Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • [GATK] quality score recalibration -knowsite

    Hi all!
    I have a problem with a step of quality score recalibration, refererred to -knowsites.

    when I try to run this command line:
    Code:
    java -Xmx4g -jar GenomeAnalysisTK.jar --num_threads 4 -l INFO /
    -R  ucsc.hg19.fasta -knownSites 00-All.vcf /
    -I chr3_bam.marked.realigned.fixed.bam -T BaseRecalibrator /
    -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate /
    -cov DinucCovariate -o chr3.recal_data.grp
    I got this error:
    Code:
    ##### ERROR A USER ERROR has occurred (version 2.3-9-ge5ebf34): 
    ##### 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 website and forum for extensive documentation and answers to 
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: No overlapping contigs found.
    ##### ERROR   knownSites contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, 
    GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, 
    GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, 
    GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, 
    GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, 
    GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, 
    GL000225.1, GL000192.1, NC_007605]
    ##### ERROR   reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, 
    chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, 
    chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, 
    chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, 
    chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, 
    chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, 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]
    ##### ERROR
    So I've downloaded another hg19.fasta from:
    ftp://ftp.broadinstitute.org/pub/seq...sembly19.fasta
    and I have :
    Code:
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A USER ERROR has occurred (version 2.3-9-ge5ebf34): 
    ##### 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 website and forum for extensive documentation and answers to 
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found.
    ##### ERROR   reads contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, 
    chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, chr4_gl000194_random, 
    chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, chr7_gl000195_random, 
    chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, 
    chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, 
    chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, 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]
    ##### ERROR   reference contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, 
    GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, 
    GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, 
    GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, 
    GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, 
    GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, 
    GL000225.1, GL000192.1, NC_007605]
    ##### ERROR
    If I build a hg19.fasta file in this way:
    Code:
    cat chrM.fa chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chr10.fa 
    chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr20.fa
     chr21.fa chr22.fa chrX.fa chrY.fa chr1_gl000191_random.fa chr1_gl000192_random.fa 
    chr4_ctg9_hap1.fa chr4_gl000193_random.fa chr4_gl000194_random.fa chr6_apd_hap1.fa 
    chr6_cox_hap2.fa chr6_dbb_hap3.fa chr6_mann_hap4.fa chr6_mcf_hap5.fa 
    chr6_qbl_hap6.fa chr6_ssto_hap7.fa chr7_gl000195_random.fa chr8_gl000196_random.fa
    chr8_gl000197_random.fa chr9_gl000198_random.fa chr9_gl000199_random.fa 
    chr9_gl000200_random.fa chr9_gl000201_random.fa chr11_gl000202_random.fa 
    chr17_ctg5_hap1.fa chr17_gl000203_random.fa chr17_gl000204_random.fa 
    chr17_gl000205_random.fa chr17_gl000206_random.fa chr18_gl000207_random.fa 
    chr19_gl000208_random.fa chr19_gl000209_random.fa chr21_gl000210_random.fa 
    chrUn_gl000211.fa chrUn_gl000212.fa chrUn_gl000213.fa chrUn_gl000214.fa 
    chrUn_gl000215.fa chrUn_gl000216.fa chrUn_gl000217.fa chrUn_gl000218.fa 
    chrUn_gl000219.fa chrUn_gl000220.fa chrUn_gl000221.fa chrUn_gl000222.fa 
    chrUn_gl000223.fa chrUn_gl000224.fa chrUn_gl000225.fa chrUn_gl000226.fa 
    chrUn_gl000227.fa chrUn_gl000228.fa chrUn_gl000229.fa chrUn_gl000230.fa 
    chrUn_gl000231.fa chrUn_gl000232.fa chrUn_gl000233.fa chrUn_gl000234.fa 
    chrUn_gl000235.fa chrUn_gl000236.fa chrUn_gl000237.fa chrUn_gl000238.fa 
    chrUn_gl000239.fa chrUn_gl000240.fa chrUn_gl000241.fa chrUn_gl000242.fa 
    chrUn_gl000243.fa chrUn_gl000244.fa chrUn_gl000245.fa chrUn_gl000246.fa 
    chrUn_gl000247.fa chrUn_gl000248.fa chrUn_gl000249.fa > /home/haloplex/bam/hg19-vcf.fa
    I got:
    Code:
    ##### ERROR MESSAGE: Input files knownSites and reference have incompatible contigs: No overlapping contigs found.
    ##### ERROR   knownSites contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, 
    GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, 
    GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, 
    GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, 
    GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, 
    GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, 
    GL000225.1, GL000192.1, NC_007605]
    ##### ERROR   reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17,
     chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_gl000191_random, chr1_gl000192_random, chr4_ctg9_hap1, chr4_gl000193_random, 
    chr4_gl000194_random, chr6_apd_hap1, chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4, chr6_mcf_hap5, chr6_qbl_hap6, chr6_ssto_hap7, 
    chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, 
    chr9_gl000201_random, chr11_gl000202_random, chr17_ctg5_hap1, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, 
    chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, 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]


    Where is a 00-All.vcf dbsnp compatible with hg19.fasta reference that I have ?
    or where is a hg19.fasta compatible with 00-All.vcf

    If it is userful:
    I use samtools faidx to build .fai and picardtool to build .dict of reference.

    thank you so much!
    Last edited by sirmark; 03-14-2013, 06:30 AM.

  • #2
    I have solved by downloading vcf format from GATK budle ftp with an ftp client



    I think that it's an important step to add in wiki

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM
    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    16 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    46 views
    0 likes
    Last Post seqadmin  
    Working...
    X