I commanded like this
java -Xmx1g -jar ../GATK/GenomeAnalysisTK.jar -I P1_novo.reordered.sorted.bam -T RealignerTargetCreator -R ../reference/hg19_ucsc.fa -o P1.intervals --known ../reference/snp.vcf
then, the following error message occurred.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.4-21-g30b937d):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Lexicographically sorted human genome sequence detected in reads.
##### ERROR For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs.
##### ERROR This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files.
##### ERROR You can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wi...php/ReorderSam
##### ERROR reads contigs = [chr1, chr10, chr11, chr11_gl000202_random, chr12, chr13, chr14, chr15, chr16, chr17, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18, chr18_gl000207_random, chr19, chr19_gl000208_random, chr19_gl000209_random, chr1_gl000191_random, chr1_gl000192_random, chr2, chr20, chr21, chr21_gl000210_random, chr22, chr3, chr4, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr5, chr6, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7, chr7_gl000195_random, chr8, chr8_gl000196_random, chr8_gl000197_random, chr9, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chrM, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249, chrX, chrY]
I downloaded reference file from ucsc and catered them by this order:
grep chr ../reference/hg19_ucsc.fa
>chr1
>chr2
>chr3
>chr4
>chr5
>chr6
>chr7
>chr8
>chr9
>chr10
>chr11
>chr12
>chr13
>chr14
>chr15
>chr16
>chr17
>chr18
>chr19
>chr20
>chr21
>chr22
>chrX
>chrY
>chrM
>chrUn_gl000211
>chrUn_gl000212
>chrUn_gl000213
>chrUn_gl000214
>chrUn_gl000215
>chrUn_gl000216
>chrUn_gl000217
>chrUn_gl000218
>chrUn_gl000219
>chrUn_gl000220
>chrUn_gl000221
>chrUn_gl000222
>chrUn_gl000223
>chrUn_gl000224
>chrUn_gl000225
>chrUn_gl000226
>chrUn_gl000227
>chrUn_gl000228
>chrUn_gl000229
>chrUn_gl000230
>chrUn_gl000231
>chrUn_gl000232
>chrUn_gl000233
>chrUn_gl000234
>chrUn_gl000235
>chrUn_gl000236
>chrUn_gl000237
>chrUn_gl000238
>chrUn_gl000239
>chrUn_gl000240
>chrUn_gl000241
>chrUn_gl000242
>chrUn_gl000243
>chrUn_gl000244
>chrUn_gl000245
>chrUn_gl000246
>chrUn_gl000247
>chrUn_gl000248
>chrUn_gl000249
as the instruction says, I commanded reordersam tool of picard like this:
java -jar ../picard/ReorderSam.jar I=P1_novo.sorted.bam O=P1_novo.reordered.sorted.bam REFERENCE=../reference/hg19_ucsc.fa
however, the result of GATK with changed bam file makes same error message.
is there any solution?
java -Xmx1g -jar ../GATK/GenomeAnalysisTK.jar -I P1_novo.reordered.sorted.bam -T RealignerTargetCreator -R ../reference/hg19_ucsc.fa -o P1.intervals --known ../reference/snp.vcf
then, the following error message occurred.
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.4-21-g30b937d):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Lexicographically sorted human genome sequence detected in reads.
##### ERROR For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs.
##### ERROR This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files.
##### ERROR You can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wi...php/ReorderSam
##### ERROR reads contigs = [chr1, chr10, chr11, chr11_gl000202_random, chr12, chr13, chr14, chr15, chr16, chr17, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18, chr18_gl000207_random, chr19, chr19_gl000208_random, chr19_gl000209_random, chr1_gl000191_random, chr1_gl000192_random, chr2, chr20, chr21, chr21_gl000210_random, chr22, chr3, chr4, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, chr5, chr6, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7, chr7_gl000195_random, chr8, chr8_gl000196_random, chr8_gl000197_random, chr9, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chrM, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249, chrX, chrY]
I downloaded reference file from ucsc and catered them by this order:
grep chr ../reference/hg19_ucsc.fa
>chr1
>chr2
>chr3
>chr4
>chr5
>chr6
>chr7
>chr8
>chr9
>chr10
>chr11
>chr12
>chr13
>chr14
>chr15
>chr16
>chr17
>chr18
>chr19
>chr20
>chr21
>chr22
>chrX
>chrY
>chrM
>chrUn_gl000211
>chrUn_gl000212
>chrUn_gl000213
>chrUn_gl000214
>chrUn_gl000215
>chrUn_gl000216
>chrUn_gl000217
>chrUn_gl000218
>chrUn_gl000219
>chrUn_gl000220
>chrUn_gl000221
>chrUn_gl000222
>chrUn_gl000223
>chrUn_gl000224
>chrUn_gl000225
>chrUn_gl000226
>chrUn_gl000227
>chrUn_gl000228
>chrUn_gl000229
>chrUn_gl000230
>chrUn_gl000231
>chrUn_gl000232
>chrUn_gl000233
>chrUn_gl000234
>chrUn_gl000235
>chrUn_gl000236
>chrUn_gl000237
>chrUn_gl000238
>chrUn_gl000239
>chrUn_gl000240
>chrUn_gl000241
>chrUn_gl000242
>chrUn_gl000243
>chrUn_gl000244
>chrUn_gl000245
>chrUn_gl000246
>chrUn_gl000247
>chrUn_gl000248
>chrUn_gl000249
as the instruction says, I commanded reordersam tool of picard like this:
java -jar ../picard/ReorderSam.jar I=P1_novo.sorted.bam O=P1_novo.reordered.sorted.bam REFERENCE=../reference/hg19_ucsc.fa
however, the result of GATK with changed bam file makes same error message.
is there any solution?
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