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I have some Problems generating Consensus-Files from MGF Files. It is the same problem as stated in #5 .
I am currently working with a toy_set to try out MaRaCluster. I have built MaRaCluster from source (master-branch) and have tried the binaries provided in releases (Version 1.01).
The Clustering via maracluster batch works well and exits without an error. But running maracluster consensus i get the following output:
MaRaCluster version 1.01.0, Build Date Jan 28 2020 09:10:12
Copyright (c) 2015-19 Matthew The. All rights reserved.
Written by Matthew The (matthewt@kth.se) in the
School of Biotechnology at the Royal Institute of Technology in Stockholm.
Issued command:
maracluster consensus --output-folder /DATA_OUTPUT/ --specOut /DATA_OUTPUT/consensus.mgf -l /DATA_OUTPUT/MaRaCluster.clusters_p5.tsv
Started Tue Apr 21 18:49:14 2020
on f777c9bdbd97
Parsing cluster file
Finished parsing cluster file
Merging clusters
Splitting /DATA_INPUT/toy_set.mgf (50%)
Splitting /DATA_INPUT/sub_folder/toy_set.mgf (100%)
Writing file /DATA_OUTPUT/consensus.part0_0_tmpfile.mgf
Finished writing file /DATA_OUTPUT/consensus.part0_0_tmpfile.mgf
Finished splitting ms2 files
Merging spectra in bin 1/1
[SpectrumList::find]: mismatch between spectrum id format of the file (index=0) and the looked-up id (scan=2000000)
Warning: index 2000000 out of bounds: /DATA_INPUT/toy_set.mgf: 1 0
Warning: index 3000000 out of bounds: /DATA_INPUT/sub_folder/toy_set.mgf: 2 0
Warning: index 2000002 out of bounds: /DATA_INPUT/toy_set.mgf: 1 2
Warning: index 3000002 out of bounds: /DATA_INPUT/sub_folder/toy_set.mgf: 2 2
Warning: index 2000003 out of bounds: /DATA_INPUT/toy_set.mgf: 1 3
Warning: index 3000003 out of bounds: /DATA_INPUT/sub_folder/toy_set.mgf: 2 3
. . . (continues with more warnings)
Processing consensus spectra.
Batch 1/1
Merging spectra
Finished merging clusters
The File consensus.mgf is afterwards NOT present in the Folder /DATA_OUTPUT
I tried to add a SCANS= attribute to the MGF FIles and even added scan= and index= to the TITLE=, which i saw on some previous issues here (#7, #5 (Archive 2.zip) and #2 ). The consensus file still does not get generated.
I am accessing the MaRaCluster binary via command line indirectly through Python.
Here are the files i used (without added attributes) + the genereated tsv file: files.zip
Greetings!
The text was updated successfully, but these errors were encountered:
Thanks for reporting this, I can indeed confirm that the mgf pipeline is broken at the moment. I suspect it's because of the changes I made here f59f9d0. I will look into it.
I have some Problems generating Consensus-Files from MGF Files. It is the same problem as stated in #5 .
I am currently working with a toy_set to try out MaRaCluster. I have built MaRaCluster from source (master-branch) and have tried the binaries provided in releases (Version 1.01).
The Clustering via
maracluster batch
works well and exits without an error. But runningmaracluster consensus
i get the following output:The File
consensus.mgf
is afterwards NOT present in the Folder/DATA_OUTPUT
I tried to add a
SCANS=
attribute to the MGF FIles and even addedscan=
andindex=
to theTITLE=
, which i saw on some previous issues here (#7, #5 (Archive 2.zip
) and #2 ). The consensus file still does not get generated.I am accessing the MaRaCluster binary via command line indirectly through Python.
Here are the files i used (without added attributes) + the genereated tsv file: files.zip
Greetings!
The text was updated successfully, but these errors were encountered: