Closed tobiasko closed 4 years ago
Hi Tobi,
One --psm
for one psm.tsv
. If you have multiple psm.tsv
, need to use multiple --psm
like what FragPipe does. Your command won't work because --psm /scratch/tobiasko/DSXXXXX/*_*/psm.tsv
will be expanded to something like --psm /scratch/tobiasko/DSXXXXX/A_1/psm.tsv /scratch/tobiasko/DSXXXXX/A_2/psm.tsv /scratch/tobiasko/DSXXXXX/A_3/psm.tsv ...
Best,
Fengchao
Ok. Not ideal. Why does the expansion work for the other parameters?
The expansion only works for the spectral files and pepXML files because there is no ambiguity (no need to specify what they are because their extension already gives such information). For psm.tsv, IonQuant need to know it is psm.tsv from Philosopher rather than other types of tsv files.
I am just re-running the command as you suggested and it looks like he is not using results from the previous execution, but starting all over again. Really?
Does "results from the previous execution" mean the *_quant.csv
file from IonQuant? If so, you can replace your pepXML paths with those *_quant.csv
.
And the rest of the command stays the same?
Yes.
Great! THX for your help! But one request: I think you should expand the README.md in this respect. The java -jar IonQuant.jar <options> <.d/.mzML/.mzXML/.pepXML/_quant.csv files>
is maybe a little brief, especially for multi experiment cases. Maybe some examples would help.
Best, Tobi
Yes, I totally agree. I am going to add more explanations and examples later.
Best,
Fengchao
Hi IonQuant developers,
my issue relates to the IonQuant parameters on the linux command line. In short, I am trying to run IonQuant on top of
philosopher pipeline
. Philosopher leaves this nicely organizsed workspace:But since it can't call
IonQuant
yet I need to do this manually. What works is using:But as soon as I start adding additional parameters like
--psm
I am running into problems:Java reports unrecognized parameters. Could it be that the unamed parameters like path to raw files or pepXMLs are parsed differently than named ones? Do you really need to add one
-psm <path>
for each file? That would be a real pain for big multi experiments.A randomly selected dry run log looks as if the FragPipeGUI does it this way:
Best, Tobi