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compomics / denovogui

Graphical user interface for de novo sequencing of tandem mass spectra
http://compomics.github.io/projects/denovogui.html
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DeNovoCLI blast generation #31

Closed CarlaCristinaUranga closed 7 years ago

CarlaCristinaUranga commented 7 years ago

Hello,

I am running DeNovoCLI but the blast file is not being generated. It has to be generated via the server becuase they are 2-3 GB files and I don't have the computing power to run it via the GUI. Any thoughts? These are my command line arguments:

java -cp DeNovoGUI-1.15.0.jar com.compomics.denovogui.cmd.IdentificationParametersCLI -out "HCD_par_decoy.par" -db uniprot_all_concatenated_target_decoy.fastaprot_all.fasta -mc 2 -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M" -pepnovo_hitlist_length 1 -pepnovo_generate_blast 1 -pnovo_activation HCD -pnovo_num_peptides 1 -novor_fragmentation HCD

Thank you very much!

Best wishes from the Mexico science rebellion,

Carla Uranga

hbarsnes commented 7 years ago

Hi Carla,

I'm afraid the BLAST feature is not yet supported on the command line. Perhaps you could try doing the de novo search via SearchGUI instead and loading the results in PeptideShaker?

Best regards, Harald

CarlaCristinaUranga commented 7 years ago

Thank you kindly for your response. This helps a lot! I have a random question for you. Is the NOVOR peptide score basically a -10logP score?

Best wishes,

Carla

On Fri, Feb 10, 2017 at 5:10 AM, Harald Barsnes notifications@github.com wrote:

Hi Carla,

I'm afraid the BLAST feature is not yet supported on the command line. Perhaps you could try doing the de novo search via SearchGUI instead and loading the results in PeptideShaker?

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/denovogui/issues/31#issuecomment-278938456, or mute the thread https://github.com/notifications/unsubscribe-auth/AVXji7efyI7BigasD2Ej8dvoHntf_vzoks5rbGG_gaJpZM4L8_SS .

hbarsnes commented 7 years ago

Hi Carla,

Is the NOVOR peptide score basically a -10logP score?

I don't know the details of how the Novor score is calculated. I'd recommend checking the Novor paper (https://www.ncbi.nlm.nih.gov/pubmed/?term=26122521) or the Novor wiki (http://wiki.rapidnovor.com/wiki/Main_Page).

Best regards, Harald