error when running the example data

[carissaxie]

Hi,

I am trying to run the sample data in zUMIs but I got an unsolvable error. Would you please check this for me? Thank you so much.

Yours, Yi

`unix305 532 % p='/stornext/General/data/user_managed/grpu_mritchie_1/YiXie/scpipe/zUMIs/' unix305 533 % bash $p/zUMIs-master.sh -f $p/ExampleData/barcoderead_HEK.1mio.fq.gz -r $p/ExampleData/cDNAread_HEK.1mio.fq.gz -c 1-6 -m 7-16 -l 50 -g $p/reference/hg38_chr22/ -a $p/reference/GRCh38.84.chr22.gtf -n chr22test -p 8 -o $p/ExampleData/ Your jobs will run on this machine.

Make sure you have more than 2.0G RAM and 8 processors available.

Your jobs will be started from filtering.

You provided these parameters: SLURM workload manager: no Summary Stats to produce: yes Start the pipeline from: filtering A custom mapped BAM: NA Custom filtered FASTQ: no Barcode read: /stornext/General/data/user_managed/grpu_mritchie_1/YiXie/scpipe/zUMIs//ExampleData/barcoderead_HEK.1mio.fq.gz cDNA read: /stornext/General/data/user_managed/grpu_mritchie_1/YiXie/scpipe/zUMIs//ExampleData/cDNAread_HEK.1mio.fq.gz Study/sample name: chr22test Output directory: /stornext/General/data/user_managed/grpu_mritchie_1/YiXie/scpipe/zUMIs//ExampleData/ Cell/sample barcode range: 1-6 UMI barcode range: 7-16 Retain cell with >=N reads: 100 Genome directory: /stornext/General/data/user_managed/grpu_mritchie_1/YiXie/scpipe/zUMIs//reference/hg38_chr22/ GTF annotation file: /stornext/General/data/user_managed/grpu_mritchie_1/YiXie/scpipe/zUMIs//reference/GRCh38.84.chr22.gtf Number of processors: 8 Read length: 50 Strandedness: 0 Cell barcode Phred: 20 UMI barcode Phred: 20

bases below phred in CellBC: 1

bases below phred in UMI: 1

Hamming Distance (UMI): 0 Hamming Distance (CellBC): 0 Plate Barcode Read: NA Plate Barcode range: NA Barcodes: NA zUMIs directory: /stornext/General/data/user_managed/grpu_mritchie_1/YiXie/scpipe/zUMIs STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript Additional STAR parameters: STRT-seq data: no InDrops data: no Library read for InDrops: NA Barcode read2(STRT-seq): NA Barcode read2 range(STRT-seq): 0-0 Bases(G) to trim(STRT-seq): 3 Subsampling reads: 0

zUMIs version 0.0.6d

Raw reads: 1000000 Filtered reads: 853296

Make sure you have approximately 11493 Mb RAM availableJul 25 15:15:10 ..... started STAR run Jul 25 15:15:10 ..... loading genome Jul 25 15:15:13 ..... processing annotations GTF Jul 25 15:15:14 ..... inserting junctions into the genome indices Jul 25 15:15:35 ..... started 1st pass mapping Jul 25 15:18:09 ..... finished 1st pass mapping Jul 25 15:18:09 ..... inserting junctions into the genome indices Jul 25 15:18:29 ..... started mapping Jul 25 15:21:08 ..... finished successfully Loading required package: optparse [1] "I am loading useful packages..." [1] "2018-07-25 15:21:27 EST" Error in installed.packages()[grep("Rsubread", installed.packages()), : subscript out of bounds Calls: as.numeric_version -> is.numeric_version Execution halted [1] "I am loading useful packages for plotting..." [1] "2018-07-25 15:22:08 EST" Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/stornext/General/data/user_managed/grpu_mritchie_1/YiXie/scpipe/zUMIs//ExampleData//zUMIs_output/expression/chr22test.dgecounts.rds', probable reason 'No such file or directory' Execution halted`

[cziegenhain]

Hey Yi,

Sorry to hear that you are having trouble with zUMIs. It looks like our internal check for the version of the Rsubread package fails. Could you tell me if you installed it and which version you have on your machine? Would also be great to know the version of R you are running.

Best,

Christoph

[carissaxie]

Hi, The versions are as follow:

Rsubread 1.29.6 R 3.5.1

Yours, Yi

[sdparekh]

Hi Yi,

I installed the same R. version and checked the condition where this error comes from and it works fine. Can you try the following chunk of code?

if(length(grep("Rsubread",installed.packages()))==0){ print("I did not find Rsubread so I am installing it...") BiocInstaller::biocLite("Rsubread",dependencies = TRUE, ask = FALSE) }else{ if(all(as.numeric_version(installed.packages()[grep("Rsubread",installed.packages()),"Version"])<'1.26.1')){ print("I need newer Rsubread so I am updating it...") BiocInstaller::biocUpdatePackages("Rsubread", ask=FALSE) } }

Please write us back what this code chunk gives you.

Best, Swati

[carissaxie]

Hi Swati,

I think I have figured it out. There is something wrong with the grep so I add [,"Package"] as a restriction and modify the zUMIs-dge.R file. Then I run the example data again and it works.

grep("Rsubread",installed.packages()) [1] 19 725 7191 dim(installed.packages()) [1] 881 16 grep("Rsubread",installed.packages()[,"Package"]) [1] 19 725

if(length(grep("Rsubread",installed.packages()))==0){ print("I did not find Rsubread so I am installing it...") BiocInstaller::biocLite("Rsubread",dependencies = TRUE, ask = FALSE) }else{ if(all(as.numeric_version(installed.packages()[grep("Rsubread",installed.packages()[,"Package"]),"Version"])<'1.26.1')){ print("I need newer Rsubread so I am updating it...") BiocInstaller::biocUpdatePackages("Rsubread", ask=FALSE) } }

Thank you again!! Yours, Yi

[sdparekh]

Hi Yi,

I am glad that you found a solution. However, it is a bit weird that it works with 'Package' and not 'Version' for you! In any case, feel free to write to us if you have any troubles.

I am closing this issue now.

Best, Swati