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Jiung-Wen / msdial

The tutorial for running MS-DIAL on Linux cluster
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How do I merge result files (*.msdial) from command lines? #1

Closed Giotto187 closed 1 year ago

Giotto187 commented 1 year ago

Thank you very much for the example, the command line version of the software works very well. But there's a problem that bothers me. When several samples are analyzed in the same batch, the graphical interface version of MSDIAL will get a combined result (row: metabolites x column: samples). The result file of each sample on the command line are output separately, so how do I merge them together? Is the RT and MZ of the final output the mean value of samples?

Jiung-Wen commented 1 year ago

Hi @Giotto187 , I believe there will also be an output file called AlignResult-XXXX.msdial (or something like that), which contains the results of all samples. Best, JC

Giotto187 commented 1 year ago

Hi JC.

Thank you very much for your reply. However, this file did not appear in my output folder. I checked my running log file and found the following line at the end. “The given key ‘0’ was not present in the dictionary.” Is this the reasion why I failed to get the merge result? Do you know how to fix it?

2022年11月1日 09:27，Jiung-Wen Chen @.***> 写道：

Hi @Giotto187 https://github.com/Giotto187 , I believe there will also be an output file called AlignResult-XXXX.msdial (or something like that), which contains the results of all samples. Best, JC

— Reply to this email directly, view it on GitHub https://github.com/Jiung-Wen/msdial/issues/1#issuecomment-1297889677, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGZF4MZVFBO723HBCA4GXDWGBWYTANCNFSM6AAAAAARSUJCFE. You are receiving this because you were mentioned.

Jiung-Wen commented 1 year ago

Hi JC. Thank you very much for your reply. However, this file did not appear in my output folder. I checked my running log file and found the following line at the end. “The given key ‘0’ was not present in the dictionary.” Is this the reasion why I failed to get the merge result? Do you know how to fix it? … 2022年11月1日 09:27，Jiung-Wen Chen @.***> 写道： Hi @Giotto187 https://github.com/Giotto187 , I believe there will also be an output file called AlignResult-XXXX.msdial (or something like that), which contains the results of all samples. Best, JC — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGZF4MZVFBO723HBCA4GXDWGBWYTANCNFSM6AAAAAARSUJCFE. You are receiving this because you were mentioned.

Do you parse parameter like "Alignment reference file ID: 0" or something like that? It's just my guess but you can try 1 instead of 0. If everything goes alright, you will see "Start aligned eic" in the log file and get the aligned result file. I hope this helps. JC

Giotto187 commented 1 year ago

Hi JC !

Thank you very much! I check my alignment parameters and update the software to the latest version (Linux 4.9), and everything worked fine. Thanks again for your help !

Kind regards, Giotto

2022年11月1日 12:30，Jiung-Wen Chen @.***> 写道：

Hi JC. Thank you very much for your reply. However, this file did not appear in my output folder. I checked my running log file and found the following line at the end. “The given key ‘0’ was not present in the dictionary.” Is this the reasion why I failed to get the merge result? Do you know how to fix it? … <x-msg://3/#> 2022年11月1日 09:27，Jiung-Wen Chen @.***> 写道： Hi @Giotto187 https://github.com/Giotto187 https://github.com/Giotto187 https://github.com/Giotto187 , I believe there will also be an output file called AlignResult-XXXX.msdial (or something like that), which contains the results of all samples. Best, JC — Reply to this email directly, view it on GitHub <#1 (comment) https://github.com/Jiung-Wen/msdial/issues/1#issuecomment-1297889677>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGZF4MZVFBO723HBCA4GXDWGBWYTANCNFSM6AAAAAARSUJCFE https://github.com/notifications/unsubscribe-auth/AKGZF4MZVFBO723HBCA4GXDWGBWYTANCNFSM6AAAAAARSUJCFE. You are receiving this because you were mentioned.

Do you parse parameter like "Alignment reference file ID: 0" or something like that? It's just my guess but you can try 1 instead of 0. If everything goes alright, you will see "Start aligned eic" in the log file and get the aligned result file. I hope this helps. JC

— Reply to this email directly, view it on GitHub https://github.com/Jiung-Wen/msdial/issues/1#issuecomment-1298013638, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKGZF4JU327WOSHMY5KHBFTWGCMFNANCNFSM6AAAAAARSUJCFE. You are receiving this because you were mentioned.