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!