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compomics / moFF

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Apache License 2.0
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Apex intensities reported as -1.0 on Linux (Ubuntu) using RAW files as input #15

Closed jgriss closed 7 years ago

jgriss commented 7 years ago

Hi!

I processed some of the CPTAC study 6 files changing from the mzML input I used previously to the original RAW files.

For some reason, all intensities are now reported as "-1.0". Here's the result and the log file: mam_050108o_CPTAC_study6_6C008_080505040419.zip

Any idea why this is happening?

Thanks for the help!

Best regards, Johannes

Maux82 commented 7 years ago

Hi,

Which of kind of input are you using ? The search result of the PeptideShaker that I provided or the result of your search engines ? With the same input and mzML file do you get result ?

One possible reason could be that the RT in input file is in second , but iin RAW file must be in minutes maybe you comment the line where I do the transformation . This happens to me a lot if I use different input from different sources like MaxQuant or PeptideShaker

Anyhow, I will take a deep look into this .

jgriss commented 7 years ago

Hi,

The input file is from my own pipeline and it works with mzML as input files.

Do I have to convert the RT from seconds into minutes? In your docs I thought it said that your tools expect RT to be in seconds.

About the code: I didn't change anything apart from the code I sent you.

Thanks for your help!

Best regards, Johannes

Maux82 commented 7 years ago

No the Rt in seconds is correct , inside the code it has converted in minute because thermo raw file store in such a way.

What the log file say for each peptide ?

Can you print for me args_txic in moff.py ? like a log.critical(args_txic) before the subprocess call here

However, I have update the master branch with a speedup improvement regadring the mzML reading( thanks to @mafreitas #14 ) , I will appreciate if you can test it, maybe this new version could fix also your problem with the rawfile. I have tested on a raw file and I did not have any problems.

Andrea