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I have downloaded dbSNP data and trying to sort the .vcf file with the command line:
java -Xms10g -Xmx20g -Djava.io.tmpdir=tmp -jar picard.jar SortVcf INPUT=00-All_chr.vcf OUTPUT=00-All_chr_sorted.vcf SEQUENCE_DICTIONARY=hg38.dict
I did add "chr" to the chromosome information in the dbSNP data.
The following is part of the log in the end of the log file after running the command line. I did not get any error message, and it ran for more than an hour, but the result file is empty.
Can anyone please help me with this?
INFO 2015-09-17 19:10:44 SortVcf read 143,025,000 records. Elapsed
time: 04:21:07s. Time for last 25,000: 3s. Last read position: chrY:2,405,259
INFO 2015-09-17 19:10:44 SortVcf read 143,050,000 records. Elapsed time: 04:21:07s. Time for last 25,000: 0s. Last read position: chrY:3,851,348
INFO 2015-09-17 19:10:44 SortVcf read 143,075,000 records. Elapsed time: 04:21:07s. Time for last 25,000: 0s. Last read position: chrY:7,480,875
INFO 2015-09-17 19:10:44 SortVcf read 143,100,000 records. Elapsed time: 04:21:07s. Time for last 25,000: 0s. Last read position: chrY:10,151,437
INFO 2015-09-17 19:10:45 SortVcf read 143,125,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:11,324,243
INFO 2015-09-17 19:10:45 SortVcf read 143,150,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:12,617,451
INFO 2015-09-17 19:10:45 SortVcf read 143,175,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:15,351,020
INFO 2015-09-17 19:10:45 SortVcf read 143,200,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:19,370,690
INFO 2015-09-17 19:10:45 SortVcf read 143,225,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:21,843,643
INFO 2015-09-17 19:10:46 SortVcf read 143,250,000 records. Elapsed time: 04:21:09s. Time for last 25,000: 0s. Last read position: chrY:57,084,728
[Thu Sep 17 19:10:59 CEST 2015] picard.vcf.SortVcf done. Elapsed time: 261.39 minutes.
Runtime.totalMemory()=12853444608
To get help, see http://broadinstitute.github.io/pica...ml#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:84)
at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:21)
at java.util.TimSort.countRunAndMakeAscending(TimSort.java:360)
at java.util.TimSort.sort(TimSort.java:234)
at java.util.Arrays.sort(Arrays.java:1512)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:218)
at htsjdk.samtools.util.SortingCollection.doneAdding(SortingCollection.java:190)
at htsjdk.samtools.util.SortingCollection.iterator(SortingCollection.java:265)
at htsjdk.samtools.util.SortingCollection.iterator(SortingCollection.java:58)
at picard.vcf.SortVcf.writeSortedOutput(SortVcf.java:171)
at picard.vcf.SortVcf.doWork(SortVcf.java:90)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Additional information:
Additional information.
[kong@hpc85 hg38]$ grep SQ hg38.dict | cut -f 2
SN:chr1
SN:chr10
SN:chr11
SN:chr11_KI270721v1_random
SN:chr12
SN:chr13
SN:chr14
SN:chr14_GL000009v2_random
SN:chr14_GL000225v1_random
SN:chr14_KI270722v1_random
SN:chr14_GL000194v1_random
SN:chr14_KI270723v1_random
SN:chr14_KI270724v1_random
SN:chr14_KI270725v1_random
SN:chr14_KI270726v1_random
SN:chr15
SN:chr15_KI270727v1_random
SN:chr16
SN:chr16_KI270728v1_random
SN:chr17
SN:chr17_GL000205v2_random
SN:chr17_KI270729v1_random
SN:chr17_KI270730v1_random
SN:chr18
SN:chr19
SN:chr1_KI270706v1_random
SN:chr1_KI270707v1_random
SN:chr1_KI270708v1_random
SN:chr1_KI270709v1_random
SN:chr1_KI270710v1_random
SN:chr1_KI270711v1_random
SN:chr1_KI270712v1_random
SN:chr1_KI270713v1_random
SN:chr1_KI270714v1_random
SN:chr2
SN:chr20
SN:chr21
SN:chr22
SN:chr22_KI270731v1_random
SN:chr22_KI270732v1_random
SN:chr22_KI270733v1_random
SN:chr22_KI270734v1_random
SN:chr22_KI270735v1_random
SN:chr22_KI270736v1_random
SN:chr22_KI270737v1_random
SN:chr22_KI270738v1_random
SN:chr22_KI270739v1_random
SN:chr2_KI270715v1_random
SN:chr2_KI270716v1_random
SN:chr3
SN:chr3_GL000221v1_random
SN:chr4
SN:chr4_GL000008v2_random
SN:chr5
SN:chr5_GL000208v1_random
SN:chr6
SN:chr7
SN:chr8
SN:chr9
SN:chr9_KI270717v1_random
SN:chr9_KI270718v1_random
SN:chr9_KI270719v1_random
SN:chr9_KI270720v1_random
SN:chr1_KI270762v1_alt
SN:chr1_KI270766v1_alt
SN:chr1_KI270760v1_alt
SN:chr1_KI270765v1_alt
SN:chr1_GL383518v1_alt
SN:chr1_GL383519v1_alt
SN:chr1_GL383520v2_alt
SN:chr1_KI270764v1_alt
SN:chr1_KI270763v1_alt
SN:chr1_KI270759v1_alt
SN:chr1_KI270761v1_alt
SN:chr2_KI270770v1_alt
SN:chr2_KI270773v1_alt
SN:chr2_KI270774v1_alt
SN:chr2_KI270769v1_alt
SN:chr2_GL383521v1_alt
SN:chr2_KI270772v1_alt
SN:chr2_KI270775v1_alt
SN:chr2_KI270771v1_alt
SN:chr2_KI270768v1_alt
SN:chr2_GL582966v2_alt
SN:chr2_GL383522v1_alt
SN:chr2_KI270776v1_alt
SN:chr2_KI270767v1_alt
SN:chr3_JH636055v2_alt
SN:chr3_KI270783v1_alt
SN:chr3_KI270780v1_alt
SN:chr3_GL383526v1_alt
SN:chr3_KI270777v1_alt
SN:chr3_KI270778v1_alt
SN:chr3_KI270781v1_alt
SN:chr3_KI270779v1_alt
SN:chr3_KI270782v1_alt
SN:chr3_KI270784v1_alt
SN:chr4_KI270790v1_alt
SN:chr4_GL383528v1_alt
SN:chr4_KI270787v1_alt
SN:chr4_GL000257v2_alt
SN:chr4_KI270788v1_alt
SN:chr4_GL383527v1_alt
SN:chr4_KI270785v1_alt
SN:chr4_KI270789v1_alt
SN:chr4_KI270786v1_alt
SN:chr5_KI270793v1_alt
SN:chr5_KI270792v1_alt
SN:chr5_KI270791v1_alt
SN:chr5_GL383532v1_alt
SN:chr5_GL949742v1_alt
SN:chr5_KI270794v1_alt
SN:chr5_GL339449v2_alt
SN:chr5_GL383530v1_alt
SN:chr5_KI270796v1_alt
SN:chr5_GL383531v1_alt
SN:chr5_KI270795v1_alt
SN:chr6_GL000250v2_alt
SN:chr6_KI270800v1_alt
SN:chr6_KI270799v1_alt
SN:chr6_GL383533v1_alt
SN:chr6_KI270801v1_alt
SN:chr6_KI270802v1_alt
SN:chr6_KB021644v2_alt
SN:chr6_KI270797v1_alt
SN:chr6_KI270798v1_alt
SN:chr7_KI270804v1_alt
SN:chr7_KI270809v1_alt
SN:chr7_KI270806v1_alt
SN:chr7_GL383534v2_alt
SN:chr7_KI270803v1_alt
SN:chr7_KI270808v1_alt
SN:chr7_KI270807v1_alt
SN:chr7_KI270805v1_alt
SN:chr8_KI270818v1_alt
SN:chr8_KI270812v1_alt
SN:chr8_KI270811v1_alt
SN:chr8_KI270821v1_alt
SN:chr8_KI270813v1_alt
SN:chr8_KI270822v1_alt
SN:chr8_KI270814v1_alt
SN:chr8_KI270810v1_alt
SN:chr8_KI270819v1_alt
SN:chr8_KI270820v1_alt
SN:chr8_KI270817v1_alt
SN:chr8_KI270816v1_alt
SN:chr8_KI270815v1_alt
SN:chr9_GL383539v1_alt
SN:chr9_GL383540v1_alt
SN:chr9_GL383541v1_alt
SN:chr9_GL383542v1_alt
SN:chr9_KI270823v1_alt
SN:chr10_GL383545v1_alt
SN:chr10_KI270824v1_alt
SN:chr10_GL383546v1_alt
SN:chr10_KI270825v1_alt
SN:chr11_KI270832v1_alt
SN:chr11_KI270830v1_alt
SN:chr11_KI270831v1_alt
SN:chr11_KI270829v1_alt
SN:chr11_GL383547v1_alt
SN:chr11_JH159136v1_alt
SN:chr11_JH159137v1_alt
SN:chr11_KI270827v1_alt
SN:chr11_KI270826v1_alt
SN:chr12_GL877875v1_alt
SN:chr12_GL877876v1_alt
SN:chr12_KI270837v1_alt
SN:chr12_GL383549v1_alt
SN:chr12_KI270835v1_alt
SN:chr12_GL383550v2_alt
SN:chr12_GL383552v1_alt
SN:chr12_GL383553v2_alt
SN:chr12_KI270834v1_alt
SN:chr12_GL383551v1_alt
SN:chr12_KI270833v1_alt
SN:chr12_KI270836v1_alt
SN:chr13_KI270840v1_alt
SN:chr13_KI270839v1_alt
SN:chr13_KI270843v1_alt
SN:chr13_KI270841v1_alt
SN:chr13_KI270838v1_alt
SN:chr13_KI270842v1_alt
SN:chr14_KI270844v1_alt
SN:chr14_KI270847v1_alt
SN:chr14_KI270845v1_alt
SN:chr14_KI270846v1_alt
SN:chr15_KI270852v1_alt
SN:chr15_KI270851v1_alt
SN:chr15_KI270848v1_alt
SN:chr15_GL383554v1_alt
SN:chr15_KI270849v1_alt
SN:chr15_GL383555v2_alt
SN:chr15_KI270850v1_alt
SN:chr16_KI270854v1_alt
SN:chr16_KI270856v1_alt
SN:chr16_KI270855v1_alt
SN:chr16_KI270853v1_alt
SN:chr16_GL383556v1_alt
SN:chr16_GL383557v1_alt
SN:chr17_GL383563v3_alt
SN:chr17_KI270862v1_alt
SN:chr17_KI270861v1_alt
SN:chr17_KI270857v1_alt
SN:chr17_JH159146v1_alt
SN:chr17_JH159147v1_alt
SN:chr17_GL383564v2_alt
SN:chr17_GL000258v2_alt
SN:chr17_GL383565v1_alt
SN:chr17_KI270858v1_alt
SN:chr17_KI270859v1_alt
SN:chr17_GL383566v1_alt
SN:chr17_KI270860v1_alt
SN:chr18_KI270864v1_alt
SN:chr18_GL383567v1_alt
SN:chr18_GL383570v1_alt
SN:chr18_GL383571v1_alt
SN:chr18_GL383568v1_alt
SN:chr18_GL383569v1_alt
SN:chr18_GL383572v1_alt
SN:chr18_KI270863v1_alt
SN:chr19_KI270868v1_alt
SN:chr19_KI270865v1_alt
SN:chr19_GL383573v1_alt
SN:chr19_GL383575v2_alt
SN:chr19_GL383576v1_alt
SN:chr19_GL383574v1_alt
SN:chr19_KI270866v1_alt
SN:chr19_KI270867v1_alt
SN:chr19_GL949746v1_alt
SN:chr20_GL383577v2_alt
SN:chr20_KI270869v1_alt
SN:chr20_KI270871v1_alt
SN:chr20_KI270870v1_alt
SN:chr21_GL383578v2_alt
SN:chr21_KI270874v1_alt
SN:chr21_KI270873v1_alt
SN:chr21_GL383579v2_alt
SN:chr21_GL383580v2_alt
SN:chr21_GL383581v2_alt
SN:chr21_KI270872v1_alt
SN:chr22_KI270875v1_alt
SN:chr22_KI270878v1_alt
SN:chr22_KI270879v1_alt
SN:chr22_KI270876v1_alt
SN:chr22_KI270877v1_alt
SN:chr22_GL383583v2_alt
SN:chr22_GL383582v2_alt
SN:chrX_KI270880v1_alt
SN:chrX_KI270881v1_alt
SN:chr19_KI270882v1_alt
SN:chr19_KI270883v1_alt
SN:chr19_KI270884v1_alt
SN:chr19_KI270885v1_alt
SN:chr19_KI270886v1_alt
SN:chr19_KI270887v1_alt
SN:chr19_KI270888v1_alt
SN:chr19_KI270889v1_alt
SN:chr19_KI270890v1_alt
SN:chr19_KI270891v1_alt
SN:chr1_KI270892v1_alt
SN:chr2_KI270894v1_alt
SN:chr2_KI270893v1_alt
SN:chr3_KI270895v1_alt
SN:chr4_KI270896v1_alt
SN:chr5_KI270897v1_alt
SN:chr5_KI270898v1_alt
SN:chr6_GL000251v2_alt
SN:chr7_KI270899v1_alt
SN:chr8_KI270901v1_alt
SN:chr8_KI270900v1_alt
SN:chr11_KI270902v1_alt
SN:chr11_KI270903v1_alt
SN:chr12_KI270904v1_alt
SN:chr15_KI270906v1_alt
SN:chr15_KI270905v1_alt
SN:chr17_KI270907v1_alt
SN:chr17_KI270910v1_alt
SN:chr17_KI270909v1_alt
SN:chr17_JH159148v1_alt
SN:chr17_KI270908v1_alt
SN:chr18_KI270912v1_alt
SN:chr18_KI270911v1_alt
SN:chr19_GL949747v2_alt
SN:chr22_KB663609v1_alt
SN:chrX_KI270913v1_alt
SN:chr19_KI270914v1_alt
SN:chr19_KI270915v1_alt
SN:chr19_KI270916v1_alt
SN:chr19_KI270917v1_alt
SN:chr19_KI270918v1_alt
SN:chr19_KI270919v1_alt
SN:chr19_KI270920v1_alt
SN:chr19_KI270921v1_alt
SN:chr19_KI270922v1_alt
SN:chr19_KI270923v1_alt
SN:chr3_KI270924v1_alt
SN:chr4_KI270925v1_alt
SN:chr6_GL000252v2_alt
SN:chr8_KI270926v1_alt
SN:chr11_KI270927v1_alt
SN:chr19_GL949748v2_alt
SN:chr22_KI270928v1_alt
SN:chr19_KI270929v1_alt
SN:chr19_KI270930v1_alt
SN:chr19_KI270931v1_alt
SN:chr19_KI270932v1_alt
SN:chr19_KI270933v1_alt
SN:chr19_GL000209v2_alt
SN:chr3_KI270934v1_alt
SN:chr6_GL000253v2_alt
SN:chr19_GL949749v2_alt
SN:chr3_KI270935v1_alt
SN:chr6_GL000254v2_alt
SN:chr19_GL949750v2_alt
SN:chr3_KI270936v1_alt
SN:chr6_GL000255v2_alt
SN:chr19_GL949751v2_alt
SN:chr3_KI270937v1_alt
SN:chr6_GL000256v2_alt
SN:chr19_GL949752v1_alt
SN:chr6_KI270758v1_alt
SN:chr19_GL949753v2_alt
SN:chr19_KI270938v1_alt
SN:chrM
SN:chrUn_KI270302v1
SN:chrUn_KI270304v1
SN:chrUn_KI270303v1
SN:chrUn_KI270305v1
SN:chrUn_KI270322v1
SN:chrUn_KI270320v1
SN:chrUn_KI270310v1
SN:chrUn_KI270316v1
SN:chrUn_KI270315v1
SN:chrUn_KI270312v1
SN:chrUn_KI270311v1
SN:chrUn_KI270317v1
SN:chrUn_KI270412v1
SN:chrUn_KI270411v1
SN:chrUn_KI270414v1
SN:chrUn_KI270419v1
SN:chrUn_KI270418v1
SN:chrUn_KI270420v1
SN:chrUn_KI270424v1
SN:chrUn_KI270417v1
SN:chrUn_KI270422v1
SN:chrUn_KI270423v1
SN:chrUn_KI270425v1
SN:chrUn_KI270429v1
SN:chrUn_KI270442v1
SN:chrUn_KI270466v1
SN:chrUn_KI270465v1
SN:chrUn_KI270467v1
SN:chrUn_KI270435v1
SN:chrUn_KI270438v1
SN:chrUn_KI270468v1
SN:chrUn_KI270510v1
SN:chrUn_KI270509v1
SN:chrUn_KI270518v1
SN:chrUn_KI270508v1
SN:chrUn_KI270516v1
SN:chrUn_KI270512v1
SN:chrUn_KI270519v1
SN:chrUn_KI270522v1
SN:chrUn_KI270511v1
SN:chrUn_KI270515v1
SN:chrUn_KI270507v1
SN:chrUn_KI270517v1
SN:chrUn_KI270529v1
SN:chrUn_KI270528v1
SN:chrUn_KI270530v1
SN:chrUn_KI270539v1
SN:chrUn_KI270538v1
SN:chrUn_KI270544v1
SN:chrUn_KI270548v1
SN:chrUn_KI270583v1
SN:chrUn_KI270587v1
SN:chrUn_KI270580v1
SN:chrUn_KI270581v1
SN:chrUn_KI270579v1
SN:chrUn_KI270589v1
SN:chrUn_KI270590v1
SN:chrUn_KI270584v1
SN:chrUn_KI270582v1
SN:chrUn_KI270588v1
SN:chrUn_KI270593v1
SN:chrUn_KI270591v1
SN:chrUn_KI270330v1
SN:chrUn_KI270329v1
SN:chrUn_KI270334v1
SN:chrUn_KI270333v1
SN:chrUn_KI270335v1
SN:chrUn_KI270338v1
SN:chrUn_KI270340v1
SN:chrUn_KI270336v1
SN:chrUn_KI270337v1
SN:chrUn_KI270363v1
SN:chrUn_KI270364v1
SN:chrUn_KI270362v1
SN:chrUn_KI270366v1
SN:chrUn_KI270378v1
SN:chrUn_KI270379v1
SN:chrUn_KI270389v1
SN:chrUn_KI270390v1
SN:chrUn_KI270387v1
SN:chrUn_KI270395v1
SN:chrUn_KI270396v1
SN:chrUn_KI270388v1
SN:chrUn_KI270394v1
SN:chrUn_KI270386v1
SN:chrUn_KI270391v1
SN:chrUn_KI270383v1
SN:chrUn_KI270393v1
SN:chrUn_KI270384v1
SN:chrUn_KI270392v1
SN:chrUn_KI270381v1
SN:chrUn_KI270385v1
SN:chrUn_KI270382v1
SN:chrUn_KI270376v1
SN:chrUn_KI270374v1
SN:chrUn_KI270372v1
SN:chrUn_KI270373v1
SN:chrUn_KI270375v1
SN:chrUn_KI270371v1
SN:chrUn_KI270448v1
SN:chrUn_KI270521v1
SN:chrUn_GL000195v1
SN:chrUn_GL000219v1
SN:chrUn_GL000220v1
SN:chrUn_GL000224v1
SN:chrUn_KI270741v1
SN:chrUn_GL000226v1
SN:chrUn_GL000213v1
SN:chrUn_KI270743v1
SN:chrUn_KI270744v1
SN:chrUn_KI270745v1
SN:chrUn_KI270746v1
SN:chrUn_KI270747v1
SN:chrUn_KI270748v1
SN:chrUn_KI270749v1
SN:chrUn_KI270750v1
SN:chrUn_KI270751v1
SN:chrUn_KI270752v1
SN:chrUn_KI270753v1
SN:chrUn_KI270754v1
SN:chrUn_KI270755v1
SN:chrUn_KI270756v1
SN:chrUn_KI270757v1
SN:chrUn_GL000214v1
SN:chrUn_KI270742v1
SN:chrUn_GL000216v2
SN:chrUn_GL000218v1
SN:chrX
SN:chrY
SN:chrY_KI270740v1_random
[kong@hpc22 dbSNP]$ grep -v "#" 00-All_chr.vcf | cut -f 1 | uniq | sort | uniq
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrMT
chrX
chrY
java -Xms10g -Xmx20g -Djava.io.tmpdir=tmp -jar picard.jar SortVcf INPUT=00-All_chr.vcf OUTPUT=00-All_chr_sorted.vcf SEQUENCE_DICTIONARY=hg38.dict
I did add "chr" to the chromosome information in the dbSNP data.
The following is part of the log in the end of the log file after running the command line. I did not get any error message, and it ran for more than an hour, but the result file is empty.
Can anyone please help me with this?
INFO 2015-09-17 19:10:44 SortVcf read 143,025,000 records. Elapsed
time: 04:21:07s. Time for last 25,000: 3s. Last read position: chrY:2,405,259
INFO 2015-09-17 19:10:44 SortVcf read 143,050,000 records. Elapsed time: 04:21:07s. Time for last 25,000: 0s. Last read position: chrY:3,851,348
INFO 2015-09-17 19:10:44 SortVcf read 143,075,000 records. Elapsed time: 04:21:07s. Time for last 25,000: 0s. Last read position: chrY:7,480,875
INFO 2015-09-17 19:10:44 SortVcf read 143,100,000 records. Elapsed time: 04:21:07s. Time for last 25,000: 0s. Last read position: chrY:10,151,437
INFO 2015-09-17 19:10:45 SortVcf read 143,125,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:11,324,243
INFO 2015-09-17 19:10:45 SortVcf read 143,150,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:12,617,451
INFO 2015-09-17 19:10:45 SortVcf read 143,175,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:15,351,020
INFO 2015-09-17 19:10:45 SortVcf read 143,200,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:19,370,690
INFO 2015-09-17 19:10:45 SortVcf read 143,225,000 records. Elapsed time: 04:21:08s. Time for last 25,000: 0s. Last read position: chrY:21,843,643
INFO 2015-09-17 19:10:46 SortVcf read 143,250,000 records. Elapsed time: 04:21:09s. Time for last 25,000: 0s. Last read position: chrY:57,084,728
[Thu Sep 17 19:10:59 CEST 2015] picard.vcf.SortVcf done. Elapsed time: 261.39 minutes.
Runtime.totalMemory()=12853444608
To get help, see http://broadinstitute.github.io/pica...ml#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:84)
at htsjdk.variant.variantcontext.VariantContextComparator.compare(VariantContextComparator.java:21)
at java.util.TimSort.countRunAndMakeAscending(TimSort.java:360)
at java.util.TimSort.sort(TimSort.java:234)
at java.util.Arrays.sort(Arrays.java:1512)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:218)
at htsjdk.samtools.util.SortingCollection.doneAdding(SortingCollection.java:190)
at htsjdk.samtools.util.SortingCollection.iterator(SortingCollection.java:265)
at htsjdk.samtools.util.SortingCollection.iterator(SortingCollection.java:58)
at picard.vcf.SortVcf.writeSortedOutput(SortVcf.java:171)
at picard.vcf.SortVcf.doWork(SortVcf.java:90)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Additional information:
Additional information.
[kong@hpc85 hg38]$ grep SQ hg38.dict | cut -f 2
SN:chr1
SN:chr10
SN:chr11
SN:chr11_KI270721v1_random
SN:chr12
SN:chr13
SN:chr14
SN:chr14_GL000009v2_random
SN:chr14_GL000225v1_random
SN:chr14_KI270722v1_random
SN:chr14_GL000194v1_random
SN:chr14_KI270723v1_random
SN:chr14_KI270724v1_random
SN:chr14_KI270725v1_random
SN:chr14_KI270726v1_random
SN:chr15
SN:chr15_KI270727v1_random
SN:chr16
SN:chr16_KI270728v1_random
SN:chr17
SN:chr17_GL000205v2_random
SN:chr17_KI270729v1_random
SN:chr17_KI270730v1_random
SN:chr18
SN:chr19
SN:chr1_KI270706v1_random
SN:chr1_KI270707v1_random
SN:chr1_KI270708v1_random
SN:chr1_KI270709v1_random
SN:chr1_KI270710v1_random
SN:chr1_KI270711v1_random
SN:chr1_KI270712v1_random
SN:chr1_KI270713v1_random
SN:chr1_KI270714v1_random
SN:chr2
SN:chr20
SN:chr21
SN:chr22
SN:chr22_KI270731v1_random
SN:chr22_KI270732v1_random
SN:chr22_KI270733v1_random
SN:chr22_KI270734v1_random
SN:chr22_KI270735v1_random
SN:chr22_KI270736v1_random
SN:chr22_KI270737v1_random
SN:chr22_KI270738v1_random
SN:chr22_KI270739v1_random
SN:chr2_KI270715v1_random
SN:chr2_KI270716v1_random
SN:chr3
SN:chr3_GL000221v1_random
SN:chr4
SN:chr4_GL000008v2_random
SN:chr5
SN:chr5_GL000208v1_random
SN:chr6
SN:chr7
SN:chr8
SN:chr9
SN:chr9_KI270717v1_random
SN:chr9_KI270718v1_random
SN:chr9_KI270719v1_random
SN:chr9_KI270720v1_random
SN:chr1_KI270762v1_alt
SN:chr1_KI270766v1_alt
SN:chr1_KI270760v1_alt
SN:chr1_KI270765v1_alt
SN:chr1_GL383518v1_alt
SN:chr1_GL383519v1_alt
SN:chr1_GL383520v2_alt
SN:chr1_KI270764v1_alt
SN:chr1_KI270763v1_alt
SN:chr1_KI270759v1_alt
SN:chr1_KI270761v1_alt
SN:chr2_KI270770v1_alt
SN:chr2_KI270773v1_alt
SN:chr2_KI270774v1_alt
SN:chr2_KI270769v1_alt
SN:chr2_GL383521v1_alt
SN:chr2_KI270772v1_alt
SN:chr2_KI270775v1_alt
SN:chr2_KI270771v1_alt
SN:chr2_KI270768v1_alt
SN:chr2_GL582966v2_alt
SN:chr2_GL383522v1_alt
SN:chr2_KI270776v1_alt
SN:chr2_KI270767v1_alt
SN:chr3_JH636055v2_alt
SN:chr3_KI270783v1_alt
SN:chr3_KI270780v1_alt
SN:chr3_GL383526v1_alt
SN:chr3_KI270777v1_alt
SN:chr3_KI270778v1_alt
SN:chr3_KI270781v1_alt
SN:chr3_KI270779v1_alt
SN:chr3_KI270782v1_alt
SN:chr3_KI270784v1_alt
SN:chr4_KI270790v1_alt
SN:chr4_GL383528v1_alt
SN:chr4_KI270787v1_alt
SN:chr4_GL000257v2_alt
SN:chr4_KI270788v1_alt
SN:chr4_GL383527v1_alt
SN:chr4_KI270785v1_alt
SN:chr4_KI270789v1_alt
SN:chr4_KI270786v1_alt
SN:chr5_KI270793v1_alt
SN:chr5_KI270792v1_alt
SN:chr5_KI270791v1_alt
SN:chr5_GL383532v1_alt
SN:chr5_GL949742v1_alt
SN:chr5_KI270794v1_alt
SN:chr5_GL339449v2_alt
SN:chr5_GL383530v1_alt
SN:chr5_KI270796v1_alt
SN:chr5_GL383531v1_alt
SN:chr5_KI270795v1_alt
SN:chr6_GL000250v2_alt
SN:chr6_KI270800v1_alt
SN:chr6_KI270799v1_alt
SN:chr6_GL383533v1_alt
SN:chr6_KI270801v1_alt
SN:chr6_KI270802v1_alt
SN:chr6_KB021644v2_alt
SN:chr6_KI270797v1_alt
SN:chr6_KI270798v1_alt
SN:chr7_KI270804v1_alt
SN:chr7_KI270809v1_alt
SN:chr7_KI270806v1_alt
SN:chr7_GL383534v2_alt
SN:chr7_KI270803v1_alt
SN:chr7_KI270808v1_alt
SN:chr7_KI270807v1_alt
SN:chr7_KI270805v1_alt
SN:chr8_KI270818v1_alt
SN:chr8_KI270812v1_alt
SN:chr8_KI270811v1_alt
SN:chr8_KI270821v1_alt
SN:chr8_KI270813v1_alt
SN:chr8_KI270822v1_alt
SN:chr8_KI270814v1_alt
SN:chr8_KI270810v1_alt
SN:chr8_KI270819v1_alt
SN:chr8_KI270820v1_alt
SN:chr8_KI270817v1_alt
SN:chr8_KI270816v1_alt
SN:chr8_KI270815v1_alt
SN:chr9_GL383539v1_alt
SN:chr9_GL383540v1_alt
SN:chr9_GL383541v1_alt
SN:chr9_GL383542v1_alt
SN:chr9_KI270823v1_alt
SN:chr10_GL383545v1_alt
SN:chr10_KI270824v1_alt
SN:chr10_GL383546v1_alt
SN:chr10_KI270825v1_alt
SN:chr11_KI270832v1_alt
SN:chr11_KI270830v1_alt
SN:chr11_KI270831v1_alt
SN:chr11_KI270829v1_alt
SN:chr11_GL383547v1_alt
SN:chr11_JH159136v1_alt
SN:chr11_JH159137v1_alt
SN:chr11_KI270827v1_alt
SN:chr11_KI270826v1_alt
SN:chr12_GL877875v1_alt
SN:chr12_GL877876v1_alt
SN:chr12_KI270837v1_alt
SN:chr12_GL383549v1_alt
SN:chr12_KI270835v1_alt
SN:chr12_GL383550v2_alt
SN:chr12_GL383552v1_alt
SN:chr12_GL383553v2_alt
SN:chr12_KI270834v1_alt
SN:chr12_GL383551v1_alt
SN:chr12_KI270833v1_alt
SN:chr12_KI270836v1_alt
SN:chr13_KI270840v1_alt
SN:chr13_KI270839v1_alt
SN:chr13_KI270843v1_alt
SN:chr13_KI270841v1_alt
SN:chr13_KI270838v1_alt
SN:chr13_KI270842v1_alt
SN:chr14_KI270844v1_alt
SN:chr14_KI270847v1_alt
SN:chr14_KI270845v1_alt
SN:chr14_KI270846v1_alt
SN:chr15_KI270852v1_alt
SN:chr15_KI270851v1_alt
SN:chr15_KI270848v1_alt
SN:chr15_GL383554v1_alt
SN:chr15_KI270849v1_alt
SN:chr15_GL383555v2_alt
SN:chr15_KI270850v1_alt
SN:chr16_KI270854v1_alt
SN:chr16_KI270856v1_alt
SN:chr16_KI270855v1_alt
SN:chr16_KI270853v1_alt
SN:chr16_GL383556v1_alt
SN:chr16_GL383557v1_alt
SN:chr17_GL383563v3_alt
SN:chr17_KI270862v1_alt
SN:chr17_KI270861v1_alt
SN:chr17_KI270857v1_alt
SN:chr17_JH159146v1_alt
SN:chr17_JH159147v1_alt
SN:chr17_GL383564v2_alt
SN:chr17_GL000258v2_alt
SN:chr17_GL383565v1_alt
SN:chr17_KI270858v1_alt
SN:chr17_KI270859v1_alt
SN:chr17_GL383566v1_alt
SN:chr17_KI270860v1_alt
SN:chr18_KI270864v1_alt
SN:chr18_GL383567v1_alt
SN:chr18_GL383570v1_alt
SN:chr18_GL383571v1_alt
SN:chr18_GL383568v1_alt
SN:chr18_GL383569v1_alt
SN:chr18_GL383572v1_alt
SN:chr18_KI270863v1_alt
SN:chr19_KI270868v1_alt
SN:chr19_KI270865v1_alt
SN:chr19_GL383573v1_alt
SN:chr19_GL383575v2_alt
SN:chr19_GL383576v1_alt
SN:chr19_GL383574v1_alt
SN:chr19_KI270866v1_alt
SN:chr19_KI270867v1_alt
SN:chr19_GL949746v1_alt
SN:chr20_GL383577v2_alt
SN:chr20_KI270869v1_alt
SN:chr20_KI270871v1_alt
SN:chr20_KI270870v1_alt
SN:chr21_GL383578v2_alt
SN:chr21_KI270874v1_alt
SN:chr21_KI270873v1_alt
SN:chr21_GL383579v2_alt
SN:chr21_GL383580v2_alt
SN:chr21_GL383581v2_alt
SN:chr21_KI270872v1_alt
SN:chr22_KI270875v1_alt
SN:chr22_KI270878v1_alt
SN:chr22_KI270879v1_alt
SN:chr22_KI270876v1_alt
SN:chr22_KI270877v1_alt
SN:chr22_GL383583v2_alt
SN:chr22_GL383582v2_alt
SN:chrX_KI270880v1_alt
SN:chrX_KI270881v1_alt
SN:chr19_KI270882v1_alt
SN:chr19_KI270883v1_alt
SN:chr19_KI270884v1_alt
SN:chr19_KI270885v1_alt
SN:chr19_KI270886v1_alt
SN:chr19_KI270887v1_alt
SN:chr19_KI270888v1_alt
SN:chr19_KI270889v1_alt
SN:chr19_KI270890v1_alt
SN:chr19_KI270891v1_alt
SN:chr1_KI270892v1_alt
SN:chr2_KI270894v1_alt
SN:chr2_KI270893v1_alt
SN:chr3_KI270895v1_alt
SN:chr4_KI270896v1_alt
SN:chr5_KI270897v1_alt
SN:chr5_KI270898v1_alt
SN:chr6_GL000251v2_alt
SN:chr7_KI270899v1_alt
SN:chr8_KI270901v1_alt
SN:chr8_KI270900v1_alt
SN:chr11_KI270902v1_alt
SN:chr11_KI270903v1_alt
SN:chr12_KI270904v1_alt
SN:chr15_KI270906v1_alt
SN:chr15_KI270905v1_alt
SN:chr17_KI270907v1_alt
SN:chr17_KI270910v1_alt
SN:chr17_KI270909v1_alt
SN:chr17_JH159148v1_alt
SN:chr17_KI270908v1_alt
SN:chr18_KI270912v1_alt
SN:chr18_KI270911v1_alt
SN:chr19_GL949747v2_alt
SN:chr22_KB663609v1_alt
SN:chrX_KI270913v1_alt
SN:chr19_KI270914v1_alt
SN:chr19_KI270915v1_alt
SN:chr19_KI270916v1_alt
SN:chr19_KI270917v1_alt
SN:chr19_KI270918v1_alt
SN:chr19_KI270919v1_alt
SN:chr19_KI270920v1_alt
SN:chr19_KI270921v1_alt
SN:chr19_KI270922v1_alt
SN:chr19_KI270923v1_alt
SN:chr3_KI270924v1_alt
SN:chr4_KI270925v1_alt
SN:chr6_GL000252v2_alt
SN:chr8_KI270926v1_alt
SN:chr11_KI270927v1_alt
SN:chr19_GL949748v2_alt
SN:chr22_KI270928v1_alt
SN:chr19_KI270929v1_alt
SN:chr19_KI270930v1_alt
SN:chr19_KI270931v1_alt
SN:chr19_KI270932v1_alt
SN:chr19_KI270933v1_alt
SN:chr19_GL000209v2_alt
SN:chr3_KI270934v1_alt
SN:chr6_GL000253v2_alt
SN:chr19_GL949749v2_alt
SN:chr3_KI270935v1_alt
SN:chr6_GL000254v2_alt
SN:chr19_GL949750v2_alt
SN:chr3_KI270936v1_alt
SN:chr6_GL000255v2_alt
SN:chr19_GL949751v2_alt
SN:chr3_KI270937v1_alt
SN:chr6_GL000256v2_alt
SN:chr19_GL949752v1_alt
SN:chr6_KI270758v1_alt
SN:chr19_GL949753v2_alt
SN:chr19_KI270938v1_alt
SN:chrM
SN:chrUn_KI270302v1
SN:chrUn_KI270304v1
SN:chrUn_KI270303v1
SN:chrUn_KI270305v1
SN:chrUn_KI270322v1
SN:chrUn_KI270320v1
SN:chrUn_KI270310v1
SN:chrUn_KI270316v1
SN:chrUn_KI270315v1
SN:chrUn_KI270312v1
SN:chrUn_KI270311v1
SN:chrUn_KI270317v1
SN:chrUn_KI270412v1
SN:chrUn_KI270411v1
SN:chrUn_KI270414v1
SN:chrUn_KI270419v1
SN:chrUn_KI270418v1
SN:chrUn_KI270420v1
SN:chrUn_KI270424v1
SN:chrUn_KI270417v1
SN:chrUn_KI270422v1
SN:chrUn_KI270423v1
SN:chrUn_KI270425v1
SN:chrUn_KI270429v1
SN:chrUn_KI270442v1
SN:chrUn_KI270466v1
SN:chrUn_KI270465v1
SN:chrUn_KI270467v1
SN:chrUn_KI270435v1
SN:chrUn_KI270438v1
SN:chrUn_KI270468v1
SN:chrUn_KI270510v1
SN:chrUn_KI270509v1
SN:chrUn_KI270518v1
SN:chrUn_KI270508v1
SN:chrUn_KI270516v1
SN:chrUn_KI270512v1
SN:chrUn_KI270519v1
SN:chrUn_KI270522v1
SN:chrUn_KI270511v1
SN:chrUn_KI270515v1
SN:chrUn_KI270507v1
SN:chrUn_KI270517v1
SN:chrUn_KI270529v1
SN:chrUn_KI270528v1
SN:chrUn_KI270530v1
SN:chrUn_KI270539v1
SN:chrUn_KI270538v1
SN:chrUn_KI270544v1
SN:chrUn_KI270548v1
SN:chrUn_KI270583v1
SN:chrUn_KI270587v1
SN:chrUn_KI270580v1
SN:chrUn_KI270581v1
SN:chrUn_KI270579v1
SN:chrUn_KI270589v1
SN:chrUn_KI270590v1
SN:chrUn_KI270584v1
SN:chrUn_KI270582v1
SN:chrUn_KI270588v1
SN:chrUn_KI270593v1
SN:chrUn_KI270591v1
SN:chrUn_KI270330v1
SN:chrUn_KI270329v1
SN:chrUn_KI270334v1
SN:chrUn_KI270333v1
SN:chrUn_KI270335v1
SN:chrUn_KI270338v1
SN:chrUn_KI270340v1
SN:chrUn_KI270336v1
SN:chrUn_KI270337v1
SN:chrUn_KI270363v1
SN:chrUn_KI270364v1
SN:chrUn_KI270362v1
SN:chrUn_KI270366v1
SN:chrUn_KI270378v1
SN:chrUn_KI270379v1
SN:chrUn_KI270389v1
SN:chrUn_KI270390v1
SN:chrUn_KI270387v1
SN:chrUn_KI270395v1
SN:chrUn_KI270396v1
SN:chrUn_KI270388v1
SN:chrUn_KI270394v1
SN:chrUn_KI270386v1
SN:chrUn_KI270391v1
SN:chrUn_KI270383v1
SN:chrUn_KI270393v1
SN:chrUn_KI270384v1
SN:chrUn_KI270392v1
SN:chrUn_KI270381v1
SN:chrUn_KI270385v1
SN:chrUn_KI270382v1
SN:chrUn_KI270376v1
SN:chrUn_KI270374v1
SN:chrUn_KI270372v1
SN:chrUn_KI270373v1
SN:chrUn_KI270375v1
SN:chrUn_KI270371v1
SN:chrUn_KI270448v1
SN:chrUn_KI270521v1
SN:chrUn_GL000195v1
SN:chrUn_GL000219v1
SN:chrUn_GL000220v1
SN:chrUn_GL000224v1
SN:chrUn_KI270741v1
SN:chrUn_GL000226v1
SN:chrUn_GL000213v1
SN:chrUn_KI270743v1
SN:chrUn_KI270744v1
SN:chrUn_KI270745v1
SN:chrUn_KI270746v1
SN:chrUn_KI270747v1
SN:chrUn_KI270748v1
SN:chrUn_KI270749v1
SN:chrUn_KI270750v1
SN:chrUn_KI270751v1
SN:chrUn_KI270752v1
SN:chrUn_KI270753v1
SN:chrUn_KI270754v1
SN:chrUn_KI270755v1
SN:chrUn_KI270756v1
SN:chrUn_KI270757v1
SN:chrUn_GL000214v1
SN:chrUn_KI270742v1
SN:chrUn_GL000216v2
SN:chrUn_GL000218v1
SN:chrX
SN:chrY
SN:chrY_KI270740v1_random
[kong@hpc22 dbSNP]$ grep -v "#" 00-All_chr.vcf | cut -f 1 | uniq | sort | uniq
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrMT
chrX
chrY
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