Hi Yuki,
thank you for the alpha version.
I have a blank + 3 abf files, lcmsdda.
- Win GUI MS-DIAL 4.36 works fine
- Win console MS-DIAL 4.36 works only with tutorial param file. If I export the params from v4.36, it doesn't work.
- Linux console alpha does not work. Log is pasted below.
.
Problems
- Paths. It seems that linux app doesn't parse the paths correctly. I had to use absolute paths to run it and the output is in the root instead of the output folder. Also the file names contain path (see ls output below)
- Blank - when I set a blank filtering, I can't set blank file. I assume this was not implemented yet.
- MSPs - I can't upload my MSP. I assume only included libraries are supported now.
- Params - I have to use a simple param file from the demo files or edit the full version exported from MS-DIAL. Most probably MSP and 'blank' definition problem.
Best regards,
Ondrej
./MsdialConsoleApp lcmsdda -i /home/ondrej/MsdialConsoleApp_linux-x64/data/ -o /home/ondrej/MsdialConsoleApp_linux-x64/out/ -m /home/ondrej/MsdialConsoleApp_linux-x64/data/Msdial-lcms-dda-Param.txt -p
Loading library files..
Start processing..
/home/ondrej/MsdialConsoleApp_linux-x64/data/blank.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\blank.msdial
Deconvoluted peak count: 2990
/home/ondrej/MsdialConsoleApp_linux-x64/data/blank.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S1.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S1.msdial
Deconvoluted peak count: 6477
/home/ondrej/MsdialConsoleApp_linux-x64/data/S1.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S2.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S2.msdial
Deconvoluted peak count: 6611
/home/ondrej/MsdialConsoleApp_linux-x64/data/S2.abf finished
/home/ondrej/MsdialConsoleApp_linux-x64/data/S3.abf
Reading data...
end peak picking
Exporting deconvolution results...
Reading data...
Exporting peak list data: /home/ondrej/MsdialConsoleApp_linux-x64/out/\S3.msdial
Deconvoluted peak count: 6525
/home/ondrej/MsdialConsoleApp_linux-x64/data/S3.abf finished
Joint aligner finished
Reading data...
0 finished
Reading data...
1 finished
Reading data...
2 finished
Reading data...
3 finished
Start finalization
Calculating basic properties
End finalization
Start aligned eic
End aligned eic
Gap filling finished
Finalization finished
Now saving the project to be used in MSDIAL GUI...
strange files
ls -alF
total 60548
drwxrwxr-x 2 ondrej ondrej 4096 říj 30 09:54 ./
drwxrwxr-x 4 ondrej ondrej 24576 říj 30 09:54 ../
-rw-rw-r-- 1 ondrej ondrej 738521 říj 30 09:54 '\AlignResult-20201030953.arf2'
-rw-rw-r-- 1 ondrej ondrej 374618 říj 30 09:54 '\AlignResult-20201030953.dcl'
-rw-rw-r-- 1 ondrej ondrej 19111850 říj 30 09:54 '\AlignResult-20201030953.EIC.aef'
-rw-rw-r-- 1 ondrej ondrej 6066618 srp 25 09:38 blank.abf
-rw-rw-r-- 1 ondrej ondrej 4704 zář 17 07:38 LIBneg_FAs.msp
-rw-rw-r-- 1 ondrej ondrej 1535 srp 21 2017 Msdial-lcms-dda-Param.txt
-rw-rw-r-- 1 ondrej ondrej 4819494 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_0.pll'
-rw-rw-r-- 1 ondrej ondrej 4929846 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_1.pll'
-rw-rw-r-- 1 ondrej ondrej 4917734 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_2.pll'
-rw-rw-r-- 1 ondrej ondrej 4923190 říj 30 09:54 '\project_2020_10_30_9_53_50_tmpFolder\peaklist_3.pll'
-rw-rw-r-- 1 ondrej ondrej 8745 říj 30 09:54 Project-20201030953.mtd2
-rw-rw-r-- 1 ondrej ondrej 5313579 srp 25 09:38 S1.abf
-rw-rw-r-- 1 ondrej ondrej 5509016 srp 25 09:38 S2.abf
-rw-rw-r-- 1 ondrej ondrej 5222554 srp 25 09:38 S3.abf