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Old 08-10-2013, 11:20 PM   #1
alpoptosis
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Default Tophat: rerunning the aborted job

One of my cluster job that ran Tophat failed. It created the bunch of tmp files. If rerun Tophat on the same directory without removing the tmp files, would it start from where it was left off? or do I have to start all over again?
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Old 08-11-2013, 04:46 AM   #2
GenoMax
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If the job failed internally TopHat may be able to resume it using the checkpoint info in "tophat_output_dir/logs/run.log" file. If the file is not there then you may have to re-run the job since the error may have occurred outside tophat.

If the file above exists then you can re-run the job by using special "tophat -R tophat_output_dir" command. Note: You do not need to provide any of the original tophat options. They read from the checkpoint file in the log directory.

Look for errors elsewhere first (from the queuing system to see if you need to addresses any other problems e.g. disk partition filling up) before re-running the job.
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Old 08-11-2013, 10:40 AM   #3
alpoptosis
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Thank you very much!
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