huiyinc
commented
4 years ago Hi Simion,
Thanks for your interest in our MSFragger-PD node. We have considered the situation of running multiple processing workflows when designing the MSFragger-PD node. The MSFragger-PD node in each processing workflow generates a temporary folder (with unique id) to store the output pepXML files, so the pepXML files should not be overwritten. One possibility is the pepXML files are not properly imported to msf files because two processing workflows are running simultaneously.
Can you please go to PD->Parallel Job Execution and change the max. number of processing workflows in parallel execution to 1 (as the figure shown below)? [image: 圖片.png]
Thank you.
Huiyin
SimionKreimer notifications@github.com 於 2020年9月16日 週三 上午3:02寫道：
Hello, I'm big fan of the software and I really appreciate the PD node. I've run into an issue where if I use two MS Fragger nodes, for example to look at lots of PTMs with each node assigned to a separate set of modifications. The searches within the MS Fragger nodes seem to finish with no issues but when the results are processed in Percolator I get a java error message, sorry I haven't copied it. Once I click OK the search finishes but the results look like only one node was used. For example I have one node running various methylation states, and the second node running phosphorylation and various oxidations and I end up with methylated peptides but no phospho. If I run the phosphorylation search separately I find ~100 phosphorylated peptides. I think it might be because the pepXML files are saved under the same name, so essentially the second search writes over the first, but that's just my hypothesis. Is there an easy fix for it other than running separate searches?
Best, Simion
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-- Hui-Yin Chang, 張彙音 Assistant Professor, 助理教授 Department of Biomedical Sciences and Engineering, 生醫科學與工程學系 National Central University (Taiwan), 國立中央大學 (台灣) 地址: 320 中壢區中大路300號 研究中心二期R3-403室 電話: (03)422-7151 ext. 27706
SimionKreimer
Hello, I'm big fan of the software and I really appreciate the PD node. I've run into an issue where if I use two MS Fragger nodes, for example to look at lots of PTMs with each node assigned to a separate set of modifications. The searches within the MS Fragger nodes seem to finish with no issues but when the results are processed in Percolator I get a java error message, sorry I haven't copied it. Once I click OK the search finishes but the results look like only one node was used. For example I have one node running various methylation states, and the second node running phosphorylation and various oxidations and I end up with methylated peptides but no phospho. If I run the phosphorylation search separately I find ~100 phosphorylated peptides. I think it might be because the pepXML files are saved under the same name, so essentially the second search writes over the first, but that's just my hypothesis. Is there an easy fix for it other than running separate searches?
Best, Simion