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statisticalbiotechnology / maracluster

Matthew The's implementation of MaRaCluster
Apache License 2.0
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maracluster producing Unsupported mzML format for MSGF+ #6

Closed BioComSoftware closed 6 years ago

BioComSoftware commented 7 years ago

Hi All,

I'm running *.mzML files created by maracluster INTO into MSGF+. The mzML files are piped into MSGF+ via an OpenMS GenericWrapper.

I get the error below. If, however, I set maracluster to create MGF and then pipe them through another GenericWrapper that calls 'msconvert' (to convert the files from MGF to mzML), MSGF+ works fine.

Is this something you can look into?

Thanks! Mike

ERROR Unsupported mzML format: /tmp/2016-11-17_021229_ubuntu_2893_1/TOPPAS_tmp/maracluster+lfq+blib.2016-11-16.Mikes/033_GenericWrapper_maracluster_python/EToolout/160812_32.mzML does not contain a child term of MS:1000767 (native spectrum identifier format) Unsupported mzML format: /tmp/2016-11-17_021229_ubuntu_2893_1/TOPPAS_tmp/maracluster+lfq+blib.2016-11-16.Mikes/033_GenericWrapper_maracluster_python/EToolout/160812_32.mzML Fatal error: Running MS-GF+ returned an error code '255'. Does the MS-GF+ executable (.jar file) exist? MSGFPlusAdapter took 01:48:40 h (wall), 0.08 s (CPU), 0.00 s (system), 0.08 s (user).

MatthewThe commented 7 years ago

I will look into this. So far I have not been able to reproduce this error on my system (direct mzML input into MSGFPlusAdapter in OpenMS 2.0, with MS-GF+ v10072), or is the error produced by the GenericWrapper?

Running the FileInfo tool of OpenMS in validation mode did reveal a couple of issues with the mzML output from MaRaCluster, including the one mentioned above. I will resolve those and get back to you. (Though it should be noted that the mzML output from msconvert shows some issues as well, so apparently the check is stricter than many tools require.)

MatthewThe commented 7 years ago

I resolved most mzML validation issues, except a few that msconvert output also produces.

Can you test if it works with this binary: maracluster.tar.gz

BioComSoftware commented 7 years ago

Awesome. I'll try it out :)

MatthewThe mailto:notifications@github.com 21 November 2016 at 11:17

I resolved most mzML validation issues, except a few that msconvert output also produces.

Can you test if it works with this binary: maracluster.tar.gz https://github.com/statisticalbiotechnology/maracluster/files/603267/maracluster.tar.gz

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MatthewThe commented 7 years ago

Have you had a chance to test the new binary?