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===Data=== ruiliu@genome-miner:~$ cd /home/kunzhang/haplotyping/Data/HL095/ ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ ls -l s_4_Indx1.* -rw-r--r-- 1 kunzhang kunzhang 114237942 2011-06-13 22:07 s_4_Indx1.bowtie.pileup -rw-r--r-- 1 kunzhang kunzhang 39977658 2011-06-13 21:28 s_4_Indx1.bowtie.sorted.bam -rw-r--r-- 1 kunzhang kunzhang 4442210 2011-06-13 22:05 s_4_Indx1.bowtie.sorted.unique.bam -rw-r--r-- 1 kunzhang kunzhang 278 2011-06-13 21:29 s_4_Indx1.bowtie.variants.txt -rw-r--r-- 1 kunzhang kunzhang 7103 2011-06-14 15:58 s_4_Indx1.hapCompare.txt -rw-r--r-- 1 kunzhang kunzhang 9399 2011-06-14 16:56 s_4_Indx1.idioGraph.txt -rw-r--r-- 1 kunzhang kunzhang 675115 2011-06-13 21:29 s_4_Indx1.log -rw-r--r-- 1 kunzhang kunzhang 273522562 2011-06-13 18:08 s_4_Indx1.txt ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ less s_4_Indx1.bowtie.pileup 1 557399 C A 25 25 25 1 ^:A f 1 557400 A A 25 0 25 1 . f 1 557401 T T 25 0 25 1 . f 1 557402 C C 25 0 25 1 . f 1 557403 A A 25 0 25 1 . c 1 557404 C C 25 0 25 1 . g 1 557405 T T 25 0 25 1 . g 1 557406 A A 25 0 25 1 . g 1 557407 G G 25 0 25 1 . g 1 557408 A A 25 0 25 1 . e 1 557409 C C 25 0 25 1 . f ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ more s_4_Indx11.log /home/kunzhang/softwares/bowtie-latest/bowtie -k 1 -l 32 -n 2 -m 1 --best --quiet -p 4 /home/kunzhang/HsGenome/1KG.ref/HsB36m s_4_Indx 11.txt s_4_Indx11.bowtie.map.1 /home/kunzhang/Exome/Data/scripts/trimTerminalMismatches.pl < s_4_Indx11.bowtie.map.1 > s_4_Indx11.bowtie.map.2 /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/bowtie2sam.pl s_4_Indx11.bowtie.map.2 > s_4_Indx11.bowtie.sam /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools import /home/kunzhang/HsGenome/1KG.ref/human_b36_male.fa.gz.fai s_4_Indx 11.bowtie.sam s_4_Indx11.bowtie.bam [sam_header_read2] 114 sequences loaded. /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools sort s_4_Indx11.bowtie.bam s_4_Indx11.bowtie.sorted java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.38/MarkDuplicates.jar ASSUME_SORTED=TRUE REMOVE_DUPLICATES=TRUE INPUT=s_4_In dx11.bowtie.sorted.bam OUTPUT=s_4_Indx11.bowtie.sorted.unique.bam METRICS_FILE=dup.metric [Tue Jun 14 15:23:03 PDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=s_4_Indx11.bowtie.sorted.bam OUTPUT=s_4_Indx11.bowtie.sorted.uni que.bam METRICS_FILE=dup.metric REMOVE_DUPLICATES=true ASSUME_SORTED=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDL ES_FOR_READ_ENDS_MAP=8000 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 TMP_DIR =/tmp/kunzhang VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=fals e CREATE_MD5_FILE=false INFO 2011-06-14 15:23:03 MarkDuplicates Start of doWork freeMemory: 374846832; totalMemory: 377225216; maxMemory: 1908932608 INFO 2011-06-14 15:23:03 MarkDuplicates Reading input file and constructing read end information. INFO 2011-06-14 15:23:03 MarkDuplicates Will retain up to 7575129 data points before spilling to disk. INFO 2011-06-14 15:23:03 MarkDuplicates Assuming input is coordinate sorted. INFO 2011-06-14 15:23:06 MarkDuplicates Read '''887559''' records. 0 pairs never matched. INFO 2011-06-14 15:23:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 733397640; totalMemory: 925368320; maxMemory : 1908932608 INFO 2011-06-14 15:23:07 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2011-06-14 15:23:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2011-06-14 15:23:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2011-06-14 15:23:09 MarkDuplicates Sorting list of duplicate records. INFO 2011-06-14 15:23:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 923987040; totalMemory: 1410072576; maxMemo ry: 1908932608 INFO 2011-06-14 15:23:09 MarkDuplicates Marking '''837865''' records as duplicates. INFO 2011-06-14 15:23:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2011-06-14 15:23:12 MarkDuplicates Before output close freeMemory: 920285040; totalMemory: 1408237568; maxMemory: 1908932 608 INFO 2011-06-14 15:23:12 MarkDuplicates After output close freeMemory: 876964080; totalMemory: 1364918272; maxMemory: 19089326 08 [Tue Jun 14 15:23:12 PDT 2011] net.sf.picard.sam.MarkDuplicates done. Runtime.totalMemory()=1364918272 /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/human_b36_male.fa s_4_Indx1 1.bowtie.sorted.unique.bam > s_4_Indx11.bowtie.pileup Use of uninitialized value in print at /home/kunzhang/Exome/Data/scripts/pileup2variants.pl line 145. Use of uninitialized value in print at /home/kunzhang/Exome/Data/scripts/pileup2variants.pl line 145. ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.bam | wc -l 887559 ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.unique.bam | wc -l 49694
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