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campbio / scruff

Single Cell RNA-seq UMI Filtering Facilitator
http://bioconductor.org/packages/scruff/
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System hangs at alignment step #185

Closed parichitran closed 2 years ago

parichitran commented 2 years ago

Hello I ran scruff tool for my celseq umi incorporated data which is actually an already demultiplexed to individual cells.So i concatenated the reads for just 10 cells and ran it.It was fine for demultiplexing.It detected the 10 cells also . When coming to run the alignment my system freezes always. I am here attaching the rscript for my code and demultiplextabfile 20220329_141402_demultiplex.txt

scruff10cells.txt Thanks in advance

zhewa commented 2 years ago

Hi. Are you running the code on Windows system? Can you paste the output of running sessionInfo() in R? Thank you.

parichitran commented 2 years ago

Hey zhewa, Sorry for the late reply.No I am using ubuntu 20.04.4 LTS sessioninfo

R version 4.1.3 (2022-03-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 BiocGenerics_0.40.0

loaded via a namespace (and not attached): [1] zlibbioc_1.40.0 compiler_4.1.3 XVector_0.34.0 tools_4.1.3 GenomeInfoDbData_1.2.7 [6] RCurl_1.98-1.6 yaml_2.3.5 data.table_1.14.2 bitops_1.0-7
Thank you