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Old 11-10-2014, 06:22 AM   #1
yuelincoln
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Default How to deal with this problem? Reordersam treat bam file

##### ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Lexicographically sorted human genome sequence detected in knownSites.
##### 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://gatkforums.broadinstitute.org...ies-reordersam
##### ERROR knownSites contigs = [chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chrM, chrX, chrY, chr9]
##### ERROR ------------------------------------------------------------------------------------------
INFO 22:20:10,569 HelpFormatter - --------------------------------------------------------------------------------

This error was happend when i run BaseRecalibrator of the bam file.
I also have used ReorderSam.jar to re-order the bam file, but it still didn't work.
java -jar /usr/local/software/picard-tools-1.105/ReorderSam.jar I=./PET19_malformed.bam O=./PET19_reorder.bam REFERENCE=/home/george/alignment/gatk_resource/ucsc.hg19.fasta CREATE_INDEX=True
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Old 11-10-2014, 01:27 PM   #2
dpryan
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Have you confirmed that the fasta file has the correct order?
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Old 11-10-2014, 09:51 PM   #3
yuelincoln
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I think fasta file order is right, because if i directly use GATK to call snp of the same bam file, all run seemed ok. But if use this file to run BaseRecalibrator, it will report this error.
So it is very confused.
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Old 11-11-2014, 07:34 AM   #4
westerman
Rick Westerman
 
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Just because one program has no problem with the order does not mean that a different program will not have a problem with the order. The ERROR message is extremely clear (for a bioinformatics program) -- it tells you both the error and what to do about it.

You say you ran ReorderSam.jar (as suggested) but the error persists. So we now need to do more heavy troubleshooting. As @dpryan says, have you confirmed your fasta file is in order. Do a:

Code:
grep '>' /home/george/alignment/gatk_resource/ucsc.hg19.fasta | more
and show us the top several lines.

It would also be nice to look inside your BAM file and see if column 3 is in correct order. I think that the following will help in this:

Code:
samtools view ./PET19_reorder.bam | cut -f 3 | grep chr | uniq -c | more
And show us the top several lines of that.
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Old 11-11-2014, 05:59 PM   #5
yuelincoln
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@westerman, thanks. Below is the results.
$ /usr/local/software/samtools-0.1.13/samtools view ./301-10.rmdup.bam | cut -f 3 | grep chr | uniq -c | more
3175288 chrM
568694 chr1
459726 chr2
351916 chr3
225789 chr4
493266 chr5
691892 chr6
348049 chr7
262928 chr8
138590 chr9
275147 chr10
209938 chr11
202256 chr12
150772 chr13
126969 chr14
193823 chr15
147602 chr16
167425 chr17
104782 chr18
73551 chr19
87570 chr20
43880 chr21
95365 chr22
529116 chrX
4396 chrY
28 chr1_gl000191_random

for hg19 is also right order.
$ head -10 /media/Analysis/gatk_resource/ucsc.hg19.fasta.fai
chrM 16571 6 50 51
chr1 249250621 16915 50 51
chr2 243199373 254252555 50 51
chr3 198022430 502315922 50 51
chr4 191154276 704298807 50 51
chr5 180915260 899276175 50 51
chr6 171115067 1083809747 50 51
chr7 159138663 1258347122 50 51
chr8 146364022 1420668565 50 51
chr9 141213431 1569959874 50 51
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Old 11-13-2014, 01:21 PM   #6
westerman
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Certainly looks good. Only that 'chr1_gl000191_random' in the BAM file is the least bit strange. Unfortunately I have no more troubleshooting advice.
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