Insufficient values in manual scale. 11 needed but only 9 provided. · Issue #31 · ShixiangWang/sigflow (original) (raw)
The Sigflow fail to extract the signatures by BayesianNMF for SBS.
Output of STDERR:
=================================================================
Name : sigflow
Author : Shixiang Wang
Version: 2.0
License: AFL 3.0
Link : https://github.com/ShixiangWang/sigflow
Doc : https://github.com/ShixiangWang/sigflow
============================== START
Parsing parameters...
------
extract : TRUE
fit : FALSE
bt : FALSE
show : FALSE
help : FALSE
version : FALSE
input : /path/to/exome.merge.maf.gz
output : /path/to/Sigflow/exome/extract_BayesianNMF/SBS_20210519_m50r30_hyper
index : ALL
mode : SBS
manual : FALSE
number : 0
max : 50
genome : hg38
nrun : 30
cores : 16
refit : FALSE
hyper : TRUE
sigprofiler : FALSE
isearch : NULL
verbose : FALSE
------
User command calling: /usr/lib/R/bin/exec/R --no-echo --no-restore --file=/opt/sigflow.R --args extract -i /path/to/exome.merge.maf.gz -o /path/to/Sigflow/exome/extract_BayesianNMF/SBS_20210519_m50r30_hyper -m SBS -g hg38 --max 50 -r 30 -T 16 --hyper
------
Reading file...
------
------
Running signature extraction pipeline...
------
An error is detected in extract process. Quit the program!
Insufficient values in manual scale. 11 needed but only 9 provided.
Warning messages:
1: In file(con, "r") :
URL 'https://bioconductor.org/config.yaml': Timeout of 60 seconds was reached
2: In file(con, "r") :
URL 'http://bioconductor.org/config.yaml': Timeout of 60 seconds was reached
Output of STDOUT:
==========start at : Tue May 25 15:57:49 CST 2021 ==========
Sig1 Sig2 Sig3 Sig4 Sig5 Sig6
1 0.24615731 0.18720205 0.027342756 0.02357352 0.04599808 0.02737249
2 0.17871662 0.13535705 0.073849690 0.03696856 0.03601408 0.01502531
3 0.26014544 0.28788830 0.030471741 0.03447861 0.04167483 0.02450295
4 0.46174631 0.17226970 0.022022158 0.02339876 0.05224561 0.02219186
5 0.16919376 0.47594024 0.194196060 0.01959926 0.01744435 0.03688851
6 0.35497207 0.17643475 0.029808545 0.02826085 0.05298947 0.02735486
7 0.04207117 0.00000000 0.005479459 0.03838119 0.86518699 0.01807443
8 0.25229011 0.04006395 0.122218724 0.27357582 0.02206503 0.09835426
9 0.39725613 0.28043876 0.028839610 0.02130957 0.04298226 0.02290072
10 0.57289246 0.11334461 0.027606416 0.02074828 0.04242611 0.02975359
11 0.37690116 0.03276671 0.154513487 0.11738752 0.02022855 0.12677601
Sig7 Sig8 Sig9 Sig10 Sig11
1 0.03315557 0.021170740 0.077021944 0.251468502 0.055532303
2 0.05643546 0.021427464 0.050244049 0.040001762 0.350268417
3 0.02333126 0.027433646 0.112332722 0.109678843 0.043594171
4 0.02154308 0.017668141 0.126070992 0.057047113 0.018656277
5 0.01150269 0.010867830 0.017815887 0.017667430 0.016329339
6 0.02448501 0.017506036 0.101635998 0.119214232 0.063057926
7 0.01208476 0.002006641 0.001677479 0.000000000 0.001682984
8 0.08629146 0.049968880 0.017403941 0.009730527 0.022656625
9 0.02328697 0.016051489 0.093759623 0.046874975 0.020837388
10 0.02384370 0.018396701 0.089446244 0.038809210 0.015405981
11 0.04850959 0.082682882 0.015687081 0.003822237 0.012131501