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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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error with run_pipeline_test.sh #187

Closed joachimdejonghe closed 8 years ago

joachimdejonghe commented 9 years ago

Hi, thank you very much for proposing the metAmos pipeline. i am running run_pipeline_test.sh after installation and run into this error: Starting Task = preprocess.PREPROCESS

****ERROR****** During preprocess, the following command failed with return code 1:

java -cp /jo/metAMOS-1.5rc3/Utilities/java:.:. outputDefaultQuality /jo/metAMOS-1.5rc3/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /jo/metAMOS-1.5rc3/Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual

****DETAILS****** Last 10 commands run before the error (/jo/metAMOS-1.5rc3/Test/test1/Logs/COMMANDS.log) |2015-03-13 17:18:47| rm /jo/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits |2015-03-13 17:18:48| rm /jo/metAMOS-1.5rc3/Test/test1/Assemble/out/.faa |2015-03-13 17:18:48| rm /jo/metAMOS-1.5rc3/Test/test1/Assemble/out/.fna |2015-03-13 17:18:48| rm /jo/metAMOS-1.5rc3/Test/test1/FindORFS/out/.faa |2015-03-13 17:18:48| rm /jo/metAMOS-1.5rc3/Test/test1/FindORFS/out/.fna |2015-03-13 17:18:48| rm /jo/metAMOS-1.5rc3/Test/test1/Logs/assemble.ok |2015-03-13 17:18:48| rm /jo/metAMOS-1.5rc3/Test/test1/Assemble/out/*.asm.contig |2015-03-13 17:18:48| rm /jo/metAMOS-1.5rc3/Test/test1/Logs/classify.ok |2015-03-13 17:19:04|# [PREPROCESS] |2015-03-13 17:19:05| java -cp /jo/metAMOS-1.5rc3/Utilities/java:.:. outputDefaultQuality /jo/metAMOS-1.5rc3/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /jo/metAMOS-1.5rc3/Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual

Last 10 lines of output (/jo/metAMOS-1.5rc3/Test/test1/Logs/PREPROCESS.log)

Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team. ****ERROR******

rm: cannot remove `/jo/metAMOS-1.5rc3/Test/test1/Logs/preprocess.ok': No such file or directory Oops, MetAMOS finished with errors! see text in red above for details. Fatal Python error: Couldn't create autoTLSkey mapping

Do you guys have any idea of whats happening ? Thank you very much for your help !!

skoren commented 9 years ago

Hi,

Do you have your PREPROCESS.log file from the Logs directory? My best guess is you have an older or missing JVM causing the error.

skoren commented 8 years ago

Closing due to inactivity.