not overlapping any simulation region, correct your input

[Former user]

command:

mutforge -x fastq -b 1000 -f 1000 -e 1000 -t target.bed -n 1 -o sv_sim -d tmp -v tmp1.var hs37d5.fa simple.par hs37d5.fa

Var file: VAR_1 DEL_1 0.5 0 chr15 74706895 TRUE 70 FALSE None VAR_2 DEL_1 0.5 1 chr15 74706895 TRUE 70 FALSE None VAR_3 DEL_2 1 0 chr21 46703297 TRUE 65 FALSE None VAR_4 DEL_2 1 1 chr21 46703297 TRUE 65 FALSE None VAR_5 DEL_3 0.5 0 chr8 145009471 TRUE 53 FALSE None VAR_6 DEL_3 0.5 1 chr8 145009471 TRUE 53 FALSE None VAR_7 DEL_4 1 0 chrX 16850737 TRUE 74 FALSE None VAR_8 DEL_4 1 1 chrX 16850737 TRUE 74 FALSE None VAR_9 DEL_5 0.5 0 chr22 23655127 TRUE 61 FALSE None VAR_10 DEL_5 0.5 1 chr22 23655127 TRUE 61 FALSE None

output: preparing simulation regions... done entering runmode 3 in file2var ... file2var done in var2bed ... done var2bed in var2fq... ERROR: feature chr15 74706895 74706966 VAR_1 DEL_1 0.5 70 None chr21 46703297 46703363 VAR_3 DEL_2 1.0 65 None chr8 145009471 145009525 VAR_5 DEL_3 0.5 53 None chrX 16850737 16850812 VAR_7 DEL_4 1.0 74 None chr22 23655127 23655189 VAR_9 DEL_5 0.5 61 None

Could you help me with this? Not sure what is the error, it is not very informative. Also is it possible to add better explanation for option -b burnin just like the plank and trunk size in FAQ?

Thanks.

[Gopi1616]

After debugging for a while, I figured this out! The chromosome was named without chr in the reference and different in bed file and var file I used. Thanks, this issue can be closed now. However I would like a good explanation for the input values like -b added in FAQ or other place