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
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