Issue with Realign Indel

Question: Issue with Realign Indel

3.1 years ago by

United States

marcosp • 0 wrote:

So I have gotten to the point where I'm realigning indels, and had my reference file (hg19) uploaded into my history into the workflow, then then following message shows up:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch
[Thu Oct 15 22:26:17 CDT 2015] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/galaxy-repl/main/scratch/tmp-gatk-sPpidD/gatk_input.fasta OUTPUT=/galaxy-repl/main/scratch/tmp-gatk-sPpidD/dict142626248728295366.tmp    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Thu Oct 15 22:26:17 CDT 2015] Executing as g2main@roundup59.tacc.utexas.edu on Linux 2.6.32-504.8.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057)
[Thu Oct 15 22:26:41 CDT 2015] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.40 minutes.
Runtime.totalMemory()=3610771456
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version exported): 
##### 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/wiki/index.php/ReorderSam
##### ERROR   reads contigs = [chr10, chr11, chr11_gl000202_random, chr12, chr13, chr14, chr15, chr16, chr17_ctg5_hap1, chr17, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18, chr18_gl000207_random, chr19, chr19_gl000208_random, chr19_gl000209_random, chr1, chr1_gl000191_random, chr1_gl000192_random, chr20, chr21, chr21_gl000210_random, chr22, chr2, chr3, chr4_ctg9_hap1, chr4, chr4_gl000193_random, chr4_gl000194_random, chr5, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6, 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]
##### ERROR ------------------------------------------------------------------------------------------

Not sure what to do. Any help is appreciated.

realign indel • 1.5k views

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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by marcosp • 0

After trying the "ReorderSam" tool, I get this message:

Fatal error: Exit code 1 ()
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch
Exception in thread "main" picard.PicardException: New reference sequence does not contain a matching contig for chr11_gl000202_random
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:229)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:110)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)

ADD REPLY • link written 3.1 years ago by marcosp • 0

3.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The problem is with the sort order of the hg19 custom reference genome in use. I believe that you obtained the version from the GATK Shared Libraries on http://usegalaxy.org, but I can let you know that it not sorted in GATK order (see the error message for details about sort order, or the GATK website).

Sorting within Galaxy can be done, is multi-stepped, and only needs to be done once to create the proper fasta file for this tool. Convert to tabular, divide the file into chromosomes that can be sorted with the "Sort" tool plus stand-alone chromosomes, combine all together again with "Concatenate" tool, convert back to fasta format, then wrap the lines to avoid problems with certain downstream tools.

Using the human genome indexed natively for the tool (hg_g1k_v37 - the 1000 Genomes version) would avoid the need to do this and avoid any potential compute resource problems due to indexing requirements for very large genomes. It is the recommended choice.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

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