Closed Irkcy closed 2 years ago
Hi Irkcy,
It looks like something was wrong in reading the files.
Could you please tell me what those ?
are from your computer:
I guess they are not English so my computer cannot display them.
Best,
Fengchao
Hi Irkcy,
It looks like something was wrong in reading the files.
Could you please tell me what those
?
are from your computer:I guess they are not English so my computer cannot display them.
Best,
Fengchao
Hi @fcyu ,
Those "?" are nothing in my computer.
Best, Irkcy
Hi Irkcy,
Thanks for your prompt reply. I guess it is due to some errors in reading the psm.tsv
. Can you re-run IonQuant? You can uncheck all tools except for IonQuant to save some time.
Best,
Fengchao
Hi Irkcy,
Thanks for your prompt reply. I guess it is due to some errors in reading the
psm.tsv
. Can you re-run IonQuant? You can uncheck all tools except for IonQuant to save some time.Best,
Fengchao
Hi @fcyu
Thanks for your prompt reply. I will re-run IonQuant as you suggest.
With kind regards, Irkcy
BTW, you can also check if there are other programs, such as antivirus, Dropbox, OneDrive, Google Drive, etc, locking or blocking the files when IonQuant is running.
Best,
Fengchao
BTW, you can also check if there are other programs, such as antivirus, Dropbox, OneDrive, Google Drive, etc, locking or blocking the files when IonQuant is running.
Best,
Fengchao
@fcyu ,thanks for pointing it out. It's a pity that there were no other programs when IonQuant was running. I tried as you suggested and it didn't work. It seems to be the same error as yesterday.
Best,
Irkcy
Hi Irkcy,
This time, the IOException
error was thrown from a different place:
2021-12-28 16:27:08 [INFO] - Writing index to Z:\lidan\WOSP00101\DDA\CAD20211212chenc_WOSP00101_DDA_60min_K562_rep1_3_Slot1-13_1_3169.quantindex
vs the last time:
2021-12-26 05:52:26 [INFO] - Calculating correlations between all other runs...
One is from writing the file, and the other is from reading the file. It looks like something was wrong with your file system. I am afraid you have to troubleshoot by yourself because I don't think I can reproduce it.
BTW, it looks like there is a message after java.io.IOException
this time, but it is not displayed correctly.
Best,
Fengchao
@Irkcy you can try to Change system locale
to English (United States)
before running FragPipe to get the error message to display properly. https://www.isunshare.com/windows-10/change-system-locale-in-windows-10.html
If you have resolved this issue already, please let us know how you resolved it.
Hi, Fragpipe Sorry for late reply. Thanks for your prompt reply. I will try as you suggest. I have resolved the issue. The DDA files was generated from two mass spectrometers. Firstly, I moved this files from the server to a local disk. Then I splited the files from two mass spectrometers into separate folders. Then I run Fragpipe separately. Finally, it worked successfully.
Best, Irkcy
---Original--- From: @.> Date: Thu, Dec 30, 2021 03:21 AM To: @.>; Cc: @.**@.>; Subject: Re: [Nesvilab/FragPipe] Label-free quantification with FragPipe(Issue #568)
@Irkcy you can try to Change system locale to English (United States) before running FragPipe to get the error message to display properly. https://www.isunshare.com/windows-10/change-system-locale-in-windows-10.html If you have resolved this issue already, please let us know how you resolved it.
— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you were mentioned.Message ID: @.***>
Hi Fragpipe,
I loaded the "LFQ-MBR" workflow. Then I added 48 .d DDA files. Alao I annotated them by editing the ‘Experiment’. On the ‘Database’ tab, I used Philosopher to add the contaminants and decoys to my FASTA file. On the ‘MSFragger’ tab, I setted "Fragment mass to tolerance" to "0.05Da", and ‘Calibration and Optimization’ to ‘None’ in the ‘Peak Matching’ section. Other parameters was followed as the default of Fragpipe. The following error occured: ERROR: java.util.concurrent.ExecutionException: java.io.IOException.
Best, Irkcy
log_2021-12-26_06-33-52.txt