Hi there,
I validated my files a few weeks ago but forgot to save the output message (something like "the file is validated"). So I tried to reproduce it again recently but had no success. The program just kept silence, no error message either. Does anyone notice this? Any suggestions?
Thanks,
MJ
Created by Meijian Guan mguan927 Hi Tom,
I notice it now. Thanks!
MJ Dear MJ,
Apologies, it changed to WAKE when I put in place the 4 letter abbreviations for centers that gave them to us. Notice the error you received when you put in WakeForest:
>validateGENIE.py: error: argument center: invalid choice: 'WakeForest' (choose from 'JHU', 'DFCI', 'GRCC', 'NKI', 'MSK', 'UHN', 'VICC', 'MDA', 'WAKE', 'YALE', 'UCSF', 'VHIO', 'UCHI', 'TJU', 'SWED', 'NWCC', 'Northwell', 'MSCC', 'IUCC', 'CORN', 'CRUK', 'COLU', 'CHOP', 'BCGSC', 'BordeauxUniCancer', 'StJude', 'JEFF', 'UBCC', 'VHIO', 'PROV')
Best,
Tom Hi Tom,
Thank you for your help. It works now. Not sure what happened, I was able to use **WakeForest** to produce those messages.
Thanks,
MJ Dear MJ,
So you are using WakeForest as your center name. Please use WAKE as your center name and also make sure you replace the `WakeForest` in your filenames to `WAKE`. These should be your commands:
```
python sage_processing/validateGENIE.py clinical sampleFile/data_clinical_supp_patient_WAKE.txt sampleFile/data_clinical_supp_sample_WAKE.txt WAKE
python sage_processing/validateGENIE.py maf sampleFile/data_mutations_extended_WAKE.txt WAKE
python sage_processing/validateGENIE.py bed sampleFile/WAKE-48-v12.bed WAKE
```
Best,
Tom Hi Tom,
I was running the following code.
```
python sage_processing/validateGENIE.py clinical sampleFile/data_clinical_supp_patient_WakeForest.txt sampleFile/data_clinical_supp_sample_WakeForest.txt WakeForest
python sage_processing/validateGENIE.py maf sampleFile/data_mutations_extended_WakeForest.txt WakeForest
python sage_processing/validateGENIE.py bed sampleFile/WakeForest-48-v12.bed WakeForest
```
Sometimes I see results as following:
```
[####################]100.00% 1/1 Done...
Downloading [####################]100.00% 798.0bytes/798.0bytes (177.5kB/s) Job-47198783324970150033252578.csv Done...
usage: validateGENIE.py [-h] [--thread THREAD] [--offline]
[--uploadToSynapse UPLOADTOSYNAPSE]
[--oncotreeLink http://oncotree.mskcc.org/oncotree/api/tumor_types.txt?version=oncotree_2017_06_21]
{maf,clinical,fusions,cnv,vcf,seg,bed,cbs,patientCounts}
file [file ...]
{JHU,DFCI,GRCC,NKI,MSK,UHN,VICC,MDA,WAKE,YALE,UCSF,VHIO,UCHI,TJU,SWED,NWCC,Northwell,MSCC,IUCC,CORN,CRUK,COLU,CHOP,BCGSC,BordeauxUniCancer,StJude,JEFF,UBCC,VHIO,PROV}
validateGENIE.py: error: argument center: invalid choice: 'WakeForest' (choose from 'JHU', 'DFCI', 'GRCC', 'NKI', 'MSK', 'UHN', 'VICC', 'MDA', 'WAKE', 'YALE', 'UCSF', 'VHIO', 'UCHI', 'TJU', 'SWED', 'NWCC', 'Northwell', 'MSCC', 'IUCC', 'CORN', 'CRUK', 'COLU', 'CHOP', 'BCGSC', 'BordeauxUniCancer', 'StJude', 'JEFF', 'UBCC', 'VHIO', 'PROV')
```
But most of the time only usage information:
```
usage: validateGENIE.py [-h] [--thread THREAD] [--offline]
[--uploadToSynapse UPLOADTOSYNAPSE]
[--oncotreeLink http://oncotree.mskcc.org/oncotree/api/tumor_types.txt?version=oncotree_2017_06_21]
{maf,clinical,fusions,cnv,vcf,seg,bed,cbs,patientCounts}
file [file ...]
{JHU,DFCI,GRCC,NKI,MSK,UHN,VICC,MDA,WAKE,YALE,UCSF,VHIO,UCHI,TJU,SWED,NWCC,Northwell,MSCC,IUCC,CORN,CRUK,COLU,CHOP,BCGSC,BordeauxUniCancer,StJude,JEFF,UBCC,VHIO,PROV}
validateGENIE.py: error: argument center: invalid choice: 'WakeForest' (choose from 'JHU', 'DFCI', 'GRCC', 'NKI', 'MSK', 'UHN', 'VICC', 'MDA', 'WAKE', 'YALE', 'UCSF', 'VHIO', 'UCHI', 'TJU', 'SWED', 'NWCC', 'Northwell', 'MSCC', 'IUCC', 'CORN', 'CRUK', 'COLU', 'CHOP', 'BCGSC', 'BordeauxUniCancer', 'StJude', 'JEFF', 'UBCC', 'VHIO', 'PROV')
```
What kind of message should I expect? I did see validation message at the first time I ran these code. Any suggestions?
MJ
Dear Meijian,
May I ask what command it is that you run?
Best,
Tom