I’m using MEGAN UE (version 6.11.6). I am trying to generate two comparison files based on rma files contained in two different directories.
$ ls tmp/* tmp/dir_ChitinaseEC32114: PH12_ChitinaseEC32114_tmp.rma PH6_ChitinaseEC32114_tmp.rma tmp/dir_Glucose1dehydrogenaseEC11147: PH12_Glucose1dehydrogenaseEC11147_tmp.rma PH6_Glucose1dehydrogenaseEC11147_tmp.rma
$ xvfb-run --auto-servernum --server-num=1 MEGAN -g -E -c rma2comparison.cmegan
where $ cat rma2comparison.cmegan,
compare mode=ABSOLUTE readAssignmentMode=readCount keep1=true ignoreUnassigned=true meganFile='tmp/dir_ChitinaseEC32114'; save file='ChitinaseEC32114_comparison.megan'; update; compare mode=ABSOLUTE readAssignmentMode=readCount keep1=true ignoreUnassigned=true meganFile='tmp/dir_Glucose1dehydrogenaseEC11147'; save file='Glucose1dehydrogenaseEC11147_comparison.megan'; quit;
The above resulted on the following error when executing the second “compare mode”.
Error: Command failed: Internal error: document already used Quit on exception
I tried also “new;” on line 3 from rma2comparison.cmegan, with no luck. This is most likely a naive situation. However, I will appreciate any help!