Genome Music Calc-Wig-Covg Uninitialized Error

Question

[NickA5133]

I am having difficulty running this function in MuSiC.

Here is the input and output returned get when I run this function:

    lailab@envy-desktop:~$ genome music bmr calc-wig-covg --wig-list Music_Files/BMR/input/LATS1_wig.txt --output-dir Music_Files/BMR/output/  --reference-sequence Music_Files/BMR/input/hg19.fa --roi-file Music_Files/BMR/input/hg19_ROI.tsv
sh: mergeBed: not found
Use of uninitialized value $tot_covd in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 229.
Use of uninitialized value $tot_at_covd in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 229.
Use of uninitialized value $tot_cg_covg in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcWigCovg.pm line 229.
...

Those three uninitialized value errors occur in the same order a number of times until the function runs to completion. At this point most of the output files appears fine, though I am not certain what they should look like. However the total_covgs file appears as follows:

#Sample    Covered_Bases    AT_Bases_Covered    CG_Bases_Covered    CpG_Bases_Covered
TCGA-05-4424-01A-22D-1855-08                
TCGA-18-3409-01A-01D-0983-08                
TCGA-22-4604-01A-01D-1267-08                
TCGA-22-4613-01A-01D-1441-08
...

I am not certain if this is a formatting issue or if I need to run additional functions to get this data, like calc-bmr.

Here is how I have the files used set up on my computer.

LATS1_wig.txt:

TCGA-05-4424-01A-22D-1855-08    Music_Files/BMR/input/wig_files/LUAD/TCGA-05-4244-01.wig
TCGA-18-3409-01A-01D-0983-08    Music_Files/BMR/input/wig_files/LUSC/TCGA-18-3409-01.wig
TCGA-22-4604-01A-01D-1267-08    Music_Files/BMR/input/wig_files/LUSC/TCGA-22-4604-01.wig
TCGA-22-4613-01A-01D-1441-08    Music_Files/BMR/input/wig_files/LUSC/TCGA-22-4613-01.wig
...

hg19_ROI.tsv:

1    11867    12229    DDX11L1
1    12611    12723    DDX11L1
1    13219    14411    DDX11L1
1    29552    30041    MIR1302-11
1    30265    30669    MIR1302-11
...

hg19.fa

>1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...

Here is an example covg file that is in the gene_covg file in the output folder:

Example 1:

#Gene    Length    Covered    AT_covd    CG_covd    CpG_covd
1/2-SBSRNA4    3199    72    30    38    4
100289134    4546    0    0    0    0
100505814    711    251    145    100    6
100507229    322    0    0    0    0
100652938    4585    1070    576    448    46
61E3.4    22050    1147    489    585    73
643750    509    0    0    0    0
A1BG    1520    1160    428    605    127
A1CF    3346    2406    1281    1049    76

Example 2:

#Gene    Length    Covered    AT_covd    CG_covd    CpG_covd
1/2-SBSRNA4    3199    0    0    0    0
100289134    4546    0    0    0    0
100505814    711    0    0    0    0
100507229    322    0    0    0    0
100652938    4585    0    0    0    0
61E3.4    22050    0    0    0    0
643750    509    0    0    0    0
A1BG    1520    0    0    0    0
A1CF    3346    0    0    0    0

Let me know if I can provide additional information that would help determine what might be causing this.

Thank you for the help!

Answer 1

[Cyriac Kandoth]

Notice the first error message that says mergeBed: not found. This means that it isn't installed ...and this is kinda my fault. calc-wig-covg uses bedtools' mergeBed, which I forgot to include as a dependency in our Ubuntu package. All your input files look correct. So simply run sudo apt-get install bedtools, and you should be good to go. bedtools won't be a dependency in the next release, as we've switched to using joinx bed-merge.