seth-ament
commented
8 years ago Hi Según,
Not entirely sure why it isn't working, though I have some thoughts. What do the first few rows of each of the tables look like in your version of the database?
Seth
On Mon, Jul 18, 2016 at 12:37 PM, Segun Jung notifications@github.com wrote:
I am interactively running the makeTRN-proximalonly-demo.R script which Seth fixed a database compatibility issue. It looks like it doesn't find any binding site for TF. I wonder whether this issue is due to the current database setup on our side.
genome.db.uri = "postgres://localhost/hg38" project.db.uri = "postgres://localhost/wholebrain" cores = 5
ptm <- proc.time()
promoter_counts = getTfbsCountsInPromoters( genome.db.uri=genome.db.uri , project.db.uri=project.db.uri , size.upstream = 10000 , size.downstream = 10000 , # define the size of the window around the TSS cores = cores ) # specify the number of cores for parallelization
proc.time() - ptm> > + + + no gene list is given, using all genes from obj@genome.db
no tf list is given. using all tfs from obj@project.db fetching promoter regions for all genes counting binding sites for each tf in each region Error in { : task 482 failed - "argument is of length zero" In addition: Warning messages: 1: closing unused connection 7 (<-localhost:11920) 2: closing unused connection 6 (<-localhost:11920) 3: closing unused connection 5 (<-localhost:11920) 4: closing unused connection 4 (<-localhost:11920) 5: closing unused connection 3 (<-localhost:11920)
user system elapsed 11.815 2.101 883.211
sessionInfo() R version 3.2.5 (2016-04-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.1 LTS
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] TReNA_0.99.51 doParallel_1.0.10 iterators_1.0.8 [4] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8 [7] S4Vectors_0.8.11 BiocGenerics_0.16.1 RPostgreSQL_0.4-1 [10] DBI_0.4-1 vbsr_0.0.5 randomForest_4.6-12 [13] glmnet_2.0-5 foreach_1.4.3 Matrix_1.2-6
loaded via a namespace (and not attached): [1] lattice_0.20-33 codetools_0.2-14 grid_3.2.5 zlibbioc_1.16.0 [5] XVector_0.10.0 compiler_3.2.5
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dauss75
paul-shannon
I am interactively running the makeTRN-proximalonly-demo.R script which Seth fixed a database compatibility issue. It looks like it doesn't find any binding site for TF. I wonder whether this issue is due to the current database setup on our side.
genome.db.uri = "postgres://localhost/hg38" project.db.uri = "postgres://localhost/wholebrain" cores = 5
promoter_counts = getTfbsCountsInPromoters( genome.db.uri=genome.db.uri , project.db.uri=project.db.uri , size.upstream = 10000 , size.downstream = 10000 , # define the size of the window around the TSS cores = cores ) # specify the number of cores for parallelization
proc.time() - ptm> > + + + no gene list is given, using all genes from obj@genome.db
no tf list is given. using all tfs from obj@project.db fetching promoter regions for all genes counting binding sites for each tf in each region Error in { : task 482 failed - "argument is of length zero" In addition: Warning messages: 1: closing unused connection 7 (<-localhost:11920) 2: closing unused connection 6 (<-localhost:11920) 3: closing unused connection 5 (<-localhost:11920) 4: closing unused connection 4 (<-localhost:11920) 5: closing unused connection 3 (<-localhost:11920)
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] TReNA_0.99.51 doParallel_1.0.10 iterators_1.0.8 [4] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8 [7] S4Vectors_0.8.11 BiocGenerics_0.16.1 RPostgreSQL_0.4-1 [10] DBI_0.4-1 vbsr_0.0.5 randomForest_4.6-12 [13] glmnet_2.0-5 foreach_1.4.3 Matrix_1.2-6
loaded via a namespace (and not attached): [1] lattice_0.20-33 codetools_0.2-14 grid_3.2.5 zlibbioc_1.16.0 [5] XVector_0.10.0 compiler_3.2.5