rseg-diff running error

[Li-Wei]

Hi I was running rseg-diff and got the following error. My command
line is

rseg-diff -c chromosome_size_rseg -o /scratch/output -i 20 -v -mode 2 -
d deadzones-k42-hg19.bed chip.bed control.bed

I allocated 8gb of memory so memory should be a problem. Anyone knows
what caused this and how to fix it?

[LOADING_DATA] chromosomes
[LOADING_DATA] dead zones
[LOADING_DATA] ocily3_fairex.bed
[LOADING_DATA] ocily3_ind.bed
[LOADING_DATA] separating deserts
[Remove duplicate reads]
[Selecting bin size] use Hideaki's empirical method: Bin size = 5381
[preparing data] binning reads ocily3_fairex
[preparing data] binning reads ocily3_ind
[preparing data] estimating parameters

DELTA (PARAMS,MIX)
1 nbdiff 9.62 10.0 12.0 10.0 0.6963 nbdiff 34.7 0.107
59.4 0.0740 0.3037
0.0284 nbdiff 10.3 10.0 13.9 10.0 0.7135 nbdiff 34.4 0.113
57.1 0.0828 0.2865
-0.001506 nbdiff 10.4 10.0 14.3 10.0 0.7165 nbdiff 34.3 0.117
56.3 0.0875 0.2835
ITR F BINS B BINS F PARAMS B PARAMS
DELTA
1 6.394 2.694nbdiff 9.93 10.0 13.7 10.0nbdiff 34.4 0.115 56.1
0.0858 1
2 13.39 8.63nbdiff 5.97 10.0 7.64 10.0nbdiff 35.0 0.0976 55.7
0.0763 0.06482
3 45.21 37.76nbdiff 2.58 10.0 3.19 10.0nbdiff 35.3 0.0945 54.7
0.0830 0.07293
4 248.8 232.8nbdiff 0.875 10.0 1.13 10.0nbdiff 35.4 0.0957 54.1
0.0900 0.05477
5 2249 2241nbdiff 0.281 10.0 0.424 10.0nbdiff 35.4 0.0999
53.9 0.0963 0.04209
61.078e+041.128e+04nbdiff 0.177 10.0 0.282 10.0nbdiff 35.4 0.103
54.0 0.0994 0.03041
71.457e+041.192e+04nbdiff 0.141 10.0 0.224 10.0nbdiff 35.5 0.104
54.0 0.101 0.009806
81.82e+041.675e+04nbdiff 0.107 10.0 0.173 10.0nbdiff 35.5 0.107
54.1 0.103 0.004742
92.093e+042.063e+04nbdiff 0.0814 10.0 0.128 10.0nbdiff 35.5 0.109
54.1 0.105 0.005095
103.396e+043.369e+04nbdiff 0.0120 10.0 0.0141 10.0nbdiff 35.6 0.115
54.2 0.112 0.005634
113.333e+053.483e+05nbdiff 4.48e-05 10.0 5.37e-05 10.0nbdiff 35.6
0.116 54.2 0.113 0.02651
124.522e+071.493e+08nbdiff 5.60e-07 10.0 5.71e-07 10.0nbdiff 35.6
0.116 54.2 0.113 0.005982
133.221e+101.979e+11nbdiff 3.55e-09 10.0 3.66e-09 10.0nbdiff 35.6
0.116 54.2 0.113 2.472e-05
14 1e+202.665e+14nbdiff 1.60e-11 10.0 1.67e-11 10.0nbdiff 35.6
0.116 54.2 0.113 2.89e-07
15 1e+203.502e+17nbdiff 6.67e-14 10.0 7.00e-14 10.0nbdiff 35.6
0.116 54.2 0.113 1.837e-09
16 1e+204.728e+18nbdiff 2.79e-16 10.0 2.93e-16 10.0nbdiff 35.6
0.116 54.2 0.113 8.246e-12
17 1e+204.728e+18nbdiff 1.18e-18 1.00e-05 1.24e-18 1.00e-05nbdiff
35.6 0.116 54.2 0.113 3.912e-
14
18 nan nannbdiff nan 5.00 nan 5.00nbdiff nan 5.00 nan
5.00 nan
rseg-diff: TwoStateScaleSplitHMM.cpp:203: double
TwoStateScaleSplitHMM::single_iteration(const std::vec
tor<double, std::allocator<double> >&, const std::vector<double,
std::allocator<double> >&, const std::
vector<double, std::allocator<double> >&, const std::vector<double,
std::allocator<double> >&, const st
d::vector<long unsigned int, std::allocator<long unsigned int> >&,
std::vector<std::pair<double, double
>, std::allocator<std::pair<double, double> > >&, std::vector<std::pair<double, double>, std::allocator
<std::pair<double, double> > >&, double&, double&, double&, double&,
double&, double&, double&, double&
, SplitDistro&, SplitDistro&) const: Assertion `finite(lp_sf) &&
finite(lp_sb) && finite(lp_ff) && fini
te(lp_fb) && finite(lp_ft) && finite(lp_bf) && finite(lp_bb) &&
finite(lp_bt)' failed.
/var/spool/torque/mom_priv/jobs/612851.mgt.SC: line 5: 27482
Aborted

[Song, Qiang]

Hi Li-Wei,

It seems that RSEG ran into some strange estimates of the domain sizes.

Could you please try the following examinations:

1. Try to visualize your data on UCSC Genome browser and see whether there is
indeed enrichment in regions you expect.

2. Run RSEG without a control sample.

This will help us to isolate the error.

Best,
Song Qiang