oolonek / isdb Goto Github PK

Hi,
from the MGF files: INCHIAUX should be InChIKey. (INCHIAUX is auxilarry information from the INCHI itself).

BEGIN IONS
PEPMASS=331.1903853
CHARGE=1+
FILENAME=PMA_000001
UNPD_ID=UNPD1
MOLECULAR_FORMULA=C20H26O4
SEQ=*..*
IONMODE=Positive
EXACTMASS=330.1831093
NAME=UNPD1
SMILES=CC(C)C1CC(=O)C(=CCC=C(C)/CC(=O)CC2=CC1OC2=O)C
INCHI=InChI=1/C20H26O4/c1-12(2)17-11-18(22)14(4)7-5-6-13(3)8-16(21)9-15-10-19(17)24-20(15)23/h6-7,10,12,17,19H,5,8-9,11H2,1-4H3/b13-6-,14-7+/t17-,19-/m1/s1
INCHIAUX=XYKVOCNWMFQQKL-NZBROFJPSA-N

Cheers
Tobias

Hello, ISDB guys,
Thank you for the wonderful ISDB software.
Recently I ran a big dataset (a mixture of dataset from Bruker MTQ-II and QE-focus, with about 77 Mbit of mgf and 30 Mbit of out files), but failed after a 30 hours of calculation.
It showed "_csv.Error: field larger than field limit" (please see the picture). Is the LCMS dataset too big?
Could you please give me any instruction?

TJ Ling

When I tryed to run the workflow I faced the error of the subject of the post.

I'm posting here the SOLUTION!

insert the following lines after import the modules:
[...]
maxInt = sys.maxsize
csv.field_size_limit(maxInt)
[...]

Hello, guys!

I'm trying to use the dereplication tool described in the research paper 'Integration of Molecular Networking and MS-MS Fragmentation for Natural Products Dereplication' , but it isn't working with my data... I can't generate any results from the workflow described in the methodology.

I noticed that the data in the .out table from older versions of GNPS (as described in the paper) is organized differently in the .clustersummary table that is generated in the current version and I even tried to edit it manually to let the columns all in the same order found previously in the .out file, but it didn't work out.

The .log file generated points to the following message:
'ERROR opening!
ERROR loading model from (in MS2ScoringModel::LoadModel())'

I did not understand what this error means ... Could someone help me?

I am attaching the files I used for the analysis and the log file.
GNPS.zip
out_teste4.zip

Regards,
Naydja

Hi
do you plan to fix UniCode/utf8 in compound names and synonyms?

Best

Hi

Is it possible to use the same workflow with the FBMN on GNPS? If yes how can I download the data .mgf and .out?