Question: Music Bmr Calc-Bmr: error
0
gravatar for Q.S.Yang
2.9 years ago by
Q.S.Yang0
China
Q.S.Yang0 wrote:

I had installed music by the guide "Installation of the MuSiC suite on unsupported Linux distributions" I am using calcRoiCovg.

the roi file : ensembl_67_cds_ncrna_and_splice_sites_hg19 (download in ubuntu)

calcRoiCovg Sample_n.bam Sample_t.bam roi.file hg19.fa test

Got this error message:

Skipping invalid ROI: 1 11867 12229 DDX11L1

Skipping invalid ROI: 1 12611 12723 DDX11L1

Skipping invalid ROI: 1 13219 14411 DDX11L1

·········

Skipping invalid ROI: Y 28124349 28124468 PRYP4

Skipping invalid ROI: Y 28132779 28132813 PRYP4

Skipping invalid ROI: Y 28133956 28134218 PRYP4

test:

NOTE:

Last line in file shows non-overlapping totals across all ROIs

Gene ROI Length Covered ATs_Covered CGs_Covered CpGs_Covered

NonOverlappingTotals 0 0 0 0

So,where did the error come from and how to fix it? Thanks!

software error • 931 views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Q.S.Yang0

Are you sure that your ROIs match up with your fasta and bam? (i.e. "1" vs "chr1")

ADD REPLYlink written 2.9 years ago by Chris Miller20k

I solved the error by using a reference fasta that uses the same chromosome names as the ROI file.

ADD REPLYlink written 2.9 years ago by Q.S.Yang0
0
gravatar for Q.S.Yang
2.9 years ago by
Q.S.Yang0
China
Q.S.Yang0 wrote:

genome music bmr calc-bmr --bmr-output bmr --roi-file roi_chr.file --gene-mr-file mr_file --reference-sequence hg19.fa --bam-list bam.txt --output-dir rr --maf-file my.maf

my bam.txt

S1 /media/qin//bam/S1b.bam /media/qin/bam/S1a.bam

S2 /media/qin//bam/S2b.bam /media/qin/bam/S2a.bam

my.maf

Hugo_Symbol Entrez_Gene_Id  Center  NCBI_Build  Chromosome  Start_Position  End_Position    Strand Variant_Classification   Variant_Type    Reference_Allele    Tumor_Seq_Allele1   Tumor_Seq_Allele2      dbSNP_RS dbSNP_Val_Status    Tumor_Sample_Barcode    Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1  Match_Norm_Seq_Allele2  Tumor_Validation_Allele1    Tumor_Validation_Allele2    Match_Norm_Validation_Allele1   Match_Norm_Validation_Allele2   Verification_Status Validation_Status   Mutation_Status Sequencing_Phase    Sequence_Source Validation_Method   Score   BAM_File    Sequencer   Tumor_Sample_UUID   Matched_Norm_Sample_UUID    HGVSc   HGVSp   HGVSp_Short Transcript_ID   Exon_Number AF in normal/AF in tumor    AF in tumor t_depth t_ref_count t_alt_count AF in normal    n_depth n_ref_count n_alt_count all_effects Allele  Gene    Feature Feature_type    Consequence cDNA_position   CDS_position    Protein_position    Amino_acids Codons  Existing_variation  ALLELE_NUM  DISTANCE    字段44    SYMBOL  SYMBOL_SOURCE   HGNC_ID BIOTYPE CANONICAL   CCDS    ENSP    SWISSPROT   TREMBL  UNIPARC RefSeq  SIFT    PolyPhen    EXON    INTRON  DOMAINS GMAF    AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF  EA_MAF  CLIN_SIG    SOMATIC PUBMED  MOTIF_NAME  MOTIF_POS   HIGH_INF_POS    MOTIF_SCORE_CHANGE  IMPACT  PICK    VARIANT_CLASS   TSL HGVS_OFFSET PHENO   MINIMISED   ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO  FILTER

rr: gene_covgs dir roi_covgs dir total_covgs

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 249.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 249.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 249.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 250.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 250.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 250.

Use of uninitialized value $sample in hash element at /usr/local/share/perl/5.20.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 250.

Loading per-sample coverages stored in rr/total_covgs

Mismatching number of samples in rr/total_covgs and bam.txt

I did not found the mismatching number of samples in total_coverage and bam.txt.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Q.S.Yang0
0
gravatar for Q.S.Yang
2.9 years ago by
Q.S.Yang0
China
Q.S.Yang0 wrote:

Chromosome names need to match between MAF, ROI file, BAM files, and FASTA file.

ADD COMMENTlink written 2.9 years ago by Q.S.Yang0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1638 users visited in the last hour