I ran MIRA with 1.2 GB (after pre processing) of my plant ion proton transcriptome data in a 120 GB RAM system. We are working through a rented server. Currently it is running and generated assembly log file of 4.2 GB. But the output directory is empty. If the assembly has over it would have created some contig files.We were observing the log file size to ensure the progress of analysis. It was running for 3days and now the size of the log assembly is not increasing.How could i know the status of MIRA running process?
It is hard to imagine how that "rented server" service works.
If you have access to the command prompt, then regardless of scientific content you can check what jobs you have still running on the server. For example if your userID is nadiya, you can try:
ps -u nadiya.
Otherwise you should check the log file itself. Again if you have access to the prompt, you can use "tail" like:
tail -n 40 whatever.log
to see the last 40 lines of the log file. If it says that you are done or error occurred then you know what to do, otherwise just wait some more.
If you do not have access to the prompt, you can download your logfile and check it accordingly.
Nevertheless, some tasks generate much output in the log file, some others are more computation-intensive with nothing to talk about, so the increase in size is not always the best indication of the status of the whole process.
Sven is right. I have used it to make comparison between Illumina and 454 outputs. I am not sure what you are asking. I can also refer you to someone who might answer most of your questions if you dont mind.
Thanks all for your reply.
MIRA author suggested that the problem we faced might be due to some temporary error with OS. We aborted the programme and started running new one. Now its running properly. As sven said MIRA author is really helpful.
Great...MIRA is a good tool but as you know already, it always depends on your goal.
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