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Job Status
Workflow FEATURE-BASED-MOLECULAR-NETWORKING (version release_18)
Status
PROGENESIS Traceback (most recent call last): File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_18/scripts/reformat_quantification.py", line 117, in <module> main() File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_18/scripts/reformat_quantification.py", line 101, in main compound_scan_mapping = progenesis_formatter.convert_to_feature_csv(args.quantification_table, args.quantification_table_reformatted) File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_18/scripts/progenesis_formatter.py", line 13, in convert_to_feature_csv input_format = pd.read_csv(input_filename, sep=",", skiprows=2) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 709, in parser_f return _read(filepath_or_buffer, kwds) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 455, in _read data = parser.read(nrows) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 1069, in read ret = self._engine.read(nrows) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 1839, in read data = self._reader.read(nrows) File "pandas/_libs/parsers.pyx", line 902, in pandas._libs.parsers.TextReader.read File "pandas/_libs/parsers.pyx", line 924, in pandas._libs.parsers.TextReader._read_low_memory File "pandas/_libs/parsers.pyx", line 978, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 965, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 2208, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 17 fields in line 5, saw 42 Tool execution terminates abnormally with exit code [1]
Usertksj (taniakeiko@gmail.com), University of Helsinki
Title
GNPS Quickstart Molecular Networking Analysis
Date Created 2021-10-15 03:40:05.0
Execution Time 0 seconds
Progress
MS2 File MGF/MSP(Progenesis QI)/mzML(MzTab-M)
quickstart_GNPS/ef0507c5-40bc-4ba1-b21b-b25668bfc9ce/featurems2/fragment_database.msp
Feature Quantification Table
quickstart_GNPS/ef0507c5-40bc-4ba1-b21b-b25668bfc9ce/featurequantification/Compound_measurement.csv
Spectral Library
speclibs/CASMI/CASMI.mgf
speclibs/GNPS-SCIEX-LIBRARY/GNPS-SCIEX-LIBRARY.mgf
speclibs/MONA/MONA.mgf
speclibs/GNPS-NIH-CLINICALCOLLECTION2/GNPS-NIH-CLINICALCOLLECTION2.mgf
speclibs/GNPS-SELLECKCHEM-FDA-PART1/GNPS-SELLECKCHEM-FDA-PART1.mgf
speclibs/GNPS-COLLECTIONS-PESTICIDES-NEGATIVE/GNPS-COLLECTIONS-PESTICIDES-NEGATIVE.mgf
speclibs/LDB_POSITIVE/LDB_POSITIVE.mgf
speclibs/GNPS-NIH-NATURALPRODUCTSLIBRARY/GNPS-NIH-NATURALPRODUCTSLIBRARY.mgf
speclibs/GNPS-NIH-CLINICALCOLLECTION1/GNPS-NIH-CLINICALCOLLECTION1.mgf
speclibs/BERKELEY-LAB/BERKELEY-LAB.mgf
speclibs/MMV_POSITIVE/MMV_POSITIVE.mgf
speclibs/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_NEGATIVE/GNPS-NIH-NATURALPRODUCTSLIBRARY_ROUND2_NEGATIVE.mgf
speclibs/GNPS-SELLECKCHEM-FDA-PART2/GNPS-SELLECKCHEM-FDA-PART2.mgf
speclibs/PNNL-LIPIDS/PNNL-LIPIDS-NEGATIVE.mgf
speclibs/PNNL-LIPIDS/PNNL-LIPIDS-POSITIVE.mgf
speclibs/GNPS-NIST14-MATCHES/GNPS-NIST14-MATCHES.mgf
speclibs/IQAMDB/IQAMDB.mgf
speclibs/GNPS-IOBA-NHC/GNPS-IOBA-NHC.mgf
speclibs/GNPS-NIH-SMALLMOLECULEPHARMACOLOGICALLYACTIVE/GNPS-NIH-SMALLMOLECULEPHARMACOLOGICALLYACTIVE.mgf
speclibs/BILELIB19/BILELIB19.mgf