_RECORDS_IN_RAM=1500000"
   end
@@ -15,14 +15,14 @@ class PicardCaller
 
   #mark_duplicates = "java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/MarkDuplicates.jar I=WT_aligned_sorted_rg.bam O=marked_dublicates.bam M=dublicate.metrcis AS=true VALIDATION_STRINGENCY=LENIENT"
   def self.mark_duplicates(bam_file_sorted, bam_file_sorted_duplicates, duplicate_metrcis, picard_tools, log_file, job_prefix, account)
-    cmd = "qsub -o #{log_file} -e #{log_file}_duplicates_errors -V -cwd -b y -hold_jid sort_#{job_prefix} -N duplicates_#{job_prefix} -l h_vmem=7G #{account} \
+    cmd = "qsub -o #{log_file} -e #{log_file}_duplicates_errors -V -cwd -b y -hold_jid sort_#{job_prefix} -N duplicates_#{job_prefix} -l h_vmem=14G #{account} \
       java -Xmx3g -jar #{picard_tools}/MarkDuplicates.jar I=#{bam_file_sorted} O=#{bam_file_sorted_duplicates} M=#{duplicate_metrcis} \
       AS=true VALIDATION_STRINGENCY=LENIENT"
   end
 
   #build_index = "java -jar ~/Downloads/picard-tools-1.56/picard-tools-1.56/BuildBamIndex.jar I=marked_dublicates.bam  VALIDATION_STRINGENCY=LENIENT"
   def self.build_index(bam_file_sorted_duplicates, picard_tools, log_file, job_prefix, account)
-    cmd = "qsub -o #{log_file} -e #{log_file}_index_errors -V -cwd -b y -hold_jid duplicates_#{job_prefix} -N index_#{job_prefix} -l h_vmem=7G #{account} \
+    cmd = "qsub -o #{log_file} -e #{log_file}_index_errors -V -cwd -b y -hold_jid duplicates_#{job_prefix} -N index_#{job_prefix} -l h_vmem=14G #{account} \
       java -Xmx3g -jar #{picard_tools}/BuildBamIndex.jar I=#{bam_file_sorted_duplicates}  VALIDATION_STRINGENCY=LENIENT"
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mutations_caller_pipeline_aws
 version: !ruby/object:Gem::Version
-  version: 0.0.17
+  version: 0.0.18
   prerelease: 
 platform: ruby
 authors: