Issues when running the sample

[tom-snir]

Hello,

I believe all dependencies are installed, but I still get an error when trying to run the basic, sample zUMIs run. I apologize for the unclear formatting, copy pasting from the terminal:

[tom@zelda ~]$ bash $p/zUMIs-master.sh -f $p/ExampleData/barcoderead_HEK.1mio.f q.gz -r $p/ExampleData/cDNAread_HEK.1mio.fq.gz -c 1-6 -m 7-16 -l 50 -g $p/refer ence/hg38_chr22/ -a $p/reference/GRCh38.84.chr22.gtf -n chr22test -p 8 -o $p/Ex ampleData Your jobs will run on this machine.

Make sure you have more than 1.9G 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 Barcode read: /private/zel/tom/zUMIs/ExampleData/barcoderead_ HEK.1mio.fq.gz cDNA read: /private/zel/tom/zUMIs/ExampleData/cDNAread_HEK .1mio.fq.gz Study/sample name: chr22test Output directory: /private/zel/tom/zUMIs/ExampleData Cell/sample barcode range: 1-6 UMI barcode range: 7-16 Genome directory: /private/zel/tom/zUMIs/reference/hg38_chr22/ GTF annotation file: /private/zel/tom/zUMIs/reference/GRCh38.84.chr2 2.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

Barcodes: NA zUMIs directory: /private/zel/tom/zUMIs STAR executable STAR samtools executable samtools Additional STAR parameters: STRT-seq data: no Barcode read2(STRT-seq): NA Barcode read2 range(STRT-seq): 0-0 Bases(G) to trim(STRT-seq): 3 Subsampling reads: 0

Raw reads: 1000000 Filtered reads: 853296

Jul 26 11:24:39 ..... started STAR run Jul 26 11:24:39 ..... loading genome Jul 26 11:24:40 ..... processing annotations GTF Jul 26 11:24:40 ..... inserting junctions into the genome indices Jul 26 11:24:48 ..... started 1st pass mapping Jul 26 11:26:00 ..... finished 1st pass mapping Jul 26 11:26:00 ..... inserting junctions into the genome indices Jul 26 11:26:09 ..... started mapping Jul 26 11:27:23 ..... finished successfully Loading required package: optparse [1] "I am loading useful packages..." [1] "2017-07-26 11:27:31 IDT" Warning message: In is.na(x[[i]]) : is.na() applied to non-(list or vector) of type 'environment' [1] "I am making annotations in SAF... This will take less than 3 minutes..." [1] "2017-07-26 11:27:37 IDT" Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Error in c(x, value) : could not find symbol "recursive" in environment of the generic function Calls: makeTxDbFromGFF ... eval -> .nextMethod -> replaceROWS -> replaceROWS -> c Execution halted [1] "I am loading useful packages..." [1] "2017-07-26 11:27:38 IDT" Warning message: In is.na(x[[i]]) : is.na() applied to non-(list or vector) of type 'environment' Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/private/zel/tom/zUMIs/ExampleData/zUMIs_output/expression/chr22test.dgecounts.rds', probable reason 'No such file or directory' Execution halted [tom@zelda ~]$

[tom-snir]

Looks like the issue I described above was solved by running this in R after loading the bioconductor library:

biocLite(c("BiocGenerics", "XVector", "S4Vectors", "IRanges", "GenomicRanges"), type="source")

I am not sure if the issue is local to me or not, but this can be closed I believe.

[cziegenhain]

Yes it looks like one of the packages was not installed properly before, sometimes there may also be issues when there are several package libraries (user/system).

Great that it works now.