This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error Running Bmr Calc-Covg

Hello,

I'm trying to run bmr calc-covg and got an warning message:

[fai_fetch] Warning - Reference 1 not found in FASTA file, returning empty sequence Failed to execute: calcRoiCovg ..,

I checked my ROI file to make sure the format is fine. The chr name only has numbers I also changed the fasta file so that the sequence header match the chr name in ROI

What could caused the error?

Thanks!

music
• 2,660 views • link
updated by Chris Miller Chris Miller • written by lili • lili

1 answer

Do all of your chromosome names match between the roi file, fasta, and bam? This includes MT/M and the short alternate haplotypes with names like chr6_cox or GL.1234

• 0 views • link
written by Chris Miller Chris Miller

Log in to answer this question.

More posts like this
  • Get calculate coverage:Runxing calcRoiCovg succeeded, but music2 bmr calc-covg failed
    written by gengshen_yin • gengshen_yin
    Dear All, for Getting calculate coverage,music2 bmr calc-covg command failed;but it is ok when i run calcRoiCovg command to get calculate coverage one by one. …
  • RUN genome music (MuSiC2) error
    written by Haitao • Haitao
    Dear All, From Install to run, I took almost one and half week, but still can not run MuSiC2 successfully. Here is my install log …
  • genome music bmr calc-covg [Run in parallel]
    written by Chirag Nepal Chirag Nepal
    I used genome music to calculate significant pathways, which works great. In the first, where coverage is calculated, genome music bmr calc-covg --gene-covg-dir geneCov_combined --bam-list …
  • Why the AT_covd CG_covg CpG_covd is zero???what happened with them?
    written by qwertyuiop201320142015 • qwertyuiop201320142015
    hi,everyone I have some problems in sample1.covg that is the part of genome music calc-covg. ``` #Gene Length Covered AT_covd CG_covd CpG_covd xuhb 13 13 …
  • genome music bmr calc-covg-helper
    written by qwertyuiop201320142015 • qwertyuiop201320142015
    ``` xuhb@xuhb-desktop:~/expirment/exam1$ genome music bmr calc-covg-helper --normal-tumor-bam-pair bam1-list --reference-sequence seq.fa --output-dir ex5 --roi-file roi --normal-min-depth 1 --tumor-min-depth 1 --min-mapq 0 Use of uninitialized value $normal_bam …
  • Genome MuSiC calcRoiCovg crashing
    written by E.Earley • E.Earley
    I'm having trouble getting calcRoiCovg to work on some paired exome alignments. I did get calcRoiCovg to finish completely and successfully on a test ROI …
  • Problem in music bmr coverage
    written by Nitish Mishra • Nitish Mishra
    Hi, I am using this command in music ``` genome music bmr calc-covg \ --bam-list /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/BAM_list \ --output-dir /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/coverage/ \ --gene-covg-dir /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Reference-Platypus/TumorVsNormal/coverage/ \ --reference-sequence /shared/unmc1/unmc_gudalab/nitish123/DbGAP/Pancreatic/hg19-Pancreatic/hg19_UCSC.fa …
  • Music Calcroicovg Core Dump: "Floating Point Exception"
    written by Alastair Droop • Alastair Droop
    <p>Hello.</p> <p>I'm having problems running music bmr calc_covg for exome data. For each of my normal/tumour <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> pairs, calcRoiCovg dies, saying "Floating point exception …
  • Problems Running Bmr Calc-Covg On Music By Washu
    written by Ashwini Patil • Ashwini Patil
    <p>Dear all, </p> <p>I am trying to run bmr calc-covg. But when I use the following command, I receive an error. </p> <pre><code>genome music bmr …
  • Error - Skipping Invalid Roi
    written by sharan.janjuha • sharan.janjuha
    <p>Hi,</p> <p>I am trying to use the command "genome music bmr calc-covg"</p> <p>genome music bmr calc-covg --bam-list=/home/duttlab/Documents/path<em>bam</em>file --output-dir=/home/duttlab/Documents/music<em>output/ --reference-sequence=/home/duttlab/Documents/GRCh37/human</em>g1k<em>v37.fasta --roi-file /home/duttlab/Documents/cervical/755/BT755</em>ROI<em>filter</em>sorted_1based.roi</p> <p>and I'm getting the …