Good morning to everyone! I hope you can help me. I ran a Bismark Methylation analysis on Galaxy.eu, but the Methylation Extractor job is running from more than 10 days without results… Is that normal?
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Hi John,
I don’t have experience with this tool, so I don’t know if is it normal or not, but your job is currently writing messages in the stdout:
galaxy@sn06:/data/jwd/main/033/262/33262638$ ll outputs/tool_stdout
-rw-r--r--. 1 galaxy galaxy 102659 Nov 11 14:27 outputs/tool_stdout
galaxy@sn06:/data/jwd/main/033/262/33262638$ tail outputs/tool_stdout
Sorting input file CpG_context_dataset_4f4e9f87-1091-4934-9033-f8c296bb8eff.dat.txt.chrchr2.methXtractor.temp by positions (using -S of 2G)
Successfully deleted the temporary input file CpG_context_dataset_4f4e9f87-1091-4934-9033-f8c296bb8eff.dat.txt.chrchr2.methXtractor.temp
Sorting input file CpG_context_dataset_4f4e9f87-1091-4934-9033-f8c296bb8eff.dat.txt.chrchr6.methXtractor.temp by positions (using -S of 2G)
Successfully deleted the temporary input file CpG_context_dataset_4f4e9f87-1091-4934-9033-f8c296bb8eff.dat.txt.chrchr6.methXtractor.temp
Sorting input file CpG_context_dataset_4f4e9f87-1091-4934-9033-f8c296bb8eff.dat.txt.chrchr16.methXtractor.temp by positions (using -S of 2G)
Successfully deleted the temporary input file CpG_context_dataset_4f4e9f87-1091-4934-9033-f8c296bb8eff.dat.txt.chrchr16.methXtractor.temp
Sorting input file CpG_context_dataset_4f4e9f87-1091-4934-9033-f8c296bb8eff.dat.txt.chrchr13.methXtractor.temp by positions (using -S of 2G)
I assigned more computational resources to this tool, so, from tomorrow, new jobs will run with 4Cores/12GB instead of 1Core/4GB.
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