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vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
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Error in vast-tools diff [if (all(totalFirst < (opt$minReads + opt$alpha + opt$beta)] #27

Closed mirimia closed 10 years ago

mirimia commented 10 years ago

Hi Tim,

More on diff. I get this error when I do two comparisons using this table. It'd say it may have happened when dealing with IR...

[mirimia@bc2 vast-tools]$ ./vast-tools diff -o vast_out/nSR100_KO/ -i INCLUSION_LEVELS_FULL-Mmu8.tab -a Embr_E18_Brain_CX_Cont_a@Embr_E18_Brain_CX_Cont_b -b Embr_E18_Brain_CX_KO_a@Embr_E18_Brain_CX_KO_b > vast_out/nSR100_KO/INCLUSION-FILTERED_nSR100_CX.tab Trying to load required package: optparse Trying to load required package: RColorBrewer Trying to load required package: reshape2 Trying to load required package: ggplot2 Trying to load required package: grid Trying to load required package: parallel Error in if (all(totalFirst < (opt$minReads + opt$alpha + opt$beta)) || : missing value where TRUE/FALSE needed Calls: mclapply -> lapply -> FUN In addition: Warning messages: 1: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 2: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 3: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 4: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion Execution halted

UBrau commented 10 years ago

Hi Manuel,

Last week fixed a bug in how the IR quality scores are handled, it may be due to that if you range combine before that. Could you check if any quality scores do not contain '@', and if that is the case, run combine again?

Ulrich

On 21/08/14 14:02, mirimia wrote:

Hi Tim,

More on diff. I get this error when I do two comparisons using this table. It'd say it may have happened when dealing with IR...

[mirimia@bc2 vast-tools]$ ./vast-tools diff -o vast_out/nSR100_KO/ -i INCLUSION_LEVELS_FULL-Mmu8.tab -a Embr_E18_Brain_CX_Cont_a@Embr_E18_Brain_CX_Cont_b -b Embr_E18_Brain_CX_KO_a@Embr_E18_Brain_CX_KO_b > vast_out/nSR100_KO/INCLUSION-FILTERED_nSR100_CX.tab Trying to load required package: optparse Trying to load required package: RColorBrewer Trying to load required package: reshape2 Trying to load required package: ggplot2 Trying to load required package: grid Trying to load required package: parallel Error in if (all(totalFirst < (opt$minReads + opt$alpha + opt$beta)) || : missing value where TRUE/FALSE needed Calls: mclapply -> lapply -> FUN In addition: Warning messages: 1: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 2: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 3: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 4: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion Execution halted

— Reply to this email directly or view it on GitHub https://github.com/vastgroup/vast-tools/issues/27.

mirimia commented 10 years ago

I'll check if I'm up to date (I think I am though). I run the combine today...

mirimia commented 10 years ago

Yes, I was mostly up to date (only missing a few edits in psiplotter.R)

mirimia commented 10 years ago

I've checked the INCLUSION file, and for some IR cases there is "...@NA,NA" rather than a number... Not sure diff expects this and could be the source of the problem...

timbitz commented 10 years ago

Thanks for checking into that Manuel. It should be fixed then in 8cc9181. That was definitely what was causing the problem.

timbitz commented 10 years ago

or fixed in 67ed2aa rather... sorry

mirimia commented 10 years ago

Sorry, Tim, I think it didn't work either (it seems to be the same error...):

[mirimia@bc2 vast-tools]$ ./vast-tools diff -o vast_out/nSR100_KO/ -i INCLUSION_LEVELS_FULL-Mmu8.tab -a Embr_E18_Brain_CX_Cont_a@Embr_E18_Brain_CX_Cont_b -b Embr_E18_Brain_CX_KO_a@Embr_E18_Brain_CX_KO_b -d INCLUSION-FILTERED_nSR100_CX.DIFF_plots > vast_out/nSR100_KO/INCLUSION-FILTERED_nSR100_CX.tab Trying to load required package: optparse Trying to load required package: RColorBrewer Trying to load required package: reshape2 Trying to load required package: ggplot2 Trying to load required package: grid Trying to load required package: parallel Error in if (all(totalFirst < (opt$minReads + opt$alpha + opt$beta)) || : missing value where TRUE/FALSE needed Calls: mclapply -> lapply -> FUN In addition: Warning messages: 1: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 2: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 3: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion 4: In parseQual(x, opt$alpha, opt$beta) : NAs introduced by coercion Execution halted