I have been using zUMIs for my RNAseq analysis for a while but ran into the following error very recently. it seems like there is an issue with the inbuilt DelayedArray package but I can't seem to figure out what.
`Using miniconda environment for zUMIs!
note: internal executables will be used instead of those specified in the YAML file!
You provided these parameters:
YAML file: /novaseqrun/demultiplex/combined/combine_samples/zUMIs.yaml
zUMIs directory: /zUMIs/zUMIs
STAR executable STAR
samtools executable samtools
pigz executable pigz
Rscript executable Rscript
RAM limit: 300
zUMIs version 2.9.7c
Wed Aug 31 20:02:04 EDT 2022
WARNING: The STAR version used for mapping is 2.7.3a and the STAR index was created using the version 2.7.1a. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR 2.7.3a.
Counting...
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Failed with error: ‘package ‘DelayedArray’ could not be loaded’
[1] "2022-08-31 20:02:12 EDT"
[1] "4.5e+08 Reads per chunk"
[1] "Warning: Barcode NA has more reads than allowed for the memory limit!\n Proceeding anyway..."
[1] "Loading reference annotation from:"
[1] "/novaseqrun/demultiplex/combined/combine_samples/results/Smartseq3_pilot_novaseq.final_annot.gtf"
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/R/libs/Matrix/libs/Matrix.so':
libgfortran.so.3: cannot open shared object file: No such file or directory
Calls: .makeSAF ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
Wed Aug 31 20:02:13 EDT 2022
Loading required package: yaml
Loading required package: Matrix
Error: package or namespace load failed for ‘Matrix’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/R/libs/Matrix/libs/Matrix.so':
libgfortran.so.3: cannot open shared object file: No such file or directory
[1] "loomR found"
Warning! HDF5 library version mismatched error
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.10.4, library is 1.10.5
SUMMARY OF THE HDF5 CONFIGURATION
General Information:
HDF5 Version: 1.10.5
Configured on: Tue Oct 22 12:02:13 UTC 2019
Configured by: conda@16247e67ecd5
Host system: x86_64-conda_cos6-linux-gnu
Uname information: Linux 16247e67ecd5 4.15.0-1059-azure #64-Ubuntu SMP Fri Sep 13 17:02:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /zUMIs/zUMIs/zUMIs-env
Compiling Options:
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Threadsafety: yes
Default API mapping: v110
With deprecated public symbols: yes
I/O filters (external): deflate(zlib)
MPE: no
Direct VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: yes
Memory allocation sanity checks: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
Bye...
/zUMIs/zUMIs/zUMIs.sh: line 307: 25321 Aborted (core dumped) ${Rexc} ${zumisdir}/misc/rds2loom.R ${yaml}
Wed Aug 31 20:02:16 EDT 2022
Descriptive statistics...
[1] "I am loading useful packages for plotting..."
[1] "2022-08-31 20:02:17 EDT"
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Error: package or namespace load failed for ‘Matrix’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/R/libs/Matrix/libs/Matrix.so':
libgfortran.so.3: cannot open shared object file: No such file or directory
Execution halted
Wed Aug 31 20:02:18 EDT 2022
`
My yaml file:
`project: Smartseq3_pilot_novaseq
sequence_files:
file1:
name: /novaseqrun/demultiplex/combined/combine_samples/Undetermined_S0R1_001.fastq.gz
base_definition:
BC(1-16)
reference:
STAR_index: /scrnaseq/hg38_STAR5idx
GTF_file: /scrnaseq/Homo_sapiens.GRCh38.99.gtf
additional_STAR_params: '--outFilterIntronMotifs RemoveNoncanonicalUnannotated'
additional_files:
out_dir: /novaseqrun/demultiplex/combined/combine_samples/results
num_threads: 100
mem_limit: 300
filter_cutoffs:
BC_filter:
num_bases: 1
phred: 20
UMI_filter:
num_bases: 1
phred: 20
barcodes:
barcode_num: null
barcode_file: /novaseqrun/demultiplex/combined/combine_samples/barcodes.txt
barcode_sharing: null #Optional for combining several barcode sequences per cell (see github wiki)
automatic: no #Give yes/no to this option. If the cell barcodes should be detected automatically. If the barcode file is given in combination with automatic barcode detection, the list of given barcodes will be used as whitelist.
BarcodeBinning: 0 #Hamming distance binning of close cell barcode sequences.
nReadsperCell: 100 #Keep only the cell barcodes with atleast n number of reads.
demultiplex: no #produce per-cell demultiplexed bam files.
Options related to counting of reads towards expression profiles
counting_opts:
introns: yes #can be set to no for exon-only counting.
intronProb: no #perform an estimation of how likely intronic reads are to be derived from mRNA by comparing to intergenic counts.
downsampling: 0 #Number of reads to downsample to. This value can be a fixed number of reads (e.g. 10000) or a desired range (e.g. 10000-20000) Barcodes with less than will not be reported. 0 means adaptive downsampling. Default: 0.
strand: 1 #Is the library stranded? 0 = unstranded, 1 = positively stranded, 2 = negatively stranded
Ham_Dist: 1 #Hamming distance collapsing of UMI sequences.
velocyto: no #Would you like velocyto to do counting of intron-exon spanning reads
primaryHit: no #Do you want to count the primary Hits of multimapping reads towards gene expression levels?
multi_overlap: no #Do you want to assign reads overlapping to multiple features?
fraction_overlap: 0 #minimum required fraction of the read overlapping with the gene for read assignment to genes
twoPass: no #perform basic STAR twoPass mapping
produce stats files and plots?
make_stats: yes
Start zUMIs from stage. Possible TEXT(Filtering, Mapping, Counting, Summarising). Default: Filtering.
Hello,
I have been using zUMIs for my RNAseq analysis for a while but ran into the following error very recently. it seems like there is an issue with the inbuilt DelayedArray package but I can't seem to figure out what.
`Using miniconda environment for zUMIs! note: internal executables will be used instead of those specified in the YAML file!
You provided these parameters: YAML file: /novaseqrun/demultiplex/combined/combine_samples/zUMIs.yaml zUMIs directory: /zUMIs/zUMIs STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: 300 zUMIs version 2.9.7c
Wed Aug 31 20:02:04 EDT 2022 WARNING: The STAR version used for mapping is 2.7.3a and the STAR index was created using the version 2.7.1a. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR 2.7.3a. Counting... Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang Failed with error: ‘package ‘DelayedArray’ could not be loaded’ [1] "2022-08-31 20:02:12 EDT" [1] "4.5e+08 Reads per chunk" [1] "Warning: Barcode NA has more reads than allowed for the memory limit!\n Proceeding anyway..." [1] "Loading reference annotation from:" [1] "/novaseqrun/demultiplex/combined/combine_samples/results/Smartseq3_pilot_novaseq.final_annot.gtf" Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/R/libs/Matrix/libs/Matrix.so': libgfortran.so.3: cannot open shared object file: No such file or directory Calls: .makeSAF ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted Wed Aug 31 20:02:13 EDT 2022 Loading required package: yaml Loading required package: Matrix Error: package or namespace load failed for ‘Matrix’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/R/libs/Matrix/libs/Matrix.so': libgfortran.so.3: cannot open shared object file: No such file or directory [1] "loomR found" Warning! HDF5 library version mismatched error The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.10.4, library is 1.10.5 SUMMARY OF THE HDF5 CONFIGURATION
General Information:
Compiling Options:
Linking Options:
Statically Linked Executables: LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/zUMIs/zUMIs/zUMIs-env/lib -Wl,-rpath-link,/zUMIs/zUMIs/zUMIs-env/lib -LzUMIs/zUMIs/zUMIs-env/lib H5_LDFLAGS: AM_LDFLAGS: -L/zUMIs/zUMIs/zUMIs-env/lib Extra libraries: -lrt -lpthread -lz -ldl -lm Archiver: /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar AR_FLAGS: cr Ranlib: /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib
Languages:
Features:
Parallel Filtered Dataset Writes: no Large Parallel I/O: no High-level library: yes Threadsafety: yes Default API mapping: v110 With deprecated public symbols: yes I/O filters (external): deflate(zlib) MPE: no Direct VFD: no dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: yes Memory allocation sanity checks: no Function stack tracing: no Strict file format checks: no Optimization instrumentation: no Bye... /zUMIs/zUMIs/zUMIs.sh: line 307: 25321 Aborted (core dumped) ${Rexc} ${zumisdir}/misc/rds2loom.R ${yaml} Wed Aug 31 20:02:16 EDT 2022 Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2022-08-31 20:02:17 EDT" Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang Error: package or namespace load failed for ‘Matrix’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/R/libs/Matrix/libs/Matrix.so': libgfortran.so.3: cannot open shared object file: No such file or directory Execution halted Wed Aug 31 20:02:18 EDT 2022 `
My yaml file: `project: Smartseq3_pilot_novaseq sequence_files: file1: name: /novaseqrun/demultiplex/combined/combine_samples/Undetermined_S0R1_001.fastq.gz base_definition:
Options related to counting of reads towards expression profiles
counting_opts: introns: yes #can be set to no for exon-only counting. intronProb: no #perform an estimation of how likely intronic reads are to be derived from mRNA by comparing to intergenic counts. downsampling: 0 #Number of reads to downsample to. This value can be a fixed number of reads (e.g. 10000) or a desired range (e.g. 10000-20000) Barcodes with less than will not be reported. 0 means adaptive downsampling. Default: 0.
strand: 1 #Is the library stranded? 0 = unstranded, 1 = positively stranded, 2 = negatively stranded
Ham_Dist: 1 #Hamming distance collapsing of UMI sequences.
velocyto: no #Would you like velocyto to do counting of intron-exon spanning reads
primaryHit: no #Do you want to count the primary Hits of multimapping reads towards gene expression levels?
multi_overlap: no #Do you want to assign reads overlapping to multiple features?
fraction_overlap: 0 #minimum required fraction of the read overlapping with the gene for read assignment to genes
twoPass: no #perform basic STAR twoPass mapping
produce stats files and plots?
make_stats: yes
Start zUMIs from stage. Possible TEXT(Filtering, Mapping, Counting, Summarising). Default: Filtering.
which_Stage: Counting
define dependencies program paths
samtools_exec: samtools #samtools executable Rscript_exec: Rscript #Rscript executable STAR_exec: STAR #STAR executable pigz_exec: pigz #pigz executable`