Entering edit mode
4.3 years ago
yueli7
▴
250
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
Error is in command line:
Ensure you have this file.
Hello, zx8754,
Thank you so much for your suggestion! I will add the code.
Best,
Yue
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?
Hello, jared.andrew07,
Thank you so much for your suggestion! I will add the code.
Best,
Yue
Hi, I encountered a similar problem at this thread: Demultiplexing RNAseq data with tag file and barcodes (single end) Did anyone find a solution?