-
Notifications
You must be signed in to change notification settings - Fork 11
Open
Description
I cloned the GitHub using:
git clone https://github.com/robinschmid/microbe_masst.git
Then installed the requirements:
pip install -r requirements.txt
Wanted to do a trial run on the provided ../examples/wender_plants.csv
Created an output directory as in jobs.py called ../output/example/
Therefore the final code in jobs.py remained:
files = [
(r"../examples/wender_plants.csv", "../output/example/feature"),
# (r"../examples/vta_filter.mgf", "../output/examples/vta_"),
]
Example of what appeared:
INFO:__main__:Starting new job for input: ../examples/wender_plants.csv
INFO:masst_batch_client:Running fast microbe masst on input n=40 spectra (total with already finished was 40 spectra)
DEBUG:masst_client:Query fastMASST id:mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00009919518 of Morphine
DEBUG:masst_client:Query fastMASST id:mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00010114208 of Paclitaxel (taxol)
DEBUG:masst_client:Query fastMASST id:mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00010111842 of Artemisinin
DEBUG:masst_client:Query fastMASST id:mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00010116841 of Physostigmine
DEBUG:masst_client:Query fastMASST id:mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00006399843 of Quinidine
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): fasst.gnps2.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): fasst.gnps2.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): fasst.gnps2.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): fasst.gnps2.org:443
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): fasst.gnps2.org:443
DEBUG:urllib3.connectionpool:https://fasst.gnps2.org:443 "POST /search HTTP/1.1" 500 265
DEBUG:root:fastMASST response=500
DEBUG:masst_client:Query fastMASST id:mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00005749386 of Emetine
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): fasst.gnps2.org:443
DEBUG:urllib3.connectionpool:https://fasst.gnps2.org:443 "POST /search HTTP/1.1" 500 265
DEBUG:root:fastMASST response=500
DEBUG:masst_client:Query fastMASST id:mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00003139483 of Rutin
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): fasst.gnps2.org:443
DEBUG:urllib3.connectionpool:https://fasst.gnps2.org:443 "POST /search HTTP/1.1" 500 265
DEBUG:root:fastMASST response=500
This ran through the entire ../examples/wender_plants.csv until finished.
There was, however, no output into ../output/examples/
Can you advise why this gave no output, when using the examples given from the Github?
Thanks in advance!
Metadata
Metadata
Assignees
Labels
No labels