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Topic: [MS-Dial 4.20] Error in JointAligner, alignment file not found (Read 5642 times) previous topic - next topic

[MS-Dial 4.20] Error in JointAligner, alignment file not found

HI,

I tried to run peak-picking and alignment with MS-Dial version 4.20 for about 12 times (different datasets and modes), and I experience problems in half of them. I got an error message saying that "error in JointAligner" right before the process finished. then when I tried to select the alignment file to export the alignment results, I found an error message saying that "There is no peak information for peak alignment. please check your ion mode setting". The peak-picking seems successful, though. i tried to re-run the alignment process once again within that project, but i got the same error message "error in JointAligner".

Has anyone experienced such problems before? and how do you solve it?

Thank you.

Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found

Reply #1 –
I would check first if raw data were converted properly.

What was your equipment/acquisition mode/data format?

Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found

Reply #2 –
At least I only found one error during the abf conversion, and I have skipped that file (RP pos). I got 3 errors with originally .raw data (RP pos metabolomics, HILIC pos and neg, though just now I could successfully redo the alignment for HILIC neg without changing any parameters) and 3 errors with .d data (RP pos lipidomics and metabolomics, RP neg lipidomics), though I don't think they matter because I converted them to .abf.

Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found

Reply #3 –
Hello,
i'm having the same problems. But when I process the same converted data on another computer, this error does not appear.

Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found

Reply #4 –
Quote from: Sergey Girel – on
I would check first if raw data were converted properly.

What was your equipment/acquisition mode/data format?

btw Sergey, how do you check if the abf files are properly converted?

Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found

Reply #5 –
Hi,

"Error occurred in JointAligner" will be shown if there is an error before going to further processes such as gap filling and filtering methods. So, maybe, I expect that it's due to "not all of files was properly processed." in the peak picking process.

candidate 1: some of files that you imported are different ionization mode.
candidate 2: some of files are not properly converted by the abf converter (check the file size, if the conversion does not work, the abf file containing around 9kb file size will be generated).
candidate 3: out of memory issue.

For candidate 3, when UC Davis's Tobias Kind tried to analyze >2000 abf files at once, MS-DIAL required around 200 GB RAM when the joint alignner is executed.

In the peak picking process for each file, MS-DIAL stores the entire MS data on the PC memory.
It means, if you set the thread size as 1, and if your abf file size is around 1GB, the program requires < 2GB RAM for the processing.
On the other hand, in the alignment process, the peak picked data (stored in *.pai2 format file) for all analysis files will be stored on the PC memory.

Although the file size of PAI2 file is around 1M, it will be elevated if you import many files.
I should export the error detail more. I am now re-writing all source codes of msdial/msfinder so that they can be executed in different OSs containing linux and mac by using the platform of .net standard 2.0 and core. In this process, I will improve this isseu.

Meanwhile, maybe, you can try to check the detail by yourself by the debug mode using the solution file of msdialworkbench.
You can download the entire source code from the below link.
http://prime.psc.riken.jp/compms/msdial/main.html

Thanks,

Hiroshi
 

Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found

Reply #6 –
Thanks for the reply, Hiroshi.

I suspect the candidate 3 as the most likely cause, because i tried to clear up some of my laptop memory, repeated the analysis, and 3 of them seemed to work out now. the last analysis still hasnt worked out yet. then i tried to reconvert some of the files from whom i got error messages for the last run, and i am rerunning the analysis now. hopefully it will be okay.

Stef
 

Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found

Reply #7 –
I was running into the exact same error and found out it may have another reason.

-> Make sure your files really contain only one run. There are instruments (like Sciex 6600) that overwrite files with the same name in case they are re-submitted (e.g., after an error or pause). Even if the original run did not contain any datapoints, there are two runs stored in one (for Sciex: wiff) file! You may not even notice because the file sizes only change marginally.

=> Solution: Conversion to mzML by MSConvert separates the runs. This means, however, that you have to convert all your files to mzML because MS-DIAL does not let you import files of different format (as far as I know).

Re: [MS-Dial 4.20] Error in JointAligner, alignment file not found

Reply #8 –
Quote from: Hiroshi Tsugawa – on
candidate 3: out of memory issue.

For candidate 3, when UC Davis's Tobias Kind tried to analyze >2000 abf files at once, MS-DIAL required around 200 GB RAM when the joint alignner is executed.

In the peak picking process for each file, MS-DIAL stores the entire MS data on the PC memory.
It means, if you set the thread size as 1, and if your abf file size is around 1GB, the program requires < 2GB RAM for the processing.
On the other hand, in the alignment process, the peak picked data (stored in *.pai2 format file) for all analysis files will be stored on the PC memory.

Although the file size of PAI2 file is around 1M, it will be elevated if you import many files.


This is really important to know. I got this error trying to process 985 mzML DIA files of ~100MB each. My VM has 64GB of RAM and the PAI2 files generated are ~3.5MB each, so that seems like plenty for this analysis. I assume that MS-DIAL builds its alignment file by combining all these individual files so the data in memory will be double that amount, but that's still a fraction of what it's using. I've rerun the analysis with some repeat samples removed, so 680 files, and I've got the same error. I'm now seeking a temporary boost to the RAM on the VM to get this analysis done.

People in the Australian Biocommons community have told me that they don't use MS-DIAL because it couldn't handle large datasets. It might help broaden the user base for the documentation to make these limits explicit.