error when genomeFile too big when running Quasr on >3 clusters
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rna seq • 90
@rna-seq-4145
Last seen 4.5 years ago

I am following up from a different post,  "problem using >3 clusters with Quasr",  as I have identified a distinct issue.

Issue: When I run:

library(QuasR)
library(parallel)
cl<-makeCluster(4)
sampleFile2<-("sample_file.txt")
genomeFile<-("reference_genome.fa")

and reference_genome.fa has more than ~1200 sequences in it, I get the following the following error:

  one node produced an error: Error on ip-172-31-10-100 processing sample /tmp/Rtmp4VPRy5/MAQC-1_S14_L001_R1_001.fastq.gzfbb2dbd9863.fastq : failed to open SAM/BAM file
  file: '/tmp/Rtmp4VPRy5/samToBam_fbb1927e6ca/5982_RPS18.sam'

when reference_genome.fa has less than ~1000 sequences in it,

It runs fine

I notice that /tmp/Rtmp4VPRy5/samToBam_fbb1927e6ca/5 does not have all the sam files in it.

Any help is most appreciated

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 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] QuasR_1.10.0         Rbowtie_1.10.0       GenomicRanges_1.22.3
[4] GenomeInfoDb_1.6.1   IRanges_2.4.6        S4Vectors_0.8.7     
[7] BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.32.3       XVector_0.10.0            
 [3] GenomicAlignments_1.6.3    zlibbioc_1.16.0           
 [5] BiocParallel_1.4.3         lattice_0.20-33           
 [7] BSgenome_1.38.0            hwriter_1.3.2             
 [9] tools_3.2.3                grid_3.2.3                
[11] SummarizedExperiment_1.0.2 Biobase_2.30.0            
[13] DBI_0.3.1                  latticeExtra_0.6-26       
[15] lambda.r_1.1.7             futile.logger_1.4.1       
[17] GenomicFiles_1.6.2         RColorBrewer_1.1-2        
[19] rtracklayer_1.30.1         futile.options_1.0.0      
[21] bitops_1.0-6               biomaRt_2.26.1            
[23] RCurl_1.95-4.7             RSQLite_1.0.0             
[25] BiocInstaller_1.20.1       GenomicFeatures_1.22.8    
[27] Rsamtools_1.22.0           Biostrings_2.38.3         
[29] ShortRead_1.28.0           XML_3.98-1.3       

 

 

 

 

quasr parallel cluster • 673 views
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Hi 'rna seq'

Creating a new post is not helpful....and please (as Martin already told you), provide a reproducible example, with publicly available data sets, in order for the community to help you.

 

Regards, Hans-Rudolf

 

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