Hi, So it turns out that your hunch was right. When our HPC guys looked further they saw that EBWT was writing its output to /tmp on the nodes which is tiny (only 2.9GB) - it is now directed to write to /local which is much bigger. We think that should sort the problem out - let you know if it fails to resolve it. Any hints on optimising the Tophat run would be great still.
Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 5 Dec 2011, at 21:00, Jeremy Goecks wrote: > Hi David, > > There should be additional information in the galaxy database about why the > job failed; take a look at stderr column of the failed job using some SQL > like this: > > -- > select * from job where state='error' and tool_id='tophat' and stderr like > '%indexing reference%' order by id desc; > -- > > If that doesn't work, try something simpler: > > -- > select * from job where state='error' and tool_id='tophat' order by id desc; > -- > > What are the errors that you see? > > Finally, please direct future questions about local Galaxy installations to > galaxy-dev (cc'd) so that the community can learn from and participate in > discussions. > > Thanks, > J. > > On Dec 5, 2011, at 10:09 AM, David Matthews wrote: > >> Hi, >> >> We have a local version of Galaxy here at Bristol and it is very nice. >> However, it does not like to run TopHat on large genomes (i.e. Human) but is >> happy with small ones (e.g. viruses). The genome we have is hg19 but missing >> chr Y and this genome works fine on the PSU version. However, we seem to be >> hitting a wall when we run it here and it seems to relate to the indexing >> part right at the begining. Here is the error output we see in the red box: >> >> An error occurred running this job:Settings: >> Output files: "/tmp/tmppA7Hrk/dataset_942.*.ebwt" >> Line rate: 6 (line is 64 bytes) >> Lines per side: 1 (side is 64 bytes) >> Offset rate: 5 (one in 32) >> FTable chars: 10 >> Strings: unpacked >> Max bucket size: default >> Max bucket size, sqrt m >> >> And here is the stuff we see when we click on the green bug (the second set >> is just the last bit of a long list of stuff): >> >> >> Error indexing reference sequence >> Returning block of 520230381 >> Getting block 6 of 7 >> Reserving size (531691900) for bucket >> Calculating Z arrays >> Calculating Z arrays time: 00:00:00 >> Entering block accumulator loop: >> 10% >> 20% >> 30% >> 40% >> 50% >> 60% >> 70% >> 80% >> 90% >> 100% >> Block accumulator loop time: 00:00:59 >> Sorting block of length 346541282 >> (Using difference cover) >> Sorting block time: 00:06:04 >> Returning block of 346541283 >> Getting block 7 of 7 >> Reserving size (531691900) for bucket >> Calculating Z arrays >> Calculating Z arrays time: 00:00:00 >> Entering block accumulator loop: >> 10% >> 20% >> 30% >> 40% >> 50% >> 60% >> 70% >> 80% >> 90% >> 100% >> Block accumulator loop time: 00:00:40 >> Sorting block of length 408062248 >> (Using difference cover) >> Sorting block time: 00:07:08 >> Returning block of 408062249 >> Exited Ebwt loop >> fchr[A]: 0 >> fchr[C]: 837200431 >> fchr[G]: 1417119193 >> fchr[T]: 1997326330 >> fchr[$]: 2835690133 >> Exiting Ebwt::buildToDisk() >> Total time for backward call to driver() for mirror index: 01:16:32 >> TopHat v1.2.0 >> We are running on our HPC and have directed the job to land on a whole node >> with 8GB of ram on board. Any ideas why the index is failing? >> >> >> Best Wishes, >> David. >> >> __________________________________ >> Dr David A. Matthews >> >> Senior Lecturer in Virology >> Room E49 >> Department of Cellular and Molecular Medicine, >> School of Medical Sciences >> University Walk, >> University of Bristol >> Bristol. >> BS8 1TD >> U.K. >> >> Tel. +44 117 3312058 >> Fax. +44 117 3312091 >> >> d.a.matth...@bristol.ac.uk >> >> >> >> >> >> >
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