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!
2 answers
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.
Chromosome names need to match between MAF, ROI file, BAM files, and FASTA file.
Log in to answer this question.
Are you sure that your ROIs match up with your fasta and bam? (i.e. "1" vs "chr1")
I solved the error by using a reference fasta that uses the same chromosome names as the ROI file.