Comments (4)
ggabernet
commented on June 29, 2024
Marie found the issue:
nextflow run qbicsoftware/rnadeseq -r dev -profile cfc,test
N E X T F L O W ~ version 19.01.0
Launching `qbicsoftware/rnadeseq` [dreamy_kirch] - revision: 0c95523fb4 [dev]
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
qbicsoftware/rnadeseq v1.0dev
----------------------------------------------------
Pipeline Release : dev
Run Name : dreamy_kirch
Gene Counts : https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/DESeq2/input/merged_gene_counts.txt
Metadata : https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/DESeq2/input/Sample_preparations.tsv
Model : https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/DESeq2/input/design.txt
Contrasts : https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/DESeq2/input/contrasts.tsv
Gene list : https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/DESeq2/input/requested_genes.txt
Project summary file: https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/rnaseqReport/summary.tsv
nf-core/rnaseq software versions: https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/rnaseqReport/software_versions.csv
Report config file: https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/rnaseqReport/config.yml
Fastqc reports : https://raw.githubusercontent.com/qbicsoftware/r-analysis-templates/master/rnaseqReport/fastqc.zip
Multiqc results : https://github.com/qbicsoftware/r-analysis-templates/blob/master/rnaseqReport/multiqc.zip?raw=true
Species : Mmusculus
Max Resources : 6 GB memory, 2 cpus, 2d time per job
Container : singularity - qbicsoftware/rnadeseq:dev
Output dir : ./results
Launch dir : /sfs/7/workspace/ws/iiiga01-QQMOI-0/test
Working dir : /sfs/7/workspace/ws/iiiga01-QQMOI-0/test/work
Script dir : /home-link/iiiga01/.nextflow/assets/qbicsoftware/rnadeseq
User : iiiga01
Config Profile : cfc,test
Config Description: Minimal test dataset to check pipeline function
Config Contact : Alexander Peltzer (@apeltzer)
Config URL : http://qbic.uni-tuebingen.de/
----------------------------------------------------
[warm up] executor > slurm
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /sfs/7/workspace/ws/iiiga01-QQMOI-0/test/work/singularity
Pulling Singularity image docker://qbicsoftware/rnadeseq:dev [cache /sfs/7/workspace/ws/iiiga01-QQMOI-0/test/work/singularity/qbicsoftware-rnadeseq-dev.img]
[84/c3e159] Submitted process > get_software_versions
[4a/dfe0b3] Submitted process > output_documentation (1)
[0c/133704] Submitted process > DESeq2 (1)
ERROR ~ Error executing process > 'get_software_versions'
Caused by:
Process `get_software_versions` terminated with an error exit status (1)
Command executed:
echo 1.0dev > v_pipeline.txt
echo 19.01.0 > v_nextflow.txt
echo $(R --version 2>&1) > v_R.txt
Rscript -e "library(RColorBrewer); write(x=as.character(packageVersion('RColorBrewer')), file='v_rcolorbrewer.txt')"
Rscript -e "library(reshape2); write(x=as.character(packageVersion('reshape2')), file='v_reshape2.txt')"
Rscript -e "library(genefilter); write(x=as.character(packageVersion('genefilter')), file='v_genefilter.txt')"
Rscript -e "library(DESeq2); write(x=as.character(packageVersion('DESeq2')), file='v_deseq2.txt')"
Rscript -e "library(ggplot2); write(x=as.character(packageVersion('ggplot2')), file='v_ggplot2.txt')"
Rscript -e "library(plyr); write(x=as.character(packageVersion('plyr')), file='v_plyr.txt')"
Rscript -e "library(vsn); write(x=as.character(packageVersion('vsn')), file='v_vsn.txt')"
Rscript -e "library(gplots); write(x=as.character(packageVersion('gplots')), file='v_gplots.txt')"
Rscript -e "library(pheatmap); write(x=as.character(packageVersion('pheatmap')), file='v_pheatmap.txt')"
Rscript -e "library(optparse); write(x=as.character(packageVersion('optparse')), file='v_optparse.txt')"
Rscript -e "library(svglite); write(x=as.character(packageVersion('svglite')), file='v_svglite.txt')"
scrape_software_versions.py &> software_versions_mqc.yaml
Command exit status:
1
Command output:
(empty)
Command error:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply
Error: package or namespace load failed for ‘DESeq2’ in rbind(info, getNamespaceInfo(env, "S3methods")):
number of columns of matrices must match (see arg 2)
Execution halted
Work dir:
/sfs/7/workspace/ws/iiiga01-QQMOI-0/test/work/84/c3e15974712128cbf3dd3ca6222d3c
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
[qbicsoftware/rnadeseq] Pipeline completed with errors
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. ```
from rnadeseq.
ggabernet
commented on June 29, 2024
And I could reproduce it in the singularity shell
Singularity qbicsoftware-rnadeseq-dev.img:/sfs/7/workspace/ws/qeaga01-randeseq-0/work/singularity> Rscript -e "library("DESeq2"); write(x=as.character(package_version("DESeq2")), file='v_deseq2.txt')"
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply
Error: package or namespace load failed for ‘DESeq2’ in rbind(info, getNamespaceInfo(env, "S3methods")):
number of columns of matrices must match (see arg 2)
Execution halted
Singularity qbicsoftware-rnadeseq-dev.img:/sfs/7/workspace/ws/qeaga01-randeseq-0/work/singularity> Rscript -e "library("DESeq2"); write(x=as.character(package_version("bioconductor-DESeq2")), file='v_deseq2.txt')"
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply
Error: package or namespace load failed for ‘DESeq2’ in rbind(info, getNamespaceInfo(env, "S3methods")):
number of columns of matrices must match (see arg 2)
Execution halted```
from rnadeseq.
ggabernet
commented on June 29, 2024
SessionInfo:
Singularity qbicsoftware-rnadeseq-dev.img:/sfs/7/workspace/ws/qeaga01-randeseq-0/work/singularity> Rscript -e "sessionInfo()"
R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS/LAPACK: /opt/conda/envs/qbicsoftware-rnadeseq-1.0dev/lib/R/lib/libRblas.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.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_3.5.1 ```
from rnadeseq.
ggabernet
commented on June 29, 2024
A local installation of conda was apparently the problem, I deinstalled conda and this issue was gone.
from rnadeseq.
Related Issues (20)
- Do another lookover of code and docu HOT 4
- Fix volcano and enrichmeht plot layout HOT 1
- Do a template update HOT 1
- The destination path is too long error on windows HOT 1
- Rename the parameter --skip_pathway_analysis to --run_pathway_analysis and have the default set to 'false' HOT 1
- Contrast that is not included in design throws error
- Remove `multiqc` and `software_versions.yml` from rnadeseq report HOT 3
- Volcano plots and PCA plot don't have correct x and y axis dimensions HOT 1
- Legend is cutoff for enriched pathway plots HOT 1
- Double-colored bar in enrichment plot, some slashes missing HOT 1
- Unreadable heatmap ticks HOT 1
- star salmon doesn't output round values HOT 2
- ## Enriched pathways not displayed properly HOT 1
- Include background gene list for pathway analysis HOT 1
- If no enriched pathway is found, it simply states so instead of throwing an error HOT 1
- Genes without 'gene_name' wont be shown in Volcano plot HOT 3
- Use --relevel parameter for PCA plotting HOT 1
- Save pipeline info to zip HOT 1
- Order the pathway heatmaps according to condition HOT 4
- Reduce pathway heatmaps to relevant samples
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from rnadeseq.