Insufficient values in manual scale. 11 needed but only 9 provided.

[YingYa]

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

[ShixiangWang]

@YingYa Thanks for your report. I think this issue is due to some plot functions can only handle signatures with number <= 9 based on the color palette. Could you re-run with added --verbose option and show again the output? So I can determine where this program stopped and fix/catch the error.

[YingYa]

Yes, I will re-run with '--verbose'.

[YingYa]

@ShixiangWang, Here is part of the output with '--verbose':

Select Run 26, which K = 11 as best solution.
Outputing signature results for SBS
==
Outputing signature object, signature and exposure matrix.
Outputing sample clusters based on relative signature exposures.
=> Running k-means clustering.
ℹ [2021-05-25 22:20:40]: Started.
✔ [2021-05-25 22:20:40]: 'Signature' object detected.
ℹ [2021-05-25 22:20:40]: Running k-means with 11 clusters...
ℹ [2021-05-25 22:20:40]: Generating a table of group and signature contribution (stored in 'map_table' attr):
ℹ [2021-05-25 22:20:40]: Assigning a group to a signature with the maximum fraction...
ℹ [2021-05-25 22:20:40]: Summarizing...
        group #1: 62 samples with Sig10 enriched.
        group #10: 114 samples with Sig1 enriched.
        group #11: 162 samples with Sig1 enriched.
        group #2: 19 samples with Sig11 enriched.
        group #3: 103 samples with Sig2 enriched.
        group #4: 245 samples with Sig1 enriched.
        group #5: 19 samples with Sig2 enriched.
        group #6: 165 samples with Sig1 enriched.
        group #7: 6 samples with Sig5 enriched.
        group #8: 64 samples with Sig4 enriched.
        group #9: 139 samples with Sig1 enriched.
! [2021-05-25 22:20:40]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
ℹ [2021-05-25 22:20:40]: 0.312 secs elapsed.
Outputing signature profile plot.
Outputing signature exposure plot.
ℹ [2021-05-25 22:20:48]: 41.695 mins elapsed.
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

[ShixiangWang]

@YingYa Thanks :). I am busy recently, but I will try to fix this issue ASAP. Please be patient.

By the way, from the output above. The major results should be properly outputted. So maybe you can plot the data by your own or directly use sigminer.

[ShixiangWang]

@YingYa Sorry for the late response. Recently I am on vocation and had no time to fix this issue. Now I am pushing a new version Sigflow 2.1 based on the modification of sigminer.

Once the new tag shows at https://hub.docker.com/r/shixiangwang/sigflow/tags?page=1&ordering=last_updated, you can pull the latest version of sigflow and retry your analysis. The issue should be properly addressed.

[YingYa]

@ShixiangWang Thanks for helping.