pNovo+ stopped in the middle of a analysis
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Teck Yew Low
Dec 3, 2015, 11:45:26 AM12/3/15
to DeNovoGUI
Hi,
I was trying to analyze a 40MB MGF files with pNovo+ but it only managed to finished 9.85% and the following message appeared:
Please advise why this is so. I managed to process the same MGF file with Novor and PepNovo.
==================================================================================================
# ------------------------------------------------------------------
# DeNovoGUI 1.9.0 Report File
#
# Originally saved by: science.bms.processi @ BMS-5P5SZ4J
# on: 03 Dec 2015, 17:43
# as: re
# ------------------------------------------------------------------
Thu Dec 03 17:33:23 CET 2015 Starting DeNovoGUI.
Thu Dec 03 17:33:23 CET 2015 Loading the spectra.
Thu Dec 03 17:33:23 CET 2015 Done loading the spectra.
Thu Dec 03 17:33:23 CET 2015 Starting de novo sequencing: 66819 spectra in 1 file using 8 threads.
Thu Dec 03 17:33:23 CET 2015 Sequencing OR6_120206_TY_BN3_Liver_3ug_AspN[Node_04].mgf using pNovo+.
####################################
# #
# Welcome to pNovo+ #
# #
# #
####################################
A subdirectory or file D:\Teck\New folder\\ already exists.
[info] FILE1 D:\Teck\New folder\OR6_120206_TY_BN3_Liver_3ug_AspN[Node_04].mgf: 66819 spectra.
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|====
This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
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|====== | 14.75% completed.terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Thu Dec 03 17:38:54 CET 2015 Sequencing OR6_120206_TY_BN3_Liver_3ug_AspN[Node_04].mgf using pNovo+ completed (5 minutes 31 seconds).
Thu Dec 03 17:38:54 CET 2015 De novo sequencing completed (5 minutes 31 seconds).
Thu Dec 03 17:38:54 CET 2015 The de novo sequencing did not generate any output files!
Thu Dec 03 17:38:54 CET 2015 Sequencing Canceled.
Best,
Teck
Harald Barsnes
Dec 3, 2015, 11:59:44 AM12/3/15
to DeNovoGUI
Hi Teck,
If one of the algorithms fails to complete in this way we'd recommend contacting the developers of the algorithm, as we have very little control over what happens inside the algorithm itself. To me it looks like a memory issue but I could be wrong. You could try with a smaller part of the same file etc, to try to narrow down the possible causes.
However, as you can see our pNovo+ support is labeled as "beta", so we'd generally recommend to use the other search engines which are more stable.
Please let us know if you mange to solve the problem through contacting the pNovo+ developers.
Best regards,
Harald
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