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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Error with v 2.02_01 #100

Closed e-manduchi closed 12 years ago

e-manduchi commented 12 years ago

I've downloaded RUM Pipeline 2.0.2_01 from github, tried to run it with the command:

RUM-Pipeline-v2.0.2_01/bin/rum_runner align -o /gpfs/fs121/h/manduchi/2218-MAM-1_RUM/ -i /gpfs/fs121/h/manduchi/RUM-Pipeline-v2.0.2_01/indexes/mm9/ --chunks 40 --name 2218-MAM-1 --alt-quant /gpfs/fs121/h/manduchi/mm9_mergedGeneModel_UCSC_20110812.txt --qsub 2218-MAM-1_1_sequence.txt

And got the following error

!!! Main log file had errors, please check /gpfs/fs121/h/manduchi/2218-MAM-1_RUM/log/rum_errors.log

RUM is not running. manduchi@gamma:~/$ more /gpfs/fs121/h/manduchi/2218-MAM-1_RUM/log/rum_errors.log 2012/08/16 11:01:58 FATAL - FAILED RUM::Script::Main (RUM-Pipeline-v2.0.2_01/bin/rum_runner align --parent --output /gpf s/fs121/h/manduchi/2218-MAM-1_RUM --lock /gpfs/fs121/h/manduchi/2218-MAM-1_RUM/.rum/lock): Error running qsub /gpfs/fs12 1/h/manduchi/2218-MAM-1_RUM/2218-MAM-1_preproc.sh: at /gpfs/fs121/h/manduchi/RUM-Pipeline-v2.0.2_01/bin/../lib/RUM/Acti on/Align.pm line 85

Can you advice?

mdelaurentis commented 12 years ago

I'll take a look at it right away.

mdelaurentis commented 12 years ago

It looks like qsub is refusing to run the preprocessing script, because the file name starts with a number (2218-MAM-1_preproc.sh). The file's name is based on the job name (the --name argument), so if you change the name so that it doesn't start with a digit, I expect that it will work.

I thought we had a check for that, but apparently either we don't or it's not working as intended. I may just change the file name so it always starts with "rum_" or something like that.

Anyway, please try using a different --name for now, and I'll let you know when I've fixed it.

e-manduchi commented 12 years ago

Thanks. So far so good. E.

On 8/16/2012 11:34 AM, Mike DeLaurentis wrote:

It looks like qsub is refusing to run the preprocessing script, because the file name starts with a number (2218-MAM-1_preproc.sh). The file's name is based on the job name (the --name argument), so if you change the name so that it doesn't start with a digit, I expect that it will work.

I thought we had a check for that, but apparently either we don't or it's not working as intended. I may just change the file name so it always starts with "rum_" or something like that.

Anyway, please try using a different --name for now, and I'll let you know when I've fixed it.

— Reply to this email directly or view it on GitHub https://github.com/PGFI/rum/issues/100#issuecomment-7789079.