Nesvilab/FragPipe

MS1 quantitation IonQuant error

Closed this issue · 4 comments

Angelwitch commented

- Upload your log file
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

- Describe the issue or question:
IonQuant error
IonQuant [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx148G -Dlibs.bruker.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.0\ext\bruker" -Dlibs.thermo.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.0\ext\thermo" -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\IonQuant-1.10.27.jar" ionquant.IonQuant --threads 42 --ionmobility 0 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\filelist_ionquant.txt --modlist D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\modmasses_ionquant.txt
IonQuant version IonQuant-1.10.27
Batmass-IO version 1.28.12
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
System OS: Windows Server 2012 R2, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 148 GB memory
2024-06-18 17:20:05 [WARNING] - There are only 1 experiments. Will not calculate MaxLFQ intensity.
2024-06-18 17:20:06 [INFO] - Collecting variable modifications from all psm.tsv files...
2024-06-18 17:20:06 [INFO] - Loading and indexing all psm.tsv files...
2024-06-18 17:20:07 [INFO] - Collecting all compensation voltages if applicable...
2024-06-18 17:20:27 [INFO] - B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash.
2024-06-18 17:20:27 [INFO] - There is no FAIMS in the dataset.
java.lang.NoSuchMethodError: 'com.google.protobuf.Internal$ProtobufList N$j.makeMutableCopy(com.google.protobuf.Internal$ProtobufList)'
at N$j.a(Unknown Source)
at N$j$a.f(Unknown Source)
at N$j$a.a(Unknown Source)
at aa.a(Unknown Source)
at k.a(Unknown Source)
at k.b(Unknown Source)
at k.a(Unknown Source)
at ionquant.IonQuant.a(Unknown Source)
at ionquant.IonQuant.main(Unknown Source)
Process 'IonQuant' finished, exit code: 1
Process returned non-zero exit code, stopping

log_2024-06-19_09-29-54.txt

fcyu commented

It was due to version incompatibility. Could you upgrade FragPipe, MFragger, and diaTracer to the latest version, and try again?

Thanks,

Fengchao

Angelwitch commented
fcyu commented

The log files were truncated by GitHub. Could you go to #1637 and upload the files there?

Thanks,

Fengchao

fcyu commented

Actually, no need to re-upload the log files. The untruncated one already tells the reason. You were still using the old version of FragPipe. Could you upgrade FragPipe?

Version info:
FragPipe version 20.0
MSFragger version 4.1
IonQuant version 1.10.27
Philosopher version 5.1.0

Also not that when you upgrade FragPipe, remember to put it in a new folder where there is no old version of FragPipe.

Best,

Fengchao