Question: Error: All columns in a tibble must be 1d or 2d objects:
0
gravatar for yueli7
9 weeks ago by
yueli7110
China
yueli7110 wrote:

Hello,

I got following error. I was trying to run the software zUMIs-zUMIs.0.0.6.

Really appreciate any help and suggestion!

Best,

Yue

$ zUMIs-zUMIs.0.0.6/zUMIs-master.sh -f barcoderead_HEK.1mio.fq.gz -r cDNAread_HEK.1mio.fq.gz -n 1 -g /home/li/reference/hg38_chr22 -a /home/li/reference/hg38_chr22/GRCh38.84.chr22.gtf  -c 1-6 -m 7-16 -l 50  -o /home/li/li01 
Your jobs will run on this machine. 


Make sure you have more than 1.9G RAM and 1 processors available. 

 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:          barcoderead_HEK.1mio.fq.gz
 cDNA read:         cDNAread_HEK.1mio.fq.gz
 Study/sample name:     1
 Output directory:      /home/li/li01
 Cell/sample barcode range: 1-6
 UMI barcode range:     7-16
 Retain cell with >=N reads:    100
 Genome directory:      /home/li/reference/hg38_chr22
 GTF annotation file:       /home/li/reference/hg38_chr22/GRCh38.84.chr22.gtf
 Number of processors:      1
 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:       /home/li/zUMIs-zUMIs.0.0.6
 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 0.0.6 




Raw reads: 1000000 
Filtered reads: 853296 

Jan 27 23:44:52 ..... started STAR run
Jan 27 23:44:52 ..... loading genome
Jan 27 23:44:52 ..... processing annotations GTF
Jan 27 23:44:52 ..... inserting junctions into the genome indices
Jan 27 23:45:01 ..... started 1st pass mapping
Jan 27 23:48:23 ..... finished 1st pass mapping
Jan 27 23:48:23 ..... inserting junctions into the genome indices
Jan 27 23:48:31 ..... started mapping
Jan 27 23:51:58 ..... finished successfully
Loading required package: optparse
[1] "I am loading useful packages..."
[1] "2020-01-27 23:52:08 EST"
[1] "I am making annotations in SAF... This will take less than 3 minutes..."
[1] "2020-01-27 23:52:12 EST"
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
'select()' returned 1:many mapping between keys and columns
[1] "I am making count tables...This will take a while!!"
[1] "2020-01-27 23:52:14 EST"

    ==========     _____ _    _ ____  _____  ______          _____  
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
   Rsubread 2.0.0

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           o 1.aligned.sorted.bam                           ||
||                                                                            ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||      Assignment details : <input_file>.featureCounts                       ||
||                      (Note that files are saved to the output directory)   ||
||                                                                            ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||      Multimapping reads : counted                                          ||
||     Multiple alignments : primary alignment only                           ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||       
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid16232 ...         ||
||    Features : 5737                                                         ||
||    Meta-features : 698                                                     ||
||    Chromosomes/contigs : 3                                                 ||
||                                                                            ||
|| Process BAM file 1.aligned.sorted.bam...                                   ||
||    Single-end reads are included.                                          ||
||    Total alignments : 853296                                               ||
||    Successfully assigned alignments : 46553 (5.5%)                         ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
 \\============================================================================    //


    ==========     _____ _    _ ____  _____  ______          _____  
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
   Rsubread 2.0.0

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           o 1.aligned.sorted.bam                           ||
||                                                                            ||
||              Annotation : R data.frame                                     ||
||      Dir for temp files : .                                                ||
||      Assignment details : <input_file>.featureCounts                       ||
||                      (Note that files are saved to the output directory)   ||
||                                                                            ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||      Multimapping reads : counted                                          ||
||     Multiple alignments : primary alignment only                           ||
|| Multi-overlapping reads : not counted                                      ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid16232 ...         ||
||    Features : 26131                                                        ||
||    Meta-features : 1190                                                    ||
||    Chromosomes/contigs : 4                                                 ||
||                                                                            ||
|| Process BAM file 1.aligned.sorted.bam...                                   ||
||    Single-end reads are included.                                          ||
||    Total alignments : 853296                                               ||
||    Successfully assigned alignments : 21890 (2.6%)                         ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
|| Write the final count table.                                               ||
|| Write the read assignment summary.                                         ||
||                                                                            ||
\\============================================================================//



Taking input= as a system command ('cut -f4 /home/li/li01/1.aligned.sorted.bam.ex.featureCounts') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
cut: /home/li/li01/1.aligned.sorted.bam.ex.featureCounts: No such file or directory
Taking input= as a system command ('cut -f10 /home/li/li01/1.barcodelist.filtered.sort.sam') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
 Error: All columns in a tibble must be 1d or 2d objects:
* Column `GE` is NULL
Backtrace:
█
1. └─global::makeGEprofile(...)
2.   └─tibble::tibble(...)
3.     └─tibble:::lst_to_tibble(xlq$output, .rows, .name_repair, lengths = xlq$lengths)
4.       └─tibble:::check_valid_cols(x)


> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.1
rna-seq R • 271 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by yueli7110
2

Error is in command line:

cut: /home/li/li01/1.aligned.sorted.bam.ex.featureCounts: No such file or directory

Ensure you have this file.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by zx87549.1k

Hello, zx8754,

Thank you so much for your suggestion! I will add the code.

Best,

Yue

ADD REPLYlink written 9 weeks ago by yueli7110

Neither do we. What command/code are you running? What are you trying to do? We can't answer/troubleshoot with no info.

It gives you an error, are you trying to pass nested dataframes or matrixes as rows of a tibble?

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by jared.andrews075.3k

Hello, jared.andrew07,

Thank you so much for your suggestion! I will add the code.

Best,

Yue

ADD REPLYlink written 9 weeks ago by yueli7110
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