Activity for saint-apms
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Asma Bankapur created ticket #18
SAINTq error: St12out_of_range
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Laura Woods posted a comment on ticket #15
Hey! I've got the same error, but I'm just working with the example data: "SAINTexpress-int.exe" "SAINTexpress_v3.6.3__2018-03-09\example input files\TIP49\inter.dat" "SAINTexpress_v3.6.3__2018-03-09\example input files\TIP49\prey.dat" "SAINTexpress_v3.6.3__2018-03-09\example input files\TIP49\bait.dat" Input files are: SAINTexpress_v3.6.3__2018-03-09\example input files\TIP49\inter.dat, SAINTexpress_v3.6.3__2018-03-09\example input files\TIP49\prey.dat, SAINTexpress_v3.6.3__2018-03-09\example input...
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Mira Sohn posted a comment on ticket #17
By any chance, is it possible to edit my ticket? I'd like to hide my bait name in the middle. Please delete my ticket if it's impossible so I can resubmit after editing.
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SAINTexpress with extremely high spectral count
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Jonathan Boulais posted a comment on ticket #16
The termination is caused by the dataset having a single control. SAINTexpress-int requires at least 2 negative controls, whereas SAINTexpress-spc can deal with a single negative control.
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SAINTexpress-int 3.6.1 char const* error
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Hi Hyungwon, I'm using SAINTexpress-int on intensity data. While I removed proteins having zero intensities, I'm getting a termination similar to Craig's : terminate called after throwing an instance of 'char const*' Aborted As a test, I ran SAINTexpress-spc using the same files and it works fine. Any help would be appreciated ! Many thanks ! Jonathan
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Hi Hyungwon, I'm using SAINTexpress-int on intensity data. While I removed proteins having zero intensities, I'm getting a termination similar to Craig's : terminate called after throwing an instance of 'char const*' Aborted Any help would be appreciated ! Many thanks ! Jonathan
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Witold Eryk created ticket #15
L is larger than the number of control IPs.
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Joan Josep Bech-Serra posted a comment on a wiki page
Hi Guo and Hyungwon, I am trying to improve my results in SAINT by adding interaction data in my analysis. However, I have some things that I need to clarify. In the example provided in the manual of SAINT you show a file with two columns: the first one with a list of GOIDs (not used by the software to compute the TopoAvgP) and the second one, the important one, with a list of genes separated with a blank space, for each GOID. I supose that the genes shown for each GOID (for example, for GO:0000002...
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Just recently moved to mac. Although I was able to build the binary on linux, I just recently moved to mac. I would be great if you could provide build instructions for this platform. Being able to build a software from source allows to have more confidence and trust in the software. Some build instructions for Windows would also be great. I am looking forward to the build instructions, and thank you so much for looking into it.
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Guo Ci Teo posted a comment on ticket #14
I have not tested it to compile in Mac. Do you have access to Windows or Linux machines? If you do, there are compiled binaries in the Precompiled_binariesfolder in the tar.gz file.
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SAINTexpress_v3.6.3__2018-03-09.tar.gz
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What did you download?
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I am also attaching the bootsrap.log
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Build on MacOS
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Armel Nicolas posted a comment on ticket #13
Ok, so I actually should not have focused on the messages. Previously I was getting the above messages but no list. Now I still get the same messages, but the list is successfully created. So whichever reason I was not getting the list for was fixed as I tried to troubleshoot the messages although they were actually unrelated. Sorry for the trouble, please close (or even delete) this bug.
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SAINTexpress-int.exe error (3.4)
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Estefany Guzman posted a comment on a wiki page
Parsing prey file prey.dat ...libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: invalid delimiter ^ I am getting this error even when utilizing the prey.dat file that came with the package. Any suggestions on how to correct the issue?
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Mike created ticket #12
SAINTexpress Imputed values
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Altuğ Kamacıoğlu posted a comment on ticket #11
Thank you, In my input files, there is PCDH7 but in result file, PCDH7 seems completely empty. Maybe it can be because bait name and the protein name is the same but it was not a problem when I'm using PSM values.
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Hyungwon Choi posted a comment on ticket #11
It seems that the data was properly run based on your list.txt file. There is a normalization step inside that scales the intensity value down in the final report (list.txt), and we replace zeros with a dot in the reporting. Unforunately the scoring algorithm must have determined that there is no significant interaction (all scores are zeros). I believe this has to do with the reproducibility across replicates. I'll look further to see if something else is wrong with the software.
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Saintexpress-int result
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Hi, which command line did you run? Was it SAINTexpress-int command? I just tried it and it ran OK. Also, you had a lot of places where you had "100" as the intensity. Are these imputed values? SAINTexpress can actually do imputation on its own, and I think you should try that instead of a plugged-in version. Usually we see a lot of missing data in the controls, but your data has no missing data at all -- which is unlikely from the raw data. Please feel free to contact me at email address: hwcho...
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Robin Journot posted a comment on ticket #10
Thank you very much, I forget to precise that I work with the SAINTexpress tool under galaxy at http://apostl.moffitt.org Best regards, Robin Journot De: "Hyungwon Choi" hwchoi912@users.sourceforge.net À: "[saint-apms:bugs]" 10@bugs.saint-apms.p.re.sourceforge.net Envoyé: Mardi 17 Septembre 2019 13:41:27 Objet: [saint-apms:bugs] #10 Error in Spec sum Hi, we will take a look and get back to you as soon as we figure it out. Hyungwon [bugs:#10] Error in Spec sum Status: open Group: v1.0 (example) Created:...
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Hi, we will take a look and get back to you as soon as we figure it out. Hyungwon
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Error in Spec sum
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rachita srivastava modified a comment on ticket #9
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Hi. I am trying to run saintexpress for IP data for a trancription factor. For me the run is getting aborted after throwing an instance of 'std::runtime_error' The command I gave was: SAINTexpress-int interaction_file.dat prey_file.dat bait_file.dat Input files are: interaction_file.dat, prey_file.dat, bait_file.dat Interaction file: "interaction_file.dat" Prey file: "prey_file.dat" Bait file: "bait_file.dat" GO file: "" Parsing prey file prey_file.dat ...done. Parsing prey file bait_file.dat ...done....
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Hi Craig, this is happening because there are interactions for which the intensities are all zero. It still tracks 0 intensities as missing observations within the software. We used to have a routine to plug zeros in, but at some point we decided not to do this for user's convenience.
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Craig Lawless posted a comment on ticket #9
Hi Hyungwon, It works with all interactions with zero intensity removed. So does SAINTexpress not treat zero intensity interactions the same as those that are missing (from control/IP replicates)? Thank you Craig
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Hi Craig, Can you try after removing all the interactions that has zero values? Hyungwon
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SAINTexpress-int Aborted
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saint-apms released /SAINTexpress_v3.6.3__2018-03-09.tar.gz
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SASI MANNE posted a comment on ticket #8
The input format was not unix compatible which was causing the error,it is fixed now. Your manual at http://crapome.org/sites/default/files/bi0815.pdf helped. For future reference "Reopen tab-delimited files generated from Mac OS X or Microsoft Windows in a text editor in a Unix environment and re-save as Unix-compatible tab-delimited files. The Unix utilities mac2unix and dos2unix may be used for this purpose. Alternatively, open each file in a nano text editor, press Ctrl+O once for saving, and...
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I'm not too sure. Your data works on mine, both on mac and linux after removing the peptide column. The only thing I can suspect is the new line character difference, even then we addressed this issue in the code.
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I wanted to know which version worked and on which OS,i used the same input files on MacOSx and using saintq_v0.0.4,still getting this error,do u have any suggestion to fix this
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Hi, I am trying to run saintq on Linux and am getting this error St12out_of_range vector::_M_range_check: __n (which is 2) >= this->size() (which is 1) I swtiched operating systems from mac to linux to see if it makes any changes in error i am getting on the same dataset. Can you check this error and see what i am doing wrong ? Thank you Sasi
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Thank you Hyungwon,i will try.
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One thing I would do is to set "normalize_control=true" instead of false. Attaching the input and output again.
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Not really, I just removed one column. I'm attaching the input and output files. Hw
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Hi, Thankyou for the quick reply,i removed the second column and tried rerunning and i am still getting the same error,did u have to change anything else in the paramter file or the input file? Thank you Sasi
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Hi, your NS_LFQ.tsv file contains protein and "peptide" labels even though the parameter file says "protein level" analysis. So you need to remove either the first or the second column in the NS_LFQ.tsv file. I just tested with your sample file and it works. Let me know if this doesn't work for you. HC
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Hi Guo and Hyungwon, I am trying to run saintq and getting the following error "St12out_of_range vector" and created a bug " #8 Out of range error",can you please look in to this and help me with the format of my param file and input files. Thank you Sasi
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Out of range error
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Sudhir Jadhao posted a comment on a wiki page
Thank you for your valuable time, I will try through CRAOome and Prohitz.
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Dear Guo and Hyungwon, Greetings for the day!! I want to analyes RIME data with saintq v4. I have downloaded the exe file and tried to run it. But I am not able install the exe file , aftter double clicking on exe file just balck window opens and get close immediately in 2 to 3 secs. Can you please help to solve above issue.
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Hi Sudhir, The file must be run from a command prompt (not a click-based program). To do this, you have to create an input parameter file placed in the same directory as the input data (spread sheet) according to the manuals and examples provided in the other zip file (saintq v0.0.4.tar.gz). If you aren't familiar with using the command line interface, then you can run the other versions of SAINT (SAINTexpress) in the CRAPome website or through ProHitz. Hope you can get it to work. Hw
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Dear Guo and Hyungwon, Greetings for the day!! I want to analyes RIME data with saintq v4. I downloaded the exe file and tried to run it. But I am not able install the exe file , aftter double clicking on exe file just balck window opens and get close immediately in 2 to 3 secs. Can you please help to solve above issue.
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Salvatore Loguercio posted a comment on ticket #7
Hi Guo, saintq 0.04 now compiles correctly on Mac OS X 10.11.2 El Capitan. Thank...
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Hi Brian, I have uploaded a new version. Please try that.
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Hi Erik, I tried what you suggested but to no avail ( on mac os x El Capitan, 10.11.2)....
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erik verschueren posted a comment on ticket #7
Hi Brian, I had a similar issue. I ended up first installing the boost and nlopt...
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Brian Capaldo created ticket #7
Make error on Mac OSX Yosemite
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hector created ticket #6
Saint express crashing
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Hi Jonas, I have included a set of sample input files in the latest version. Best,...
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Jonas Grossmann created ticket #5
Proper InputFiles not available
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New visualization tool for AP-MS data
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